Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle.

Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.

The cycling and aging mouse female reproductive tract at single-cell resolution.

The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction.

Unwinding Limb Development.

The molecular mechanisms underpinning vertebrate body plan evolution are beginning to be unravelled. In this issue of Cell, Kvon et al. spectacularly demonstrate how transplanting snake-specific genetic changes found uniquely in serpent enhancers leads to limb loss in mice.

Enhancer evolution across 20 mammalian species.

The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution.

Strand-resolved mutagenicity of DNA damage and repair.

DNA base damage is a major source of oncogenic mutations1. Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation2. Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication3,4, we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts5. The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution.

CTCF and cohesin: linking gene regulatory elements with their targets.

Current epigenomics approaches have facilitated the genome-wide identification of regulatory elements based on chromatin features and transcriptional regulator binding and have begun to map long-range interactions between regulatory elements and their targets. Here, we focus on the emerging roles of CTCF and the cohesin in coordinating long-range interactions between regulatory elements. We discuss how species-specific transposable elements may influence such interactions by remodeling the CTCF binding repertoire and suggest that cohesin's association with enhancers, promoters, and sites defined by CTCF binding has the potential to form developmentally regulated networks of long-range interactions that reflect and promote cell-type-specific transcriptional programs.

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of TF binding locations between species, we identified thousands of TF regions of highly constrained TF binding intensity. Although individual mutations in bound sequence motifs can influence TF binding, most binding differences occur in the absence of nearby sequence variations. Instead, combinatorial binding was found to be significant for genetic and evolutionary stability; cobound TFs tend to disappear in concert and were sensitive to genetic knockout of partner TFs. The large, qualitative differences in genomic regions bound between closely related mammals, when contrasted with the smaller, quantitative TF binding differences among Drosophila species, illustrate how genome structure and population genetics together shape regulatory evolution.

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.

CTCF-binding locations represent regulatory sequences that are highly constrained over the course of evolution. To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals. Our data indicate that activation of retroelements has produced species-specific expansions of CTCF binding in rodents, dogs, and opossum, which often functionally serve as chromatin and transcriptional insulators. We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago. Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages.

DNA lesion bypass and the stochastic dynamics of transcription-coupled repair.

DNA base damage is a major source of oncogenic mutations and disruption to gene expression. The stalling of RNA polymerase II (RNAP) at sites of DNA damage and the subsequent triggering of repair processes have major roles in shaping the genome-wide distribution of mutations, clearing barriers to transcription, and minimizing the production of miscoded gene products. Despite its importance for genetic integrity, key mechanistic features of this transcription-coupled repair (TCR) process are controversial or unknown. Here, we exploited a well-powered in vivo mammalian model system to explore the mechanistic properties and parameters of TCR for alkylation damage at fine spatial resolution and with discrimination of the damaged DNA strand. For rigorous interpretation, a generalizable mathematical model of DNA damage and TCR was developed. Fitting experimental data to the model and simulation revealed that RNA polymerases frequently bypass lesions without triggering repair, indicating that small alkylation adducts are unlikely to be an efficient barrier to gene expression. Following a burst of damage, the efficiency of transcription-coupled repair gradually decays through gene bodies with implications for the occurrence and accurate inference of driver mutations in cancer. The reinitation of transcription from the repair site is not a general feature of transcription-coupled repair, and the observed data is consistent with reinitiation never taking place. Collectively, these results reveal how the directional but stochastic activity of TCR shapes the distribution of mutations following DNA damage.

Pervasive lesion segregation shapes cancer genome evolution.

Cancers arise through the acquisition of oncogenic mutations and grow by clonal expansion1,2. Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. We characterize this process in mutagen-induced mouse liver tumours and show that DNA replication across persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multiallelic and combinatorial genetic diversity. The phasing of lesions enables accurate measurement of strand-biased repair processes, quantification of oncogenic selection and fine mapping of sister-chromatid-exchange events. Finally, we demonstrate that lesion segregation is a unifying property of exogenous mutagens, including UV light and chemotherapy agents in human cells and tumours, which has profound implications for the evolution and adaptation of cancer genomes.

BIONIC: biological network integration using convolutions.

Biological networks constructed from varied data can be used to map cellular function, but each data type has limitations. Network integration promises to address these limitations by combining and automatically weighting input information to obtain a more accurate and comprehensive representation of the underlying biology. We developed a deep learning-based network integration algorithm that incorporates a graph convolutional network framework. Our method, BIONIC (Biological Network Integration using Convolutions), learns features that contain substantially more functional information compared to existing approaches. BIONIC has unsupervised and semisupervised learning modes, making use of available gene function annotations. BIONIC is scalable in both size and quantity of the input networks, making it feasible to integrate numerous networks on the scale of the human genome. To demonstrate the use of BIONIC in identifying new biology, we predicted and experimentally validated essential gene chemical-genetic interactions from nonessential gene profiles in yeast.

