The underappreciated diversity of bile acid modifications.

The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.

Current advances in primate genomics: novel approaches for understanding evolution and disease.

Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.

Human prostate organoid generation and the identification of prostate development drivers using inductive rodent tissues.

The reactivation of developmental genes and pathways during adulthood may contribute to pathogenesis of diseases such as prostate cancer. Analysis of the mechanistic links between development and disease could be exploited to identify signalling pathways leading to disease in the prostate. However, the mechanisms underpinning prostate development require further characterisation to interrogate fully the link between development and disease. Previously, our group developed methods to produce prostate organoids using induced pluripotent stem cells (iPSCs). Here, we show that human iPSCs can be differentiated into prostate organoids using neonatal rat seminal vesicle mesenchyme in vitro. The organoids can be used to study prostate development or modified to study prostate cancer. We also elucidated molecular drivers of prostate induction through RNA-sequencing analyses of the rat urogenital sinus and neonatal seminal vesicles. We identified candidate drivers of prostate development evident in the inductive mesenchyme and epithelium involved with prostate specification. Our top candidates included Spx, Trib3, Snai1, Snai2, Nrg2 and Lrp4. This work lays the foundations for further interrogation of the reactivation of developmental genes in adulthood, leading to prostate disease.

Static and dynamic magnetic properties of circular and square cobalt nanodots in hexagonal cells.

In this work we performed a detailed numerical analysis to investigate the static and dynamic magnetic properties of hexagonal cells of square and circular cobalt nanodots as a function of the distance between them and the external magnetic field to which they are subjected. By simulating hysteresis curves with the external magnetic field applied parallel and perpendicular to the plane of these nanostructures, we can conclude that the cobalt nanodots presented a significant perpendicular magnetic anisotropy. We also obtained that the coercivity increases with decreasing volume, which implies that the circular dots have a higher coercivity than the square dots. Furthermore, we studied the dynamic susceptibility of these systems and found that it is possible to control both the position and the number of resonance peaks by controlling the geometry and the distance between the magnetic nanodots. This work provides useful information on the behaviour of cobalt nanodot arrays, opening paths for the design and improvement of two-dimensional technological devices.

Relative contributions of the supraspinatus cord and strap tendons to shoulder abduction and translation.

BACKGROUND: The supraspinatus (SS) is formed by a larger anterior bipennate muscle with a cord-like tendon and a posterior unipennate muscle with a strap-like tendon. There is a tendinous connection between the 2 SS subunits. Yet, the relative mechanical contribution of the SS cord and SS strap musculotendinous units to load transmission and subsequent shoulder abduction force is unknown. We hypothesized that a simulated SS cord vs. an SS strap tear would generate less shoulder abduction force and, further, an intact SS cord would offset the expected abduction loss from an SS strap tear, but the inverse would not be true. MATERIALS AND METHODS: Twenty fresh-frozen cadaveric specimens were tested in a shoulder simulator with physiological load vectors applied to the upper and lower subscapularis, SS cord, SS strap, infraspinatus, and teres minor. The roles of the SS cord and SS strap muscles were delineated by varying their loads, while keeping constant loads on other muscles. The randomized testing trials included a native condition and 4 test cases that simulated tears by dropping the load and force transfer via the SS cord-to-SS strap connection by adding the load. Testing was completed at both 0° and 30° of abduction. During each test, shoulder abduction force, rotator cuff strains, and humeral translation were measured. RESULTS: Simulated isolated SS cord and SS strap tears led to a significantly lower shoulder abduction force (P < .001). A simulated cord tear at 0° and 30° reduced the abduction force by 53% and 38%, respectively. A simulated strap tear at 0° and 30° dropped the abduction force by 27% and 23%, respectively. The decline in the abduction force was larger for the SS cord tear vs. SS strap tear (P ≤ .001). An SS cord tear with full-load transfer to the strap was able to recover to native values at both 0° and 30° (P ≥ .288). Likewise, an SS strap tear with full-load transfer to the SS cord showed a similar recovery to native values at both 0° and 30° (P ≥ .155). During full-load transfer, the tendon strain followed the loading pattern. An SS cord tear or SS strap tear did not cause a change in humeral translation (P ≥ .303). DISCUSSION: The mechanical findings support the efficacy of nonoperative treatment of small (<10 mm) SS tears,11 because an intact SS strap tendon can effectively offset the abduction loss of a torn SS cord tear and vice versa.

