Dynamic Control of X Chromosome Conformation and Repression by a Histone H4K20 Demethylase.

Chromatin modification and higher-order chromosome structure play key roles in gene regulation, but their functional interplay in controlling gene expression is elusive. We have discovered the machinery and mechanism underlying the dynamic enrichment of histone modification H4K20me1 on hermaphrodite X chromosomes during C. elegans dosage compensation and demonstrated H4K20me1's pivotal role in regulating higher-order chromosome structure and X-chromosome-wide gene expression. The structure and the activity of the dosage compensation complex (DCC) subunit DPY-21 define a Jumonji demethylase subfamily that converts H4K20me2 to H4K20me1 in worms and mammals. Selective inactivation of demethylase activity eliminates H4K20me1 enrichment in somatic cells, elevates X-linked gene expression, reduces X chromosome compaction, and disrupts X chromosome conformation by diminishing the formation of topologically associating domains (TADs). Unexpectedly, DPY-21 also associates with autosomes of germ cells in a DCC-independent manner to enrich H4K20me1 and trigger chromosome compaction. Our findings demonstrate the direct link between chromatin modification and higher-order chromosome structure in long-range regulation of gene expression.

Functional Selectivity in Cytokine Signaling Revealed Through a Pathogenic EPO Mutation.

Cytokines are classically thought to stimulate downstream signaling pathways through monotonic activation of receptors. We describe a severe anemia resulting from a homozygous mutation (R150Q) in the cytokine erythropoietin (EPO). Surprisingly, the EPO R150Q mutant shows only a mild reduction in affinity for its receptor but has altered binding kinetics. The EPO mutant is less effective at stimulating erythroid cell proliferation and differentiation, even at maximally potent concentrations. While the EPO mutant can stimulate effectors such as STAT5 to a similar extent as the wild-type ligand, there is reduced JAK2-mediated phosphorylation of select downstream targets. This impairment in downstream signaling mechanistically arises from altered receptor dimerization dynamics due to extracellular binding changes. These results demonstrate how variation in a single cytokine can lead to biased downstream signaling and can thereby cause human disease. Moreover, we have defined a distinct treatable form of anemia through mutation identification and functional studies.

A comprehensive analysis of clinical and polygenic germline influences on somatic mutational burden.

Tumor mutational burden (TMB), the total number of somatic mutations in the tumor, and copy number burden (CNB), the corresponding measure of aneuploidy, are established fundamental somatic features and emerging biomarkers for immunotherapy. However, the genetic and non-genetic influences on TMB/CNB and, critically, the manner by which they influence patient outcomes remain poorly understood. Here, we present a large germline-somatic study of TMB/CNB with >23,000 individuals across 17 cancer types, of which 12,000 also have extensive clinical, treatment, and overall survival (OS) measurements available. We report dozens of clinical associations with TMB/CNB, observing older age and male sex to have a strong effect on TMB and weaker impact on CNB. We additionally identified significant germline influences on TMB/CNB, including fine-scale European ancestry and germline polygenic risk scores (PRSs) for smoking, tanning, white blood cell counts, and educational attainment. We quantify the causal effect of exposures on somatic mutational processes using Mendelian randomization. Many of the identified features associated with TMB/CNB were additionally associated with OS for individuals treated at a single tertiary cancer center. For individuals receiving immunotherapy, we observed a complex relationship between PRSs for educational attainment, self-reported college attainment, TMB, and survival, suggesting that the influence of this biomarker may be substantially modified by socioeconomic status. While the accumulation of somatic alterations is a stochastic process, our work demonstrates that it can be shaped by host characteristics including germline genetics.

A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress.