Leveraging Machine Learning for Advanced Nanoscale X-ray Analysis: Unmixing Multicomponent Signals and Enhancing Chemical Quantification.

Energy dispersive X-ray (EDX) spectroscopy in the transmission electron microscope is a key tool for nanomaterials analysis, providing a direct link between spatial and chemical information. However, using it for precisely determining chemical compositions presents challenges of noisy data from low X-ray yields and mixed signals from phases that overlap along the electron beam trajectory. Here, we introduce a novel method, non-negative matrix factorization based pan-sharpening (PSNMF), to address these limitations. Leveraging the Poisson nature of EDX spectral noise and binning operations, PSNMF retrieves high-quality phase spectral and spatial signatures via consecutive factorizations. After validating PSNMF with synthetic data sets of different noise levels, we illustrate its effectiveness on two distinct experimental cases: a nanomineralogical lamella, and supported catalytic nanoparticles. Not only does PSNMF obtain accurate phase signatures, but data sets reconstructed from the outputs have demonstrably lower noise and better fidelity than from the benchmark denoising method of principle component analysis.

Polyploidisation pleiotropically buffers ageing in hepatocytes.

BACKGROUND & AIMS: Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. METHODS: We performed single-nucleus RNA sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent strains that were haploinsufficient for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. RESULTS: We observed that ageing in wild-type mice results in nuclei polyploidy and a marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in the CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A-haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbations. CONCLUSIONS: Our results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome. IMPACT AND IMPLICATIONS: The functional role of hepatocyte polyploidisation during ageing is poorly understood. Using single-nucleus RNA sequencing and BaseScope approaches, we have studied ploidy dynamics during ageing in murine livers with non-deleterious genetic perturbations. We have identified that hepatocytes present different cellular states and the ability to buffer ageing-associated dysfunctions. Tetraploid nuclei exhibit robust transcriptional networks and are better adapted to genomically overcome perturbations. Novel therapeutic interventions aimed at attenuating age-related changes in tissue function could be exploited by manipulation of ploidy dynamics during chronic liver conditions.

Expert Consensus on Pediatric Urodynamics Reporting Using Modified Delphi Technique.

PURPOSE: Urodynamic testing (UDS) is an important tool in the management of pediatric lower urinary tract conditions. There have been notable efforts to standardize pediatric UDS nomenclature and technique, but no formal guidelines exist on essential elements to include in a clinical report. We sought to identify ideal structure and elements of a pediatric UDS assessment based on expert consensus. MATERIALS AND METHODS: Pediatric urologists regularly performing UDS were queried using a Delphi process. Participants were invited representing varied geographic, experience, and societal involvement. Participants underwent 3 rounds of questionnaires between November 2022 and August 2023 focusing on report organization, elements, definitions, and automated electronic health record clinical decision support. Professional billing requirements were also considered. Consensus was defined as 80% agreeing either in favor of or against a topic. Elements without consensus were discussed in subsequent rounds. RESULTS: A diverse sample of 30 providers, representing 27 institutions across 21 US states; Washington, District of Columbia; and Canada completed the study. Participants reported interpreting an average number of 5 UDS reports per week (range 1-22). The finalized consensus report identifies 93 elements that should be included in a pediatric UDS report based on applicable study conditions and findings. CONCLUSIONS: This consensus report details the key elements and structure agreed upon by an expert panel of pediatric urologists. Further standardization of documentation should aid collaboration and research for patients undergoing UDS. Based on this information, development of a standardized UDS report template using electronic health record implementation principles is underway, which will be openly available for pediatric urologists.

Urological outcomes in adult females born with anorectal malformation or Hirschsprung disease.

INTRODUCTION: Women born with anorectal malformation (ARM) or Hirschsprung disease (HD) may have impaired urologic function resulting in sequelae in adulthood. This study assessed and compared self-reported urinary outcomes in adult females born with ARM or HD to a reference population. METHODS: This was an IRB approved, cross-sectional study of female-born patients with ARM or HD, who completed surveys between November 2021 and August 2022. Female patients between the ages of 18 and 80 years were included. Lower Urinary Tract Symptom Questionnaires were administered through REDCap and the responses were compared to a reference population using Chi-squared or Fisher's exact tests. RESULTS: Sixty-six born female patients answered the questionnaires, two of them identified as non-binary. The response rate was 76%. Median age was 31.6 years. The majority were born with cloaca (56.3%), followed by other type of ARMs (28.1%), complex malformation (9.4%), and HD (6.3%). A history of bladder reconstruction was present for 26.6%. Catheterization through a channel or native urethra was present in 18.8%. Two had ureterostomies and were excluded from the analysis. Seven had chronic kidney disease or end-stage renal disease, three with a history of kidney transplantation. Patients with cloaca had significantly higher rates of urinary incontinence, urinary tract infection, and social problems due to impaired urological functioning, when compared to an age-matched reference population (Table 3). CONCLUSION: This study emphasizes the need for a multi-disciplinary team that includes urology and nephrology following patients with ARM long term, especially within the subgroup of cloaca. LEVEL OF EVIDENCE: III.