The efficacy and safety of systemic corticosteroids as first line treatment for granulomatous lymphocytic interstitial lung disease.

BACKGROUND: Granulomatous and lymphocytic interstitial lung disease (gl-ILD) is a major cause of morbidity and mortality among patients with common variable immunodeficiency. Corticosteroids are recommended as first-line treatment for gl-ILD, but evidence for their efficacy is lacking. OBJECTIVES: This study analyzed the effect of high-dose corticosteroids (≥0.3 mg/kg prednisone equivalent) on gl-ILD, measured by high-resolution computed tomography (HRCT) scans, and pulmonary function test (PFT) results. METHODS: Patients who had received high-dose corticosteroids but no other immunosuppressive therapy at the time (n = 56) and who underwent repeated HRCT scanning or PFT (n = 39) during the retrospective and/or prospective phase of the Study of Interstitial Lung Disease in Primary Antibody Deficiency (STILPAD) were included in the analysis. Patients without any immunosuppressive treatment were selected as controls (n = 23). HRCT scans were blinded, randomized, and scored using the Hartman score. Differences between the baseline and follow-up HRCT scans and PFT were analyzed. RESULTS: Treatment with high-dose corticosteroids significantly improved HRCT scores and forced vital capacity. Carbon monoxide diffusion capacity significantly improved in both groups. Of 18 patients, for whom extended follow-up data was available, 13 achieved a long-term, maintenance therapy independent remission. All patients with relapse were retreated with corticosteroids, but only one-fifth of them responded. Two opportunistic infections were found in the corticosteroid treatment group, while overall infection rate was similar between cohorts. CONCLUSIONS: Induction therapy with high-dose corticosteroids improved HRCT scans and PFT results of patients with gl-ILD and achieved long-term remission in 42% of patients. It was not associated with major side effects. Low-dose maintenance therapy provided no benefit and efficacy was poor in relapsing disease.

Assessing mental health among students in the UAE: A cross-sectional study utilizing the DASS-21 scale.

Background: The escalating worldwide concerns for mental health, significantly amplified by the COVID-19 pandemic, necessitates understanding the impact on vulnerable populations, such as university students. This study aims to investigate the prevalence and implications of depression, anxiety, and stress among university students in the United Arab Emirates (UAE) using the Depression, Anxiety, and Stress Scale-21 Items (DASS-21). Methods: This study utilized convenience sampling to investigate the mental health of undergraduates in UAE universities using a bilingual DASS-21 questionnaire via Google Forms. Analysis was conducted using SPSS version 29.0, employing descriptive statistics, Chi-squared tests, Mann-Whitney tests, Kruskal-Wallis tests, and Multinomial Logistic Regression to analyze relationships between sociodemographic variables and mental health scores. Results: The study examined 332 students, with most female participants (81 %, n = 269) and individuals aged 18-20 (89.8 %, n = 298). It revealed higher mean DASS scores among females: Depression (M = 15.80, p = 0.030), Anxiety (M = 17.63, p < 0.001), and Stress (M = 22.61, p < 0.001). Fourth-year students exhibited the highest DASS scores for depression (M = 30.33, p = 0.002), anxiety (M = 21.33, p = 0.002), and stress (M = 27.00, p = 0.005). Younger participants aged 18-20 had an odds ratio (OR) of 4.925 for depression, indicating they were approximately five times more likely to experience depression. Conclusions: This study reveals gender, age, and academic-year variations in depression, anxiety, and stress among UAE university students. Specifically, our findings indicate higher levels of anxiety and stress among females and reveal academic-year and age-related patterns in mental health conditions. University support services in the UAE should better address student needs, including counseling focused on high school to university transition challenges.

Feeding during hibernation shifts gene expression toward active season levels in brown bears (Ursus arctos).