The conserved transcriptional regulator heat shock factor 1 (Hsf1) is a key sensor of proteotoxic and other stress in the eukaryotic cytosol. We surveyed Hsf1 activity in a genome-wide loss-of-function library in Saccaromyces cerevisiae as well as ~78,000 double mutants and found Hsf1 activity to be modulated by highly diverse stresses. These included disruption of a ribosome-bound complex we named the Ribosome Quality Control Complex (RQC) comprising the Ltn1 E3 ubiquitin ligase, two highly conserved but poorly characterized proteins (Tae2 and Rqc1), and Cdc48 and its cofactors. Electron microscopy and biochemical analyses revealed that the RQC forms a stable complex with 60S ribosomal subunits containing stalled polypeptides and triggers their degradation. A negative feedback loop regulates the RQC, and Hsf1 senses an RQC-mediated translation-stress signal distinctly from other stresses. Our work reveals the range of stresses Hsf1 monitors and elucidates a conserved cotranslational protein quality control mechanism.

A bivalent tarantula toxin activates the capsaicin receptor, TRPV1, by targeting the outer pore domain.

Toxins have evolved to target regions of membrane ion channels that underlie ligand binding, gating, or ion permeation, and have thus served as invaluable tools for probing channel structure and function. Here, we describe a peptide toxin from the Earth Tiger tarantula that selectively and irreversibly activates the capsaicin- and heat-sensitive channel, TRPV1. This high-avidity interaction derives from a unique tandem repeat structure of the toxin that endows it with an antibody-like bivalency. The "double-knot" toxin traps TRPV1 in the open state by interacting with residues in the presumptive pore-forming region of the channel, highlighting the importance of conformational changes in the outer pore region of TRP channels during activation.

Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.

Cyclic dinucleotides (CDNs) have central roles in bacterial homeostasis and virulence by acting as nucleotide second messengers. Bacterial CDNs also elicit immune responses during infection when they are detected by pattern-recognition receptors in animal cells. Here we perform a systematic biochemical screen for bacterial signalling nucleotides and discover a large family of cGAS/DncV-like nucleotidyltransferases (CD-NTases) that use both purine and pyrimidine nucleotides to synthesize a diverse range of CDNs. A series of crystal structures establish CD-NTases as a structurally conserved family and reveal key contacts in the enzyme active-site lid that direct purine or pyrimidine selection. CD-NTase products are not restricted to CDNs and also include an unexpected class of cyclic trinucleotide compounds. Biochemical and cellular analyses of CD-NTase signalling nucleotides demonstrate that these cyclic di- and trinucleotides activate distinct host receptors and thus may modulate the interaction of both pathogens and commensal microbiota with their animal and plant hosts.

In men with LUTS in primary care, a standardized intervention reduced symptoms by a small amount at 12 mo.

SOURCE CITATION: Drake MJ, Worthington J, Frost J, et al. Treatment of lower urinary tract symptoms in men in primary care using a conservative intervention: cluster randomised controlled trial. BMJ. 2023;383:e075219. 37967894.

Hyper-active RAS/MAPK introduces cancer-specific mitotic vulnerabilities.

Aneuploidy, the incorrect number of whole chromosomes, is a common feature of tumors that contributes to their initiation and evolution. Preventing aneuploidy requires properly functioning kinetochores, which are large protein complexes assembled on centromeric DNA that link mitotic chromosomes to dynamic spindle microtubules and facilitate chromosome segregation. The kinetochore leverages at least two mechanisms to prevent aneuploidy: error correction and the spindle assembly checkpoint (SAC). BubR1, a factor involved in both processes, was identified as a cancer dependency and therapeutic target in multiple tumor types; however, it remains unclear what specific oncogenic pressures drive this enhanced dependency on BubR1 and whether it arises from BubR1's regulation of the SAC or error-correction pathways. Here, we use a genetically controlled transformation model and glioblastoma tumor isolates to show that constitutive signaling by RAS or MAPK is necessary for cancer-specific BubR1 vulnerability. The MAPK pathway enzymatically hyperstimulates a network of kinetochore kinases that compromises chromosome segregation, rendering cells more dependent on two BubR1 activities: counteracting excessive kinetochore-microtubule turnover for error correction and maintaining the SAC. This work expands our understanding of how chromosome segregation adapts to different cellular states and reveals an oncogenic trigger of a cancer-specific defect.

