The rockefeller university

Colibactin, a human microbiome-derived genotoxin, promotes colorectal cancer by damaging the host gut epithelial genomes. While colibactin is synthesized via a hybrid non-ribosomal peptide synthetase (NRPS)polyketide synthase (PKS) pathway, known as pks or clb, the structural details of its biosynthetic enzymes remain limited, hindering our understanding of its biosynthesis and clinical application. In this study, we report the cryo-EM structures of two colibactin-producing PKS enzymes, ClbC and ClbI, captured in different reaction states using a substrate-mimic crosslinker. Our structural analysis revealed the binding sites of carrier protein (CP) domains of the ClbC and ClbI on their ketosynthase (KS) domains. Further, we identified a novel NRPS-PKS docking interaction between ClbI and its upstream enzyme, ClbH, mediated by the C-terminal peptide ClbH and the dimeric interface of ClbI, establishing a 1:2 stoichiometry. These findings advance our understanding of colibactin assembly line and provide broader insights into NRPS-PKS natural product biosynthesis mechanisms.

Lung cancer continues to be the leading cause of cancer-related deaths globally. Unraveling the regulators behind lung cancer growth and its metastatic spread, along with understanding the underlying mechanisms, is crucial for developing novel and effective therapeutic strategies. While much research has focused on identifying potential oncogenes or tumor suppressors, the roles of certain genes can vary depending on the context and may even exhibit contradictory effects. In this study, we demonstrate that acyl-CoA binding domain containing 3 (ACBD3), a Golgi resident protein, promotes primary lung cancer growth by recruiting phosphatidylinositol (PI)-4-kinase III beta (PI4KB) to the Golgi, thereby enhancing oncogenic secretion in chromosome 1q-amplified lung cancer cells. Conversely, in chromosome 1q-diploid lung cancer cells, ACBD3 acts as a suppressor of lung cancer metastasis by inhibiting the NOTCH signaling pathway and reducing cancer cell motility. This highlights the intricacy of cancer progression and cautions against simplistic approaches targeting individual oncogenes for cancer therapy.

Endothelial cells form the inner layer of blood vessels and play key roles in circulatory system development and function. A variety of endothelial cell types have been described through gene expression and transcriptome studies; nonetheless, the transcriptional programs that specify endothelial cell fate and maintenance are not well understood. To uncover such regulatory programs, we studied the C. elegans head mesodermal cell (HMC), a noncontractile mesodermal cell bearing molecular and functional similarities to vertebrate endothelial cells. Here, we demonstrate that a Forkhead transcription factor, LET-381, is required for HMC fate specification and maintenance of HMC gene expression. DMD-4, a DMRT transcription factor, acts downstream of and in conjunction with LET-381 to mediate these functions. Independently of LET-381, DMD-4 also represses the expression of genes associated with a different, non-HMC, mesodermal fate. Our studies uncover essential roles for FoxF transcriptional regulators in endothelial cell development and suggest that FoxF co-functioning target transcription factors promote specific non-contractile mesodermal fates.

Nguni sheep (Ovis aries) are indigenous to the Southern Africa region and common within the smallholder and poor resources farming systems. They are well adapted to different agroecological regions. However, limited genomic resources such as high-quality reference genomes have hindered our understanding of its adaptation and establishment of an effective breeding program. To address this, we assembled a chromosomal-level genome of Nguni sheep using a combination of PacBio HiFi reads and Omni-C reads. The genome size was estimated to be 2.9 Gb with a contig/scaffold N50 74 Mb and 99.6 Mb and a genome completeness of 96.1%, as estimated by the Benchmarking Universal Single-Copy Orthologs (BUSCO) program. The final genome encompassed a total of 25,926 protein-coding genes. The findings of this study provide a valuable genomic resource for understanding the adaptability of the Nguni sheep and the establishment of effective breeding programs.

Hearing hinges upon the ear's ability to enhance its responsiveness by means of an energy-expending active process that amplifies the very mechanical inputs that it detects. This process is defined by four properties that, although seemingly unrelated, consistently occur together: amplification, sharp frequency tuning, compressive nonlinearity, and spontaneous otoacoustic emission. In nonmammal tetrapods, the active process is evident in individual hair cells. The hair bundles of the bullfrog, for example, exhibit all four attributes by operating near a Hopf bifurcation-a critical regime in which these properties naturally coalesce. In mammals, however, the delicate nature of the cochlea has restricted the evidence for an active process to studies in vivo, where it is generally attributed to the collective effort of the outer hair cells that energize the traveling wave along the cochlear spiral. As a result, the cellular mechanisms that underlie the properties of mammalian hearing remain contested, with uncertainty about whether criticality plays a role in the cochlea's active process. Here we show that, when placed in a recording chamber that closely mimics the in vivo physiological environment, a segment of the mammalian cochlea ex vivo displays the features of the active process-amplification, frequency tuning, compressive nonlinearity, and the generation of distortion products. We show that this process operates locally, independently of traveling waves, and that the sensory epithelium achieves active amplification by operating near criticality at a Hopf bifurcation. The results reveal the existence of a unified biophysical principle that underlies auditory processing across species and even phyla.

Type 2 immunity is orchestrated by IL-4 and IL-13 signaling, initiated by binding to receptors that are specific to each cytokine or to the shared heterodimeric receptor comprising the IL-4R alpha and IL-13R alpha 1 subunits. Here, we report that sexually dimorphic IL13RA1 transcription is regulated by estrogen and characterize an IL-13R alpha 1 isoform (referred to here as IL-13R alpha 1-LOR1a) created through facultative splicing to an alternative terminal exon composed of primate-specific retrotransposable elements (RTEs). At the mRNA level, RTE exonization replaces regulatory sequences in the canonical 3 ' untranslated region (3 ' UTR) implicated in IL13RA1 mRNA stability. Moreover, alternative splicing removes critical domains in the cytoplasmic tail, rendering the IL-13R alpha 1-LOR1a isoform partially signaling defective at the protein level. When coexpressed, the IL-13R alpha 1-LOR1a isoform antagonizes the function of the canonical receptor, reducing cellular responsiveness to IL-4 and IL-13. Thus, the balance of the two IL13RA1 isoforms appears to fine-tune type 2 cytokine signaling and downstream immune responses.

Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project (CGP) began in early 2020 to facilitate the generation of near error-free, chromosome-resolved reference genomes for all cetacean species. Towards that goal, and using the methods, goals and genome assembly quality standards of the Vertebrate Genomes Project (VGP), we generated 13 new reference genomes across eight of the 14 cetacean families. Additionally, we summarize the genome assembly characteristics for 18 species, including these newly-generated and five published genome assemblies that meet the completeness and quality standards. We infer ancestral linkage groups (ALG) for cetaceans, showing that the ancestral karyotype of 22 ALGs is largely conserved in extant species, except for Ziphiidae, and for Balaenidae and Kogiidae, which exhibit similar independent fusions. Gene annotation, characterization of historical demography, heterozygosity and runs of homozygosity (ROH) reveal important information for conservation applications. By comparing the new reference genomes to previous draft assemblies, we show that the reference genomes have enhanced characteristics that will support and promote scientific research. Specifically, the genomes improve resolution and characterization of repetitive elements, provide validation (or exclusion) of genes linked to complex traits, and allow more complete characterization of gene regions such as the highly complex Major Histocompatibility Complex (MHC) Class I and II gene clusters that are important for population health.

Background: Recent single-cell studies indicated that IL-17-producing T cells (T17) have diverse subsets expressing IL-17A, IL-17F, or a combination in human psoriasis skin. However, it is unknown how T17 subsets are differently regulated by IL-23 versus IL-17A blockade. Objective: We sought to investigate how systemic monoclonal antibody injections blocking IL-23 versus IL-17A differently modify immune cell transcriptomes in human psoriasis skin. Methods: We analyzed a total of 93 human skin single-cell libraries, including 42 psoriasis pretreatment lesional skin, 25 psoriasis pretreatment nonlesional skin, 12 psoriasis posttreatment after IL-23 inhibition, 4 psoriasis posttreatment after IL-17A inhibition, and 10 control skin samples. ClinicalTrials.gov NCT04630652. Results: Of the six T17 subsets identified, an IL17A+IFNG+ subset and an IL17F+IL102 subset expressed the IL-23 receptor along with other inflammatory cytokines, and IL-23 inhibition downregulated these potentially pathogenic T17 subsets. In contrast, T17 cells expressing both IL-17A and IL-17F did not express the IL-23 receptor, and the percentage of this potentially nonpathogenic T17 subset increased after IL-23 inhibition. In addition, the expression of the IL-17-negative regulation genes, such as TNFAIP3, increased in myeloid cells more after IL-23 inhibition than after IL-17A inhibition. Conclusions: This study suggests multiple immune mechanisms of how IL-23 inhibition can modify the complex inflammatory environment present in psoriatic skin, highlighting the roles of specific T17 subsets in psoriasis development and background skin protection. (J Allergy Clin Immunol 2025;155:1898-912.)

The lack of T cells in tumors is a major hurdle to successful immune checkpoint therapy (ICT). Therefore, ther-apeutic strategies promoting T cell recruitment into tumors are warranted to improve the treatment efficacy. Here, we report that Fc-optimized anti-cytotoxic T lymphocyte antigen 4 (CTLA-4) antibodies are potent re-modelers of tumor vasculature that increase tumor-associated high endothelial venules (TA-HEVs), special-ized blood vessels supporting lymphocyte entry into tumors. Mechanistically, this effect is dependent on the Fc domain of anti-CTLA-4 antibodies and CD4+ T cells and involves interferon gamma (IFNy). Unexpectedly, we find that the human anti-CTLA-4 antibody ipilimumab fails to increase TA-HEVs in a humanized mouse model. However, increasing its Fc effector function rescues the modulation of TA-HEVs, promotes CD4+ and CD8+ T cell infiltration into tumors, and sensitizes recalcitrant tumors to programmed cell death protein 1 (PD-1) blockade. Our findings suggest that Fc-optimized anti-CTLA-4 antibodies could be used to repro-gram tumor vasculature in poorly immunogenic cold tumors and improve the efficacy of ICT.

PurposeIn the receptor organs of the inner ear, hair cells detect mechanical stimuli such as sounds and accelerations by deflection of their hair bundles. Myosin regulatory light chain (RLC) and non-muscle myosin II (NM2) are expressed at the apical surfaces of hair cells, and NM2 and the phosphorylation of RLC by myosin light chain kinase (MLCK) have earlier been shown to regulate the shapes of hair cells' apical surfaces in rodents. The aim of our study was to elucidate the function of myosin molecules on hair cell physiology.MethodsWe investigated the expression of NM2 and RLC in the bullfrog's saccule by immunostaining. Using NM2 and MLCK inhibitors, we measured the stiffness, spontaneous oscillation, and resting open probability of frog hair bundles. Six to ten saccules from pleural animals were used in each experiment. In addition, we recorded auditory brainstem responses in ten mice after transtympanic injection of an MLCK inhibitor.ResultsWe confirmed the expression of NM2A/B and MYL9 on the apical surfaces of hair cells and of NM2A and MYL12A in hair bundles. We found that NM2 and MLCK inhibitors reduce the stiffness of hair bundles from the bullfrog's saccule. Moreover, MLCK inhibition inhibits the spontaneous oscillation of hair bundles and increases the resting open probability of transduction channels. In addition, MLCK inhibition elevates hearing thresholds in mice.ConclusionWe conclude that NM2 and the phosphorylation of RLC modulate the physiological function of hair cells and thereby help to set the normal operating conditions of hair bundles.