Hibernation in bears involves a suite of metabolical and physiological changes, including the onset of insulin resistance, that are driven in part by sweeping changes in gene expression in multiple tissues. Feeding bears glucose during hibernation partially restores active season physiological phenotypes, including partial resensitization to insulin, but the molecular mechanisms underlying this transition remain poorly understood. Here, we analyze tissue-level gene expression in adipose, liver, and muscle to identify genes that respond to midhibernation glucose feeding and thus potentially drive postfeeding metabolical and physiological shifts. We show that midhibernation feeding stimulates differential expression in all analyzed tissues of hibernating bears and that a subset of these genes responds specifically by shifting expression toward levels typical of the active season. Inferences of upstream regulatory molecules potentially driving these postfeeding responses implicate peroxisome proliferator-activated receptor gamma (PPARG) and other known regulators of insulin sensitivity, providing new insight into high-level regulatory mechanisms involved in shifting metabolic phenotypes between hibernation and active states.

Race and outcomes after percutaneous coronary intervention: Insights from the Blue Cross Blue Shield of Michigan Cardiovascular Consortium.

BACKGROUND: Current studies show similar in-hospital outcomes following percutaneous coronary intervention (PCI) between Black and White patients. Long-term outcomes and the role of individual and community-level socioeconomic factors in differential risk are less understood. METHODS: We linked clinical registry data from PCIs performed between January, 2013 and March, 2018 at 48 Michigan hospitals to Medicare Fee-for-service claims. We analyzed patients of Black and White race. We used propensity score matching and logistic regression models to estimate the odds of 90-day readmission and Cox regression to evaluate the risk of postdischarge mortality. We used mediation analysis to evaluate the proportion of association mediated by socioeconomic factors. RESULTS: Of the 29,317 patients included in this study, 10.28% were Black and 89.72% were White. There were minimal differences between groups regarding post-PCI in-hospital outcomes. Compared with White patients, Black patients were more likely to be readmitted within 90-days of discharge (adjusted OR 1.62, 95% CI [1.32-2.00]) and had significantly higher risk of all-cause mortality (adjusted HR 1.45, 95% CI 1.30-1.61) when adjusting for age and gender. These associations were significantly mediated by dual eligibility (proportion mediated [PM] for readmission: 11.0%; mortality: 21.1%); dual eligibility and economic well-being of the patient's community (PM for readmission: 22.3%; mortality: 43.0%); and dual eligibility, economic well-being of the community, and baseline clinical characteristics (PM for readmission: 45.0%; mortality: 87.8%). CONCLUSIONS: Black patients had a higher risk of 90-day readmission and cumulative mortality following PCI compared with White patients. Associations were mediated by dual eligibility, community economic well-being, and traditional cardiovascular risk factors. Our study highlights the need for improved upstream care and streamlined postdischarge care pathways as potential strategies to improve health care disparities in cardiovascular disease.

Stereotactic Body Radiation Therapy Salvage for Lymph Node Recurrent Prostate Cancer in the Era of PSMA PET Imaging.