Gradient-index Alvarez lenses: publisher's note.

This publisher's note contains a correction to Appl. Opt.62, 3485 (2023)APOPAI0003-693510.1364/AO.487089.

Gradient-index Alvarez lenses.

Gradient-index Alvarez lenses (GALs), a new, to the best of our knowledge, type of freeform optical component, are surveyed in this work for their unique properties in generating variable optical power. GALs display similar behavior to conventional surface Alvarez lenses (SALs) by means of a freeform refractive index distribution that has only recently been achievable in fabrication. A first-order framework is described for GALs including analytical expressions for their refractive index distribution and power variation. A useful feature of Alvarez lenses for introducing bias power is also detailed and is helpful for both GALs and SALs. The performance of GALs is studied, and the value of three-dimensional higher-order refractive index terms is demonstrated in an optimized design. Last, a fabricated GAL is demonstrated along with power measurements agreeing closely with the developed first-order theory.

Perinatal Morbidity in Healthy Obese Pregnant Individuals Delivered by Elective Repeat Cesarean at Term.

OBJECTIVE: This study aimed to compare the risks of adverse perinatal outcomes by body mass index (BMI) categories in healthy pregnant individuals delivered by term elective repeat cesarean (ERCD) to describe an optimal timing of delivery in otherwise healthy patients at the highest-risk BMI threshold. STUDY DESIGN: A secondary analysis of a prospective cohort of pregnant individuals undergoing ERCD at 19 centers in the Maternal-Fetal Medicine Units Network from 1999 to 2002. Nonanomalous singletons undergoing prelabor ERCD at term were included. The primary outcome was composite neonatal morbidity; secondary outcomes included composite maternal morbidity and individual components of the composites. Patients were stratified by BMI classes and to identify a BMI threshold for which morbidity was the highest. Outcomes were then examined by completed week's gestation, between BMI classes. Multivariable logistic regression was used to calculate adjusted odds ratios (aOR) and 95% confidence intervals (CI). RESULTS: A total of 12,755 patients were included in analysis. Patient's with BMI ≥ 40 had the highest rates of newborn sepsis, neonatal intensive care unit admissions, and wound complications. While a weight-related response was observed between BMI class and neonatal composite morbidity (p < 0.001), only those with BMI ≥ 40 had significantly higher odds of composite neonatal morbidity (aOR: 1.4, 95% CI: 1.0-1.8). In analyses of patients with BMI ≥ 40 (n = 1,848), there was no difference in the incidence of composite neonatal or maternal morbidity across weeks' gestation at delivery; however, as gestational age approached 39 to 40 weeks, rates of adverse neonatal outcomes decreased, only to increase again at 41 weeks' gestation. Of note, the odds of the primary neonatal composite were the highest at 38 weeks compared with 39 weeks (aOR: 1.5, 95% CI: 1.1-2.0). CONCLUSION: Neonatal morbidity is significantly higher in pregnant individuals with BMI ≥40 delivering by ERCD. Despite this increased perinatal morbidity, delivery prior to 39 and after 41 weeks in these patients is associated with increased neonatal risks. KEY POINTS: · Obese patients without additional comorbidities have higher rates of neonatal morbidity.. · Patients with BMI ≥ 40 carry the highest odds of poor perinatal outcomes.. · Earlier timing of delivery does not appear to reduce this risk..

Multi-material freeform gradient-index spectrometers.

With the advent of 3D printing optical elements, new techniques for manufacturing gradient-index (GRIN) optics have been realized that blend multiple materials in the deposition process. A method to achieve spectral splitting using multi-material GRIN optics is presented. The GRIN is additionally used to generate optical power, allowing for planar entrance and exit surfaces. It is shown that this simultaneous focusing and spectral splitting is not feasible with a two-material GRIN. A comparative design study is then conducted using three and four-material GRIN. A four-material design with optimized materials is also presented to showcase the potential for this new design form.

Achromatization of multi-material gradient-index singlets.

Recent advancements in additive manufacturing have enabled new methods of fabricating gradient-index (GRIN) optics by blending multiple materials in the deposition process. A design study highlighting the advantages of multi-material GRIN optics is presented. It is shown that additional materials in the GRIN allow for higher orders of color correction. A new multi-material refractive index representation, which constrains the GRIN to real materials, is also presented.