Mutation protocols share with sexual reproduction the physiological role of producing genetic variation within 'constraints that deconstrain'.

Because the universe of possible DNA sequences is inconceivably vast, organisms have evolved mechanisms for exploring DNA sequence space while substantially reducing the hazard that would otherwise accrue to any process of random, accidental mutation. One such mechanism is meiotic recombination. Although sexual reproduction imposes a seemingly paradoxical 50% cost to fitness, sex evidently prevails because this cost is outweighed by the advantage of equipping offspring with genetic variation to accommodate environmental vicissitudes. The potential adaptive utility of additional mechanisms for producing genetic variation has long been obscured by a presumption that the vast majority of mutations are deleterious. Perhaps surprisingly, the probability for adaptive variation can be increased by several mechanisms that generate mutations abundantly. Such mechanisms, here called 'mutation protocols', implement implicit 'constraints that deconstrain'. Like meiotic recombination, they produce genetic variation in forms that minimize potential for harm while providing a reasonably high probability for benefit. One example is replication slippage of simple sequence repeats (SSRs); this process yields abundant, reversible mutations, typically with small quantitative effect on phenotype. This enables SSRs to function as adjustable 'tuning knobs'. There exists a clear pathway for SSRs to be shaped through indirect selection favouring their implicit tuning-knob protocol. Several other molecular mechanisms comprise probable components of additional mutation protocols. Biologists might plausibly regard such mechanisms of mutation not primarily as sources of deleterious genetic mistakes but also as potentially adaptive processes for 'exploring' DNA sequence space.

Cough in Children and Adults: Diagnosis, Assessment and Management (CICADA). Summary of an updated position statement on chronic cough in Australia.

INTRODUCTION: Cough is the most common symptom leading to medical consultation. Chronic cough results in significant health care costs, impairs quality of life, and may indicate the presence of a serious underlying condition. Here, we present a summary of an updated position statement on cough management in the clinical consultation. MAIN RECOMMENDATIONS: Assessment of children and adults requires a focused history of chronic cough to identify any red flag cough pointers that may indicate an underlying disease. Further assessment with examination should include a chest x-ray and spirometry (when age > 6 years). Separate paediatric and adult diagnostic management algorithms should be followed. Management of the underlying condition(s) should follow specific disease guidelines, as well as address adverse environmental exposures and patient/carer concerns. First Nations adults and children should be considered a high risk group. The full statement from the Thoracic Society of Australia and New Zealand and Lung Foundation Australia for managing chronic cough is available at https://lungfoundation.com.au/resources/cicada-full-position-statement. CHANGES IN MANAGEMENT AS A RESULT OF THIS STATEMENT: Algorithms for assessment and diagnosis of adult and paediatric chronic cough are recommended. High quality evidence supports the use of child-specific chronic cough management algorithms to improve clinical outcomes, but none exist in adults. Red flags that indicate serious underlying conditions requiring investigation or referral should be identified. Early and effective treatment of chronic wet/productive cough in children is critical. Culturally specific strategies for facilitating the management of chronic cough in First Nations populations should be adopted. If the chronic cough does not resolve or is unexplained, the patient should be referred to a respiratory specialist or cough clinic.

Enhancing exercise performance and recovery through sodium bicarbonate supplementation: introducing the ingestion recovery framework.