PURPOSE OF REVIEW: Our understanding of patterns of prostate cancer recurrence after primary treatment of localized disease has significantly evolved since the development of positron emission tomography (PET) agents targeting prostate cancer. Previously, most biochemical recurrences were not associated with imaging correlates when restaging with computed tomography (CT), magnetic resonance imaging (MRI), or bone scintigraphy and, hence, were typically assumed to represent occult metastases. A rising prostate specific antigen (PSA) after previous local therapy prompting a PET scan showing uptake limited to regional lymph nodes is an increasingly common clinical scenario as advanced prostate cancer imaging becomes more widely utilized. The optimal management strategy for patients who have lymph node recurrent prostate cancer is both unclear and evolving, particularly in terms of local and regionally directed therapies. Stereotactic body radiation therapy (SBRT) utilizes ablative radiation doses with steep gradients to achieve local tumor control while sparing nearby normal tissues. SBRT is an attractive therapeutic modality due to its efficacy, favorable toxicity profile, and flexibility to administer elective doses to areas of potential occult involvement. The purpose of this review is to briefly describe how SBRT is being implemented in the era of PSMA PET for the management of solely lymph node recurrent prostate cancer. RECENT FINDINGS: SBRT has been shown to effectively control individual lymph node tumor deposits within the pelvis and retroperitoneum for prostate cancer and is well-tolerated with a favorable toxicity profile. However, a major limitation thus far has been the lack of prospective trials supporting the use of SBRT for oligometastatic nodal recurrent prostate cancer. As further trials are conducted, its exact role in the treatment paradigm of recurrent prostate cancer will be better established. Although PET-guided SBRT appears feasible and potentially beneficial, there is still considerable uncertainty about the use of elective nodal radiotherapy (ENRT) in patients with nodal recurrent oligometastatic prostate cancer. PSMA PET has undoubtedly advanced imaging of recurrent prostate cancer, revealing anatomic correlates for disease recurrence that previously went undetected. At the same time, SBRT continues to be explored in prostate cancer with feasibility, a favorable risk profile, and satisfactory oncologic outcomes. However, much of the existing literature comes from the pre-PSMA PET era and integration of this novel imaging approach has led to greater focus on new and ongoing clinical trials to rigorously evaluate this approach and compare to other established treatment modalities utilized for oligometastatic, nodal recurrence of prostate cancer.

Investigation of the opto-thermo-mechanical properties of antimicrobial PET/TiO2 fiber using the transport of intensity equation technique.

The transport of intensity equation (TIE) technique is used to investigate the effect of stretching and annealing conditions on the optical features and antimicrobial activity of polyethylene terephthalate (PET) fibers treated with TiO2 nanoparticles. The main core of this paper gets the most preferable optical and mechanical properties for PET/TiO2 fiber which maintains its antibacterial activity. The variation of the refractive index of untreated PET/TiO2 fiber along its axis is studied. The computed tomography technique is used to investigate the morphology of the tested fiber and the distribution of TiO2 nanoparticles inside the fiber. The effect of stretching on the refractive index and the density of TiO2 nanoparticles of drawn PET/TiO2 fibers are carried out. The antimicrobial activity of the PET/TiO2 fibers are evaluated before and after stretching. The PET/TiO2 fibers are annealed at different temperatures and durations. The influence of annealing on the variation of the refractive index of PET/TiO2 fiber along its axis and the distribution of TiO2 is investigated.

Prenylated Benzophenones from Vismia Guianensis Reduced Nematode Growth and Chemotaxis.

Biopesticides are generally considered a safer and more environmentally friendly alternative to conventional pesticides. Plant metabolites display a range of pest specific activity ranging from antimicrobial to larvicidal and nematocidal. We herein describe the evaluation of a Guyanese collection of Vismia guianensis (Clusiaceae) for anthelmintic activity. The bioassay-guided evaluation of the hexane extract yielded the new prenylated benzophenone 8,9-epoxyvismiaphenone F (1). The final structures were elucidated based on spectral analysis and comparison to the known metabolite. To evaluate the anthelmintic efficacy of these compounds, Caenorhabditis elegans were exposed to the compounds via a ring assay model. Post-exposure, the numbers of live C. elegans in the compound (middle), bacteria ring were recorded for 3 d, as well as the total number of live worms for each plate. Compound 1 reduced C. elegans' overall growth and reproduction, suggesting that these prenylated benzophenones may hold some promise as natural pesticides.

Loss of ephrin B2 receptor (EPHB2) sets lipid rheostat by regulating proteins DGAT1 and ATGL inducing lipid droplet storage in prostate cancer cells.

