Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection.

BACKGROUND: Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. METHODS: We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. RESULTS: We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA-protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. CONCLUSIONS: This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Incidence of Surgical Reintervention for Benign Prostatic Hyperplasia Following Prostatic Urethral Lift, Transurethral Resection of the Prostate, and Photoselective Vaporization of the Prostate: A TriNetX Analysis.

Background: Prostatic urethral lift, or UroLift, has gained popularity as a treatment for lower urinary tract symptoms associated with benign prostatic hyperplasia (BPH). Surgical reintervention rates are a reliable indicator for treatment durability. Objective: The objective of this study was to utilize TriNetX, a third-party database, to investigate the incidence of surgical reintervention following UroLift, transurethral resection of the prostate (TURP), and photoselective vaporization of the prostate (PVP) procedures for BPH from 2015 to 2018. Design setting and participants: Male patients aged 18-100 yr diagnosed with BPH were identified in the TriNetX Diamond Network database between January 2015 and December 2018. Cohorts of individuals undergoing their first UroLift procedure were built using Current Procedural Terminology and International Classification of Diseases 10th Revision codes. TURP and PVP cohorts were built as comparison groups. The cohorts were then queried for subsequent BPH-related procedures. Outcome measurements and statistical analysis: Reprocedure rates were assessed and descriptive statistics were used. Results and limitations: The mean age at first-time UroLift was 70.1 ± 9.4 yr (n = 14 343). Cumulative reprocedure rates collected after first-time UroLift included 1 yr after UroLift (5.1%, n = 14 343) and 4 yr after UroLift (16.1%, n = 710), with an average annual increase of +3.6% per year following 1 yr after the procedure. Comparatively, TURP (n = 22 071) and PVP (n = 14 110) had 4-yr reprocedure rates of 7.5% and 7.8%, respectively, during the same timeframe. Limitations include a lack of clinical data and loss of follow-up data outside the Diamond Network. Conclusions: The reprocedure rate of UroLift at 4 yr is double the rate of TURP and PVP. In appropriately selected patients, UroLift might be a suitable option for those who desire symptomatic relief from BPH with minimal erectile and ejaculatory side effects. However, the risk of secondary surgical intervention should be considered when considering BPH treatments. Patient summary: We compared the reintervention rates of prostatic urethral lift (PUL), transurethral resection of the prostate (TURP), and photoselective vaporization of the prostate (PVP) using the TriNetX database, and have found that the highest reintervention rates were for PUL of 16% at 4 yr of follow-up, compared with about 8% for those who had TURP and PVP. Interestingly, the most common reintervention was the same operation at 1 yr. This has important implications when counseling patients about the durability of these various outlet procedures for BPH.

Basophils Play a Protective Role in the Recovery of Skin Barrier Function from Mechanical Injury in Mice.

Physical trauma disrupts skin barrier function. How the skin barrier recovers is not fully understood. We evaluated in mice the mechanism of skin barrier recovery after mechanical injury inflicted by tape stripping. Tape stripping disrupted skin barrier function as evidenced by increased transepidermal water loss. We show that tape stripping induces IL-1-, IL-23-, and TCRγδ+-dependent upregulation of cutaneous Il17a and Il22 expression. We demonstrate that IL-17A and IL-22 induce epidermal hyperplasia, promote neutrophil recruitment, and delay skin barrier function recovery. Neutrophil depletion improved the recovery of skin barrier function and decreased epidermal hyperplasia. Single-cell RNA sequencing and flow cytometry analysis of skin cells revealed basophil infiltration into tape-stripped skin. Basophil depletion upregulated Il17a expression, increased neutrophil infiltration, and delayed skin barrier recovery. Comparative analysis of genes differentially expressed in tape-stripped skin of basophil-depleted mice and Il17a-/- mice indicated that basophils counteract the effects of IL-17A on the expression of epidermal and lipid metabolism genes important for skin barrier integrity. Our results demonstrate that basophils play a protective role by downregulating Il17a expression after mechanical skin injury, thereby counteracting the adverse effect of IL-17A on skin barrier function recovery, and suggest interventions to accelerate this recovery.

Roots selectively decompose litter to mine nitrogen and build new soil carbon.

Plant-microbe interactions in the rhizosphere shape carbon and nitrogen cycling in soil organic matter (SOM). However, there is conflicting evidence on whether these interactions lead to a net loss or increase of SOM. In part, this conflict is driven by uncertainty in how living roots and microbes alter SOM formation or loss in the field. To address these uncertainties, we traced the fate of isotopically labelled litter into SOM using root and fungal ingrowth cores incubated in a Miscanthus x giganteus field. Roots stimulated litter decomposition, but balanced this loss by transferring carbon into aggregate associated SOM. Further, roots selectively mobilized nitrogen from litter without additional carbon release. Overall, our findings suggest that roots mine litter nitrogen and protect soil carbon.

Illuminating the daily life experiences of adolescents with and without ADHD: protocol for an ecological momentary assessment study.

INTRODUCTION: Adolescents with attention-deficit/hyperactivity disorder (ADHD) are at elevated risk of a range of difficulties, among which emotion regulation, peer and co-occurring mental health problems are prominent challenges. To better support adolescents with ADHD, ecologically valid interventions that can be embedded in daily life to target the most proximal antecedents of these challenges are needed. Ecological momentary assessment (EMA) designs are ideally suited to meeting this need. METHODS AND ANALYSES: In the mental health in the moment ADHD study, we will use an EMA design to capture the daily life experiences of approximately 120 adolescents aged 11-14 years with a clinical diagnosis of ADHD and the same number of age-matched and gender-matched peers without a diagnosis of ADHD. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the role of emotion regulation and peer problems in mediating the links between characteristics of ADHD and commonly co-occurring outcomes such as anxiety, depression and conduct problems. The results can help inform interventions to support improved peer functioning and emotion regulation for adolescents with ADHD. ETHICS AND DISSEMINATION: This study received a favourable ethical opinion through the National Health Service ethical review board and the University of Edinburgh PPLS Research Ethics panel. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders, such as those with ADHD, their families and clinicians.

Fungivorous nematodes drive microbial diversity and carbon cycling in soil.

Soil bacteria and fungi mediate terrestrial biogeochemical cycling, but we know relatively little about how trophic interactions influence their community composition, diversity, and function. Specifically, it is unclear how consumer populations affect the activity of microbial taxa they consume, and therefore the interaction of those taxa with other members of the microbial community. Due to its extreme diversity, studying trophic dynamics in soil is a complex feat. Seeking to address these challenges, we performed a microcosm-based consumer manipulation experiment to determine the impact of a common fungal-feeding nematode (Aphelenchus avenae) on soil microbial community composition, diversity, and activity (e.g., C cycling parameters). Fungivory decreased fungal and bacterial α-diversity and stimulated C and N cycling, possibly via cascading impacts of fungivory on bacterial communities. Our results present experimental evidence that soil trophic dynamics are intimately linked with microbial diversity and function, factors that are key in understanding global patterns in biogeochemical cycling.

Acute effects of vasoactive medications in patients with parallel circulation awaiting hybrid or Norwood procedure.

Background: Vasoactive medications are frequently used in the preoperative stage to balance the pulmonary and systemic blood flow. However, not much is known about the effects of these agents during this stage. Aims: The primary objective of this study was to characterize the acute effects of vasoactive medications in children with parallel circulation before either the hybrid or Norwood procedure. Setting and Designs: This is a single-center, cross-sectional, retrospective study. Methods: Hemodynamic and systemic oxygen delivery data were captured from patients' vital signs, arterial blood gases, near-infrared spectroscopy monitoring (NIRS). Data for each patient were collected before the initiation of a vasoactive medication and again 6 h after. Statistical Analysis: Data were analyzed using paired t-tests, and analysis of covariance. Results: A total of 139 patients were identified. After data extraction the following patients were included before the initial intervention: 7 were on milrinone, 22 were on dopamine, and 17 were on dobutamine. Dopamine and dobutamine were found to significantly increase systolic blood pressure. Only dopamine increased pH (mean difference 0.04), decreased paCO2 (mean difference -7.1), decreased lactate (mean difference -0.6 mmol/L), and decreased in bedside Qp: Qs (mean difference -7.5) after continuous infusion for 6 h. Milrinone was not associated with any significant hemodynamic change. Conclusion: In this study, dopamine was independently associated with improvement in markers of systemic oxygen delivery 6 h after initiation. Dobutamine and dopamine were associated with increased in blood pressure. Well-powered studies are required to detect changes in lactate and NIRS.

Assessing the quality of RNA isolated from human breast tissue after ambient room temperature exposure.

High quality human tissue is essential for molecular research, but pre-analytical conditions encountered during tissue collection could degrade tissue RNA. We evaluated how prolonged exposure of non-diseased breast tissue to ambient room temperature (22±1°C) impacted RNA quality. Breast tissue received between 70 to 190 minutes after excision was immediately flash frozen (FF) or embedded in Optimal Cutting Temperature (OCT) compound upon receipt (T0). Additional breast tissue pieces were further exposed to increments of 60 (T1 = T0+60 mins), 120 (T2 = T0+120 mins) and 180 (T3 = T0+180 mins) minutes of ambient room temperature before processing into FF and OCT. Total exposure, T3 (T0+180 mins) ranged from 250 minutes to 370 minutes. All samples (FF and OCT) were stored at -80°C before RNA isolation. The RNA quality assessment based on RNA Integrity Number (RIN) showed RINs for both FF and OCT samples were within the generally acceptable range (mean 7.88±0.90 to 8.52±0.66). No significant difference was observed when RIN at T0 was compared to RIN at T1, T2 and T3 (FF samples, p = 0.43, 0.56, 0.44; OCT samples, p = 0.25, 0.82, 1.0), or when RIN was compared between T1, T2 and T3. RNA quality assessed by quantitative real-time PCR (qRT-PCR) analysis of beta-actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin A (CYPA), and porphobilinogen deaminase (PBGD) transcripts showed threshold values (Ct) that indicate abundant and intact target nucleic acid in all samples (mean ranging from 14.1 to 25.3). The study shows that higher RIN values were obtained for non-diseased breast tissue up to 190 minutes after resection and prior to stabilization. Further experimental exposure up to 180 minutes had no significant effect on RIN values. This study strengthens the rationale for assessing RIN and specific gene transcript levels as an objective method for determining how suitable RNA will be for a specific research purpose ("fit-for purpose").

The effect of prescribing antibiotics with opioids on the development of opioid use disorder: a national database study.

The goal of this study was to examine the impact of inpatient- or emergency department- prescribed antibiotic treatment in combination with opioids on the risk of developing opioid use disorder 12 months following discharge from the hospital. The authors conducted a propensity score-matched cohort study with data from the TriNetX Research Network database to identify adult subjects (18-65 years old) with no previous history of an opioid use disorder. Three cohorts were defined for the analyses: subjects who were prescribed an opioid, opioid in combination with an antibiotic, or an antibiotic while in the emergency department or inpatient unit, from the years 2012 to 2018. The diagnosis of an Opioid Related Disorder (F11.10-F11.20) 12 months following discharge from the emergency department or inpatient unit was then observed within the cohorts following the index event as identified by the ICD-10 procedural coding system. Primary analysis (propensity-score matched on age and sex) showed that opioids prescribed in combination with antibiotics had a protective effect against the development of opioid use disorder. This effect was consistent throughout all of the years included in this study with the smallest protective effect observed in 2018 (2012 risk ratio = 1.27 (95% CI: 1.23, 1.32); 2018 risk ratio: 1.03 (95% CI: 1.01, 1.05). These findings suggest that opioids prescribed in combination with antibiotics in the hospital setting are protective against the development of OUD at later time points following hospital discharge.

Understanding the Origins of Problem Geomagnetic Storms Associated with "Stealth" Coronal Mass Ejections.

Geomagnetic storms are an important aspect of space weather and can result in significant impacts on space- and ground-based assets. The majority of strong storms are associated with the passage of interplanetary coronal mass ejections (ICMEs) in the near-Earth environment. In many cases, these ICMEs can be traced back unambiguously to a specific coronal mass ejection (CME) and solar activity on the frontside of the Sun. Hence, predicting the arrival of ICMEs at Earth from routine observations of CMEs and solar activity currently makes a major contribution to the forecasting of geomagnetic storms. However, it is clear that some ICMEs, which may also cause enhanced geomagnetic activity, cannot be traced back to an observed CME, or, if the CME is identified, its origin may be elusive or ambiguous in coronal images. Such CMEs have been termed "stealth CMEs". In this review, we focus on these "problem" geomagnetic storms in the sense that the solar/CME precursors are enigmatic and stealthy. We start by reviewing evidence for stealth CMEs discussed in past studies. We then identify several moderate to strong geomagnetic storms (minimum Dst < - 50  nT) in solar cycle 24 for which the related solar sources and/or CMEs are unclear and apparently stealthy. We discuss the solar and in situ circumstances of these events and identify several scenarios that may account for their elusive solar signatures. These range from observational limitations (e.g., a coronagraph near Earth may not detect an incoming CME if it is diffuse and not wide enough) to the possibility that there is a class of mass ejections from the Sun that have only weak or hard-to-observe coronal signatures. In particular, some of these sources are only clearly revealed by considering the evolution of coronal structures over longer time intervals than is usually considered. We also review a variety of numerical modelling approaches that attempt to advance our understanding of the origins and consequences of stealthy solar eruptions with geoeffective potential. Specifically, we discuss magnetofrictional modelling of the energisation of stealth CME source regions and magnetohydrodynamic modelling of the physical processes that generate stealth CME or CME-like eruptions, typically from higher altitudes in the solar corona than CMEs from active regions or extended filament channels.

Basophil-derived IL-4 promotes cutaneous Staphylococcus aureus infection.

Superficial cutaneous Staphylococcus aureus (S. aureus) infection in humans can lead to soft tissue infection, an important cause of morbidity and mortality. IL-17A production by skin TCRγδ+ cells in response to IL-1 and IL-23 produced by epithelial and immune cells is important for restraining S. aureus skin infection. How S. aureus evades this cutaneous innate immune response to establish infection is not clear. Here we show that mechanical injury of mouse skin by tape stripping predisposed mice to superficial skin infection with S. aureus. Topical application of S. aureus to tape-stripped skin caused cutaneous influx of basophils and increased Il4 expression. This basophil-derived IL-4 inhibited cutaneous IL-17A production by TCRγδ+ cells and promoted S. aureus infection of tape-stripped skin. We demonstrate that IL-4 acted on multiple checkpoints that suppress the cutaneous IL-17A response. It reduced Il1 and Il23 expression by keratinocytes, inhibited IL-1+IL-23-driven IL-17A production by TCRγδ+ cells, and impaired IL-17A-driven induction of neutrophil-attracting chemokines by keratinocytes. IL-4 receptor blockade is shown to promote Il17a expression and enhance bacterial clearance in tape-stripped mouse skin exposed to S. aureus, suggesting that it could serve as a therapeutic approach to prevent skin and soft tissue infection.

Unusual Case of Nephrotic Syndrome From Light Chain Amyloidosis in a 37-Year-Old Patient.

Amyloidosis with renal involvement is a well-known cause of nephrotic syndrome. Immunoglobulin light-chain amyloidosis (AL), which is a result of monoclonal light-chain deposition in the kidney from plasma cell dyscrasia, is rare before the age of 40 and typically occurs in old patients. Most cases of renal amyloidosis in young patients are secondary to chronic inflammatory disease. We are reporting a case of a 37-year-old male who was transferred to our hospital for evaluation of possibly acquired bleeding disorder. He was initially presented to an outside hospital with bleeding per rectum for three days duration and one-week history of abdominal pain and bloating. He was found to have nephrotic range proteinuria with hypoalbuminemia and hyperlipidemia. A kidney biopsy was performed to identify the cause of his nephrotic syndrome, and a biopsy showed AL amyloidosis. Bone marrow biopsy performed showed plasma cell myeloma, and the patient was started on induction chemotherapy. Even though the incidence of AL amyloidosis is low before age of 40, we should always perform monoclonal gammopathy workup in patients with nephrotic syndrome regardless of the age. Prompt bone marrow biopsy should be performed to confirm the diagnosis, and starting the treatment as one of the factors that affect the prognosis of AL amyloidosis is early diagnosis.

Subungual Nail Erythrasma Presenting as Melanonychia: A Rare Finding.

Nail pathology may reflect a wide array of localized and systemic dermatological conditions. Certain nail findings such as melanonychia can create diagnostic challenges even to nail experts. We report a case of a 78-year-old man who presented with melanonychia of the great toe. Nail clipping showed focal melanin deposition, and dermoscopy demonstrated a region of localized erythema in the lunula concerning for possible melanocytic neoplasm. Subsequent nail biopsy showed numerous vertically oriented filamentous bacteria and coccobacilli within the nail plate consistent with a diagnosis of subungual nail erythrasma. Nail erythrasma is a rare entity. Additionally, this case highlights a new clinical presentation of nail erythrasma as melanonychia.

Soil microbial succession following surface mining is governed primarily by deterministic factors.

Understanding the successional dynamics governing soil microbial community assembly following disturbance can aid in developing remediation strategies for disturbed land. However, the influences shaping microbial communities during succession following soil disturbance remain only partially understood. One example of a severe disturbance to soil is surface mining for natural resources, which displaces communities and changes the physical and chemical soil environment. These changes may alter community composition through selective pressure on microbial taxa (i.e. deterministic processes). Dispersal and ecological drift may also shape communities following disturbance (i.e. stochastic processes). Here, the relative influence of stochastic and deterministic processes on microbial community succession was investigated using a chronosequence of reclaimed surface mines ranging from 2-32 years post-reclamation. Sequencing of bacterial and fungal ribosomal gene amplicons coupled with a linear modeling approach revealed that following mine reclamation, while bacterial communities are modestly influenced by stochastic factors, the influence of deterministic factors was ∼7 × greater. Fungal communities were influenced only by deterministic factors. Soil organic matter, texture, and pH emerged as the most influential environmental factors on both bacterial and fungal communities. Our results suggest that management of deterministic soil characteristics over a sufficient time period could increase the microbial diversity and productivity of mine soils.

Neighborhood affluence protects against antenatal smoking: evidence from a spatial multiple membership model.

A spatial multiple membership model formalizes the effect of neighborhood affluence on antenatal smoking. The data are geocoded New Jersey birth certificate records linked to United States census tract-level data from 1999 to 2007. Neighborhood affluence shows significant spatial autocorrelation and local clustering. Better model fit is observed when incorporating the spatial clustering of neighborhood affluence into multivariate analyses. Relative to the spatial multiple membership model, the multilevel model that ignores spatial clustering produced downwardly biased standard errors; the effective sample size of the key parameter of interest (neighborhood affluence) is also lower. Residents of communities located in high-high affluence clusters likely have better access to health-promoting institutions that regulate antenatal smoking behaviors.

Strong upward neighborhood mobility and preterm birth: a matched-sibling design approach.

PURPOSE: Much cross-sectional work reports an association between neighborhood disadvantage and adverse birth outcomes. Limitations of this work include that mothers with pre-existing unmeasured morbidity may "select" into, or out of, certain neighborhoods. This selection issue remains a key rival explanation for work concerned with place-based disparities in birth outcomes. We move beyond a cross-sectional approach and exploit a sibling-linked data set in California to test whether upwardly mobile mothers, who move from a very high to a very low disadvantaged neighborhood, exhibit a lower than expected risk of preterm birth (PTB) (i.e., delivery <37 weeks). METHODS: We used a matched-sibling design for 461,061 sibling pairs (i.e., 922,122 births total) to mothers in urban areas in who gave birth in California from 2005 to 2010. We linked mother's address at two time points (i.e., two sibling birth dates) to a census-derived composite indicator of neighborhood disadvantage. Conditional logistic regression methods controlled for mother's risk of PTB in the sibling delivered before the move when estimating the relation between strong upward mobility and preterm of the subsequent birth after the move. RESULTS: As hypothesized, strong upward mobility (relative to no mobility) varies inversely with the odds of PTB of the second sibling (odds ratio [OR] for PTB = 0.83, 95% confidence interval: 0.74, 0.93). CONCLUSIONS: Mothers moving from very high to very low disadvantaged neighborhoods show a reduced odds of PTB. Our findings, if replicated, raise the possibility that improvements in neighborhood quality may improve perinatal health in a relatively short time span.

Neighborhood disadvantage across the transition from adolescence to adulthood and risk of metabolic syndrome.

This study investigates the association between neighborhood disadvantage from adolescence to young adulthood and metabolic syndrome using a life course epidemiology framework. Data from the United States-based National Longitudinal Study of Adolescent to Adult Health (n = 9500) and a structural equation modeling approach were used to test neighborhood disadvantage across adolescence, emerging adulthood, and young adulthood in relation to metabolic syndrome. Adolescent neighborhood disadvantage was directly associated with metabolic syndrome in young adulthood. Evidence supporting an indirect association between adolescent neighborhood disadvantage and adult metabolic syndrome was not supported. Efforts to improve cardiometabolic health may benefit from strategies earlier in life.

Racial and Ethnic Patterning of Low Birth Weight, Normal Birth Weight, and Macrosomia.

Both low birthweight (<2500 g; LBW) and macrosomia (>4000 g) are considered adverse birth outcomes and are associated with later poor health conditions, yet the social determinants of macrosomia are understudied. In this study, we explore patterning of LBW, normal birthweight, and macrosomia by