Sodium bicarbonate (SB) supplementation is an ergogenic strategy for athletes competing in high-intensity exercise, but the efficacy of SB for accelerating recovery from exercise and thus improving performance during repeated bouts of exercise is not fully understood. In a similar fashion to using SB as a pre-exercise buffer, it is possible accelerated restoration of blood pH and bicarbonate following an exercise bout mechanistically underpins the use of SB as a recovery aid. Physiological mechanisms contributing to beneficial effects for SB during repeated bout exercise could be more far-reaching however, as alterations in strong ion difference (SID) and attenuated cellular stress response might also contribute to accelerated recovery from exercise. From inspection of existing literature, ingestion of 0.3 g kg-1 body mass SB ~60-90 min pre-exercise seems to be the most common dosage strategy, but there is evidence emerging for the potential application of post-exercise supplementation timing, gradual SB doses throughout a competition day, or even ingestion during exercise. Based on this review of literature, an SB ingestion recovery framework is proposed to guide athletes and practitioners on the use of SB to enhance performance for multiple bouts of exercise.

Cytisinicline increased smoking abstinence at 6 and 12 wk.

SOURCE CITATION: Rigotti NA, Benowitz NL, Prochaska J, et al. Cytisinicline for smoking cessation: a randomized clinical trial. JAMA. 2023;330:152-160. 37432430.

Systematic Review of Literature Citing the ISCHEMIA Trial.

PURPOSE OF REVIEW: Optimal therapy for patients with chronic coronary artery disease (CCD) has long been a topic under investigation and a subject of debate. Seeking to clarify appropriate management, the International Study of Comparative Health Effectiveness with Medical and Invasive Approaches (ISCHEMIA) trial compared medical management versus coronary angiography for patients with stable ischemic heart disease. Its reception in the medical community has been met with both acclaim and criticism. In light of such disparate views of this trial, a systematic review of the literature citing the ISCHEMIA trial was performed. RECENT FINDINGS: All articles citing the ISCHEMIA trial on PubMed as of July 21, 2023, were compiled and underwent qualitative analysis. A total of 430 articles were evaluated; 109 (25.3%) did not offer substantial commentary on ISCHEMIA and cite it as background evidence for further study. Of the commentary articles, the majority (224, 52.1%) gave balanced, honest appraisals of the ISCHEMIA trial. A total of 46 (10.7%) strongly praised the trial while another 39 (9.1%) were strongly critical of the results. Almost three-quarters of the literature citing the ISCHEMIA trial was commentary in nature, with roughly equal distribution across the spectrum of praise and criticism. Despite being one of the largest studies on CCD and coronary revascularization ever conducted, the impact of ISCHEMIA on the cardiology community appears to be mixed.

A large-scale assessment of eastern whip-poor-will (Antrostomus vociferus) occupancy across a gradient of forest management intensity using autonomous recording units.

Conservationists spend considerable resources to create and enhance wildlife habitat. Monitoring how species respond to these efforts helps managers allocate limited resources. However, monitoring efforts often encounter logistical challenges that are exacerbated as geographic extent increases. We used autonomous recording units (ARUs) and automated acoustic classification to mitigate the challenges of assessing Eastern Whip-poor-will (Antrostomus vociferus) response to forest management across the eastern USA. We deployed 1263 ARUs in forests with varying degrees of management intensity. Recordings were processed using an automated classifier and the resulting detection data were used to assess occupancy. Whip-poor-wills were detected at 401 survey locations. Across our study region, whip-poor-will occupancy decreased with latitude and elevation. At the landscape scale, occupancy decreased with the amount of impervious cover, increased with herbaceous cover and oak and evergreen forests, and exhibited a quadratic relationship with the amount of shrub-scrub cover. At the site-level, occupancy was negatively associated with basal area and brambles (Rubus spp.) and exhibited a quadratic relationship with woody stem density. Implementation of practices that create and sustain a mosaic of forest age classes and a diverse range of canopy closure within oak (Quercus spp.) dominated landscapes will have the highest probability of hosting whip-poor-wills. The use of ARUs and a machine learning classifier helped overcome challenges associated with monitoring a nocturnal species with a short survey window across a large spatial extent. Future monitoring efforts that combine ARU-based protocols and mappable fine-resolution structural vegetation data would likely further advance our understanding of whip-poor-will response to forest management.