Lipid droplet (LD) accumulation in cancer results from aberrant metabolic reprograming due to increased lipid uptake, diminished lipolysis and/or de novo lipid synthesis. Initially implicated in storage and lipid trafficking in adipocytes, LDs are more recently recognized to fuel key functions associated with carcinogenesis and progression of several cancers, including prostate cancer (PCa). However, the mechanisms controlling LD accumulation in cancer are largely unknown. EPHB2, a tyrosine kinase (TKR) ephrin receptor has been proposed to have tumor suppressor functions in PCa, although the mechanisms responsible for these effects are unclear. Given that dysregulation in TRK signaling can result in glutaminolysis we postulated that EPHB2 might have potential effects on lipid metabolism. Knockdown strategies for EPHB2 were performed in prostate cancer cells to analyze the impact on the net lipid balance, proliferation, triacylglycerol-regulating proteins, effect on LD biogenesis, and intracellular localization of LDs. We found that EPHB2 protein expression in a panel of human-derived prostate cancer cell lines was inversely associated with in vivo cell aggressiveness. EPHB2 silencing increased the proliferation of prostate cancer cells and concurrently induced de novo LD accumulation in both cytoplasmic and nuclear compartments as well as a "shift" on LD size distribution in newly formed lipid-rich organelles. Lipid challenge using oleic acid exacerbated the effects on the LD phenotype. Loss of EPHB2 directly regulated key proteins involved in maintaining lipid homeostasis including, increasing lipogenic DGAT1, DGAT2 and PLIN2 and decreasing lipolytic ATGL and PEDF. A DGAT1-specific inhibitor abrogated LD accumulation and proliferative effects induced by EPHB2 loss. In conclusion, we highlight a new anti-tumor function of EPHB2 in lipid metabolism through regulation of DGAT1 and ATGL in prostate cancer. Blockade of DGAT1 in EPHB2-deficient tumors appears to be effective in restoring the lipid balance and reducing tumor growth.

Defining the temporal evolution of gut dysbiosis and inflammatory responses leading to hepatocellular carcinoma in Mdr2 -/- mouse model.

BACKGROUND: Emerging evidence implicates the gut microbiome in liver inflammation and hepatocellular carcinoma (HCC) development. We aimed to characterize the temporal evolution of gut dysbiosis, in relation to the phenotype of systemic and hepatic inflammatory responses leading to HCC development. In the present study, Mdr2 -/- mice were used as a model of inflammation-based HCC. Gut microbiome composition and function, in addition to serum LPS, serum cytokines/chemokines and intrahepatic inflammatory genes were measured throughout the course of liver injury until HCC development. RESULTS: Early stages of liver injury, inflammation and cirrhosis, were characterized by dysbiosis. Microbiome functional pathways pertaining to gut barrier dysfunction were enriched during the initial phase of liver inflammation and cirrhosis, whilst those supporting lipopolysaccharide (LPS) biosynthesis increased as cirrhosis and HCC ensued. In parallel, serum LPS progressively increased during the course of liver injury, corresponding to a shift towards a systemic Th1/Th17 proinflammatory phenotype. Alongside, the intrahepatic inflammatory gene profile transitioned from a proinflammatory phenotype in the initial phases of liver injury to an immunosuppressed one in HCC. In established HCC, a switch in microbiome function from carbohydrate to amino acid metabolism occurred. CONCLUSION: In Mdr2 -/- mice, dysbiosis precedes HCC development, with temporal evolution of microbiome function to support gut barrier dysfunction, LPS biosynthesis, and redirection of energy source utilization. A corresponding shift in systemic and intrahepatic inflammatory responses occurred supporting HCC development. These findings support the notion that gut based therapeutic interventions could be beneficial early in the course of liver disease to halt HCC development.

Environment and pathogens shape local and regional adaptations to climate change in the chocolate tree, Theobroma cacao L.

Predicting the potential fate of a species in the face of climate change requires knowing the distribution of molecular adaptations across the geographic range of the species. In this work, we analysed 79 genomes of Theobroma cacao, an Amazonian tree known for the fruit from which chocolate is produced, to evaluate how local and regional molecular signatures of adaptation are distributed across the natural range of the species. We implemented novel techniques that incorporate summary statistics from multiple selection scans to infer selective sweeps. The majority of the molecular adaptations in the genome are not shared among populations. We show that ~71.5% of genes under selection also show significant associations with changes in environmental variables. Our results support the interpretation that these genes contribute to local adaptation of the populations in response to abiotic factors. We also found strong patterns of molecular adaptation in a diverse array of disease resistance genes (6.5% of selective sweeps), suggesting that differential adaptation to pathogens also contributes significantly to local adaptations. Our results are consistent with the interpretation that local selective pressures are more important than regional selective pressures in explaining adaptation across the range of a species.

