Boston VA Research Institute

Innate immune detection of Gram-negative bacteria depends on sensing of cytosolic lipopolysaccharide (cLPS) by the non-canonical inflammasome, mediated in humans by NLRP11 and caspase-4 (CASP4). Activation of this pathway in human macrophages triggers gasdermin-D activation and pyroptotic cell death. Although CASP4 directly binds LPS in vitro, additional host factors are required for efficient activation in vivo. Here, we show that NLRP11, a primate-specific pattern recognition receptor, facilitates CASP4 recognition of cLPS and promotes non-canonical inflammasome activation. NLRP11 functions upstream CASP4, forming an ASC-independent complex that requires a conserved CASP4 p20 residue, binds cLPS, and enhances CASP4-dependent LPS recognition. Mutational analyses demonstrate that in human macrophages, in addition to LPS binding and CASP4 catalytic activity, CASP4 interaction with NLRP11 is essential for efficient pyroptosis. Together, these findings establish NLRP11 as a primate-specific determinant that enhances CASP4-mediated cLPS detection and non-canonical inflammasome activation, revealing a mechanism for human-specific regulation of innate immunity.

Understanding oocyte and ovarian aging has become critically important, as trends in family planning evolve, with many women choosing to have children later in life. The ovary, a crucial organ in female reproduction, is particularly susceptible to age-related changes and is one of the organs that exhibit functional deterioration most distinctly with age. The aging of female reproductive systems also affects longevity and various health outcomes. A better understanding of both oocyte and ovarian aging will lay the cornerstone to elucidate the phenomenon of longevity in women. Here, clinical data from 400 women of various ages undergoing intracytoplasmic sperm injection (ICSI) have been analyzed, including Anti-Müllerian Hormone (AMH) and Follicle-Stimulating Hormone (FSH) levels, the number of recovered oocytes, blastocyst rates, pregnancy rates, and live birth rates. Our analyses revealed significant differences in the aforementioned rates between patients of young and advanced age. For the biomarker analysis, we further utilised a novel predictive performance of age-associated gene expression signatures for oocyte aging, demonstrating its potential to provide molecular-level insights into oocyte quality over time. By analyzing RNA sequencing data generated from human oocytes of different ages, a genome-wide landscape of age-associated gene expression has been described. Additionally, metabolome profiling has been performed on young and reproductively aged mice, serving as a model for human ovaries. Changes in metabolites of the murine ovaries during aging have been recorded. In conjunction with traditional biomarkers, multiomics data represent a transformative approach in reproductive health, and they may offer personalised risk assessments and interventions to mitigate age-related fertility decline in women. Our metabolome profiling provides a valuable resource for elucidating the metabolomic basis of ovarian aging. Our findings offer novel insights into systemic shifts associated with oocyte and ovarian aging. This integrated approach may unlock new avenues for fertility preservation, ovarian rejuvenation, and assisted reproduction.

Segmental copy-number gains are major contributors to human genetic variation and disease, but how these alterations arise remains incompletely understood. Here, based on the analyses of both experimental evolution and human disease genomes, we describe a general mechanism of segmental copy-number gain from a rearrangement process termed ‘breakage–replication/fusion’. The hallmark genomic feature of breakage–replication/fusion is adjacent parallel breakpoints: two or more rearrangement breakpoints derived from replication of a single ancestral DNA end. We show that adjacent parallel breakpoints are a widespread feature of DNA duplications in human disease genomes and experimental models of chromothripsis. In addition to adjacent parallel breakpoints, breakage–replication/fusion also explains two other patterns of complex rearrangements with unclear provenance: chains of short (≤1 kb) insertions and high-level amplification consisting of inverted segments. Together, these findings revise the mechanistic model for chromothripsis and provide a new conceptual framework for understanding the origin of segmental DNA duplication during genome evolution.

Double-strand breaks (DSBs) are the most deleterious lesions experienced by our genome. Yet, DSBs are intentionally induced during gamete formation to promote the exchange of genetic material between homologous chromosomes. While the conserved topoisomerase-like enzyme Spo11 catalyzes DSBs, additional regulatory proteins— referred to as “Spo11 accessory factors”— regulate the number, timing, and placement of DSBs during meiotic prophase ensuring that SPO11 does not wreak havoc on the genome. Despite the importance of the accessory factors, they are poorly conserved at the sequence level suggesting that these factors may adopt unique functions in different species. In this work, we present a detailed analysis of the genetic and physical interactions between the DSB factors in the nematode Caenorhabditis elegans providing new insights into conserved and novel functions of these proteins. This work shows that HIM-5 is the determinant of X-chromosome-specific crossovers and that its retention in the nucleus is dependent on DSB-1, the sole accessory factor that interacts with SPO-11. We further provide evidence that HIM-5 mediates interactions with the different accessory factors sub-groups, providing insights into how components on the DNA loops may interact with the chromosome axis.

Recent studies have found non-immunological roles of the classical complement pathway (CP) in brain development and its involvement in neuropsychiatric and neurodegenerative diseases. However, multiple complement activation pathways exist beyond the CP, but their expression and function remain poorly understood in the brain. Using MERFISH, we constructed a comprehensive spatial transcriptomic atlas of the complement system in mouse brains from late embryonic stage to adulthood. Here we show that most complement genes are expressed locally with a remarkable degree of cellular, spatial, and temporal heterogeneity and that complement regulatory mechanisms are distinct from the periphery. Beyond confirming the known expression of the CP, our measurements reveal endogenous expression of the alternative pathway (AP), notably the AP activator Masp3 in immature brains. Masp3 deficiency alters molecular structure of the brain and causes working spatial memory defects, indicating a role of Masp3 in brain maturation, potentially via modulation of AP activity.

Although in vitro neuronal models are accessible and versatile systems for functional electrophysiological studies, the spontaneous and random formation of neural circuits often compromises the structural control and reproducibility. Here, we introduce a robust method for engineering human neuronal networks in vitro with single-cell precision and reproducibility. Our integrated platform combines direct laser-written microstructure templates and soft lithography-based fabrication of microscaffolds with functional multielectrode array recordings. This system enables high-throughput production of diverse circuit designs and allows for the exact placement of neurons within confined microenvironments. The system enables precise recording of spontaneous neuronal activity, as well as electrical and optogenetic stimulations. Using this approach, we constructed reproducible, bottom-up neuronal circuits composed of a defined number of human neurons. As a proof of principle, we employed these circuits to investigate ephaptic coupling, which refers to the modulation of neuronal activity by endogenous electric fields. Although it is believed to play a role in neural computations and cardiac conduction and is associated with epilepsy and arrhythmia, its mechanisms are unclear due to limitations in experimental models, both in vivo and in vitro. By controlling axonal proximity within microchannels and the number of neurons in the engineered circuits, we can quantify ephaptic coupling at different strengths, which validates theoretical predictions, including reduced action potential velocity, increased activity synchronization, and lower stimulation thresholds. Furthermore, the platform has broad potential for studying synaptic and nonsynaptic interactions, myelination processes, advancing disease modeling, and fundamental neuroscience research.

Staphylococcus aureus is a leading cause of fatal infections worldwide. It encodes diverse genes that contribute to the organism's high intrinsic resistance to antibiotics. Understanding the biological roles of these genes and how their features contribute to intrinsic resistance may enable better antibiotic therapies. Here, we investigate AuxB, an intrinsic resistance factor to compounds that target the cell envelope. We find that AuxB interacts directly with the cell cycle regulator GpsB and the eukaryotic-like serine/threonine kinase PknB, another intrinsic resistance factor that is proposed to sense and respond to cell wall status. Based on our findings, we propose that AuxB impacts cell physiology through three mechanisms: (i) by antagonizing PknB's penicillin-binding protein and Ser/Thr kinase-associated domain function; (ii) by coordinating the phosphorylation of cell division proteins; and (iii) by forming a homodimer that interacts with GpsB hexamers to enable the formation of extended GpsB interaction networks.