Comparison of the Ultrasonography Features of the Breast in Women with Fibroadenoma and Those with Other Breast Lumps.

BACKGROUND: Fibroadenoma (FA) is documented as the most common benign breast disease typically presenting as a lump. A wide variety of other diseases including breast cancer can similarly present as lumps hence the need for further differentiation. Ultrasonography plays a vital role in the evaluation and treatment of breast lumps with histological analysis as the gold standard. OBJECTIVE: This study compared the physical and sonographic features of the breast in women with FA and women with breast lumps due to other diseases. MATERIALS AND METHODS: This is a single-centre comparative study. Clinical and sonographic breast evaluations of the recruited patients with lumps were done and reported using the American College of Radiology Breast Imaging Reporting and Data System score. The lumps were biopsied, and histological diagnosis was documented. Clinical and imaging features of the breasts of women with FA were then compared with those of women with lumps from other breast diseases, and collated data were analysed using SPSS Statistical version 23.0. RESULTS: Data from 118 subjects (59 in each group) were used for this study. There was a significant difference in the physical and sonographic appearance of FA concerning the patient's age, parity, change in lesion size, perilesional architecture, echogenicity, borders, capsule and background breast density. No FA was found in women with less dense breasts. CONCLUSION: The sonographic features of breasts showed some differences from the corresponding features of FA and other breast lesions. This has the potential to increase the efficiency of pre-operative diagnosis of FA and could be further applied in developing diagnostic criteria for FA in our environment.

Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses.

Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary relationships and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention's Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses.

Is the future female for turtles? Climate change and wetland configuration predict sex ratios of a freshwater species.

Climate change and land-use change are leading drivers of biodiversity decline, affecting demographic parameters that are important for population persistence. For example, scientists have speculated for decades that climate change may skew adult sex ratios in taxa that express temperature-dependent sex determination (TSD), but limited evidence exists that this phenomenon is occurring in natural settings. For species that are vulnerable to anthropogenic land-use practices, differential mortality among sexes may also skew sex ratios. We sampled the spotted turtle (Clemmys guttata), a freshwater species with TSD, across a large portion of its geographic range (Florida to Maine), to assess the environmental factors influencing adult sex ratios. We present evidence that suggests recent climate change has potentially skewed the adult sex ratio of spotted turtles, with samples following a pattern of increased proportions of females concomitant with warming trends, but only within the warmer areas sampled. At intermediate temperatures, there was no relationship with climate, while in the cooler areas we found the opposite pattern, with samples becoming more male biased with increasing temperatures. These patterns might be explained in part by variation in relative adaptive capacity via phenotypic plasticity in nest site selection. Our findings also suggest that spotted turtles have a context-dependent and multi-scale relationship with land use. We observed a negative relationship between male proportion and the amount of crop cover (within 300 m) when wetlands were less spatially aggregated. However, when wetlands were aggregated, sex ratios remained consistent. This pattern may reflect sex-specific patterns in movement that render males more vulnerable to mortality from agricultural machinery and other threats. Our findings highlight the complexity of species' responses to both climate change and land use, and emphasize the role that landscape structure can play in shaping wildlife population demographics.

Outcomes of limited stage primary bone diffuse large B-cell lymphoma in the rituximab era: a multicenter, retrospective study.

Primary bone diffuse large B cell lymphoma (DLBCL) is a rare variant of extranodal non-Hodgkin lymphoma (NHL) historically treated with induction chemotherapy followed by consolidative radiation therapy (RT). It remains unknown whether RT confers additional benefit following rituximab-based chemoimmunotherapy (CIT) induction in patients with limited-stage disease. We conducted a multicenter retrospective analysis of patients treated between 2005 and 2019 using rituximab-based CIT regimens with or without consolidative RT to discern whether consolidative RT adds benefit in patients with stage I-II disease that could be encompassed in one radiation field. A total of 112 patients were included: 78 received CIT and radiation (RT group), and 34 received CIT alone (no RT group). The OS at 10 years was 77.9% in the RT group and 89.0% in the no RT group (p = 0.42). The RFS at 10 years was 73.5% in the RT group and 80.3% in the no RT group (p = 0.88). Neither improved OS nor RFS was associated with the addition of consolidative RT. Subgroup analysis of patients only achieving a partial response after CIT suggests that these patients may benefit from consolidative RT.

Open Abdomen in Elderly Patients With Surgical Sepsis: Predictors of Mortality.

INTRODUCTION: Elderly patients are frequently presenting with emergency surgical conditions. The open abdomen technique is widely used in abdominal emergencies needing rapid control of intrabdominal contamination. However, specific predictors of mortality identifying candidates for comfort care are understudied. METHODS: The 2013-2017 the American College of Surgeons-National Surgical Quality Improvement Program database was queried for emergent laparotomies performed in geriatric patients with sepsis or septic shock in whom fascial closure was delayed. Patients with acute mesenteric ischemia were excluded. The primary outcome was 30-d mortality. Univariable analysis, followed by multivariable logistic regression, was performed. Mortality was computed for combinations of the five predictors with the highest odds ratios (OR). RESULTS: A total of 1399 patients were identified. The median age was 73 (69-79) y, and 54.7% were female. 30-d mortality was 50.6%. In the multivariable analysis, the most important predictors were as follows: American Society of Anesthesiologists status 5 (OR = 4.80, 95% confidence interval [CI], 1.85-12.49 P = 0.002), dialysis dependence (OR = 2.65, 95% CI 1.54-4.57, P < 0.001), congestive hearth failure (OR = 2.53, 95% CI 1.52-4.21, P < 0.001), disseminated cancer (OR = 2.61, 95% CI 1.55-4.38, P < 0.001), and preoperative platelet count of <100,000 cells/µL (OR = 1.87, 95% CI 1.15-3.04, P = 0.011). The presence of two or more of these factors resulted in over 80% mortality. The absence of all these risk factors results in a survival rate of 62.1%. CONCLUSIONS: In elderly patients, surgical sepsis or septic shock requiring an open abdomen for surgical management is highly lethal. The presence of several combinations of preoperative comorbidities is associated with a poor prognosis and can identify patients who can benefit from timely initiation of palliative care.

Outcomes of plastic surgical reconstruction in extremity and truncal soft tissue sarcoma: Results from the US Sarcoma Collaborative.

BACKGROUND: This study aimed to define how utilization of plastic surgical reconstruction (PSR) affects perioperative outcomes, locoregional recurrence-free survival (LRRFS), and overall survival (OS) after radical resection of extremity and truncal soft tissue sarcoma (ETSTS). The secondary aim was to determine factors associated with PSR. METHODS: Patients who underwent resection of ETSTS between 2000 and 2016 were identified from a multi-institutional database. PSR was defined as complex primary closure requiring a plastic surgeon, skin graft, or tissue-flap reconstruction. Outcomes included PSR utilization, postoperative complications, LRRFS, and OS. RESULTS: Of 2750 distinct operations, 1060 (38.55%) involved PSR. Tissue-flaps (854, 80.57%) were most commonly utilized. PSR was associated with a higher proportion of R0 resections (83.38% vs. 74.42%, p < 0.001). Tissue-flap PSR was associated with local wound complications (odds ratio: 1.81, confidence interval: 1.21-2.72, p = 0.004). Neither PSR nor postoperative complications were independently associated with LRRFS or OS. High-grade tumors (1.60, 1.13-2.26, p = 0.008) and neoadjuvant radiation (1.66, 1.20-2.30, p = 0.002) were associated with the need for PSR. CONCLUSION: Patients with ETSTS undergoing resection with PSR experienced acceptable rates of complications and a higher rate of negative margins, which were associated with improved LRRFS and OS. High tumor grade and neoadjuvant radiation were associated with requirement of PSR.