Epidemiology of hospitalized patients with COVID-19 in a tertiary care hospital.

INTRODUCTION: COVID-19, caused by the betacoronavirus SARS-CoV-2, has overwhelmed the world's health systems. OBJECTIVE: To describe the epidemiological characteristics of patients treated in a tertiary care hospital. METHODS: A retrospective cohort study of patients diagnosed with or suspected of having COVID-19 from March 23 to July 31, 2020 was conducted. RESULTS: 4,401 patients were hospitalized at Central Military Hospital, out of which 35 % were beneficiaries, 26 % civilians, 28 % active military personnel, and only 11 %, retired military personnel. Male gender predominated, both in hospitalized patients and in those who died, as well as the O+ group and absence of comorbidities; among the observed comorbidities, the main ones were overweight and diabetes. Hospitalized patients' median age was 49 years, while median age of those who died was 62 years; women older than 51 years had a higher risk of dying. Adjusted case fatality rate was 18.5 %; 50 % died within the first six days. CONCLUSIONS: In this study, the epidemiological characteristics and main comorbidities in Mexican patients with SARS-CoV-2 infection were identified.

INTRODUCCIÓN: COVID-19, causada por el betacoronavirus SARS-CoV-2, ha saturado los sistemas de salud del mundo. OBJETIVO: Describir las características epidemiológicas de los pacientes atendidos en un hospital de tercer nivel. MÉTODOS: Se realizó una cohorte retrospectiva de pacientes con diagnóstico o sospecha de COVID-19, del 23 de marzo al 31 de julio de 2020. RESULTADOS: En el Hospital Central Militar se hospitalizaron 4401 pacientes, 35 % derechohabientes, 26 % civiles, 28 % militares en activo y solo 11 %, militares retirados. Predominó el sexo masculino, tanto en los pacientes hospitalizados como en los que fallecieron, el grupo O+ y la ausencia de comorbilidades; entre las comorbilidades que se observaron, las principales fueron el sobrepeso y la diabetes. La mediana de edad de los pacientes hospitalizados fue de 49 años, mientras que 62 años fue la edad de quienes fallecieron; las mujeres mayores de 51 años tuvieron mayor riesgo de fallecer. La tasa de letalidad ajustada fue de 18.5 %; 50 % falleció durante los primeros seis días. CONCLUSIONES: En este estudio se lograron identificar las características epidemiológicas y se destacaron las principales comorbilidades en pacientes mexicanos con infección por SARS-CoV-2.

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations.

BACKGROUND: Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao - a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated. RESULTS: Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo. CONCLUSIONS: We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.

Tripolar chromosome segregation drives the association between maternal genotype at variants spanning PLK4 and aneuploidy in human preimplantation embryos.

Aneuploidy is prevalent in human embryos and is the leading cause of pregnancy loss. Many aneuploidies arise during oogenesis, increasing with maternal age. Superimposed on these meiotic aneuploidies are frequent errors occurring during early mitotic divisions, contributing to widespread chromosomal mosaicism. Here we reanalyzed a published dataset comprising preimplantation genetic testing for aneuploidy in 24 653 blastomere biopsies from day-3 cleavage-stage embryos, as well as 17 051 trophectoderm biopsies from day-5 blastocysts. We focused on complex abnormalities that affected multiple chromosomes simultaneously, seeking insights into their formation. In addition to well-described patterns such as triploidy and haploidy, we identified 4.7% of blastomeres possessing characteristic hypodiploid karyotypes. We inferred this signature to have arisen from tripolar chromosome segregation in normally fertilized diploid zygotes or their descendant diploid cells. This could occur via segregation on a tripolar mitotic spindle or by rapid sequential bipolar mitoses without an intervening S-phase. Both models are consistent with time-lapse data from an intersecting set of 77 cleavage-stage embryos, which were enriched for the tripolar signature among embryos exhibiting abnormal cleavage. The tripolar signature was strongly associated with common maternal genetic variants spanning the centrosomal regulator PLK4, driving the association we previously reported with overall mitotic errors. Our findings are consistent with the known capacity of PLK4 to induce tripolar mitosis or precocious M-phase upon dysregulation. Together, our data support tripolar chromosome segregation as a key mechanism generating complex aneuploidy in cleavage-stage embryos and implicate maternal genotype at a quantitative trait locus spanning PLK4 as a factor influencing its occurrence.

Heterogeneity of human prostate carcinoma-associated fibroblasts implicates a role for subpopulations in myeloid cell recruitment.

BACKGROUND: Carcinoma-associated fibroblasts (CAF) are a heterogeneous group of cells within the tumor microenvironment (TME) that can promote tumorigenesis in the prostate. By understanding the mechanism(s) by which CAF contributes to tumor growth, new therapeutic targets for the management of this disease may be identified. These studies determined whether unique sub-populations of human prostate CAF can be identified and functionally characterized. METHODS: Single-cell RNA-seq of primary human prostate CAF followed by unsupervised clustering was utilized to generate cell clusters based on differentially expressed (DE) gene profiles. Potential communication between CAF and immune cells was analyzed using in vivo tissue recombination by combining CAF or normal prostate fibroblasts (NPF) with non-tumorigenic, initiated prostate epithelial BPH-1 cells. Resultant grafts were assessed for inflammatory cell recruitment. RESULTS: Clustering of 3321 CAF allows for visualization of six subpopulations, demonstrating heterogeneity within CAF. Sub-renal capsule recombination assays show that the presence of CAF significantly increases myeloid cell recruitment to resultant tumors. This is supported by significantly increased expression of chemotactic chemokines CCL2 and CXCL12 in large clusters compared to other subpopulations. Bayesian analysis topologies also support differential communication signals between chemokine-related genes of individual clusters. Migration of THP-1 monocyte cells in vitro is stimulated in the presence of CAF conditioned medium (CM) compared with NPF CM. Further in vitro analyses suggest that CAF-derived chemokine CCL2 may be responsible for CAF-stimulated migration of THP-1 cells, since neutralization of this chemokine abrogates migration capacity. CONCLUSIONS: CAF clustering based on DE gene expression supports the concept that clusters have unique functions within the TME, including a role in immune/inflammatory cell recruitment. These data suggest that CCL2 produced by CAF may be involved in the recruitment of inflammatory cells, but may also directly regulate the growth of the tumor. Further studies aimed at characterizing the subpopulation(s) of CAF which promote immune cell recruitment to the TME and/or stimulate prostate cancer growth and progression will be pursued.

PEDF regulates plasticity of a novel lipid-MTOC axis in prostate cancer-associated fibroblasts.

Prostate tumors make metabolic adaptations to ensure adequate energy and amplify cell cycle regulators, such as centrosomes, to sustain their proliferative capacity. It is not known whether cancer-associated fibroblasts (CAFs) undergo metabolic re-programming. We postulated that CAFs augment lipid storage and amplify centrosomal or non-centrosomal microtubule-organizing centers (MTOCs) through a pigment epithelium-derived factor (PEDF)-dependent lipid-MTOC signaling axis. Primary human normal prostate fibroblasts (NFs) and CAFs were evaluated for lipid content, triacylglycerol-regulating proteins, MTOC number and distribution. CAFs were found to store more neutral lipids than NFs. Adipose triglyceride lipase (ATGL) and PEDF were strongly expressed in NFs, whereas CAFs had minimal to undetectable levels of PEDF or ATGL protein. At baseline, CAFs demonstrated MTOC amplification when compared to 1-2 perinuclear MTOCs consistently observed in NFs. Treatment with PEDF or blockade of lipogenesis suppressed lipid content and MTOC number. In summary, our data support that CAFs have acquired a tumor-like phenotype by re-programming lipid metabolism and amplifying MTOCs. Normalization of MTOCs by restoring PEDF or by blocking lipogenesis highlights a previously unrecognized plasticity in centrosomes, which is regulated through a new lipid-MTOC axis.This article has an associated First Person interview with the first author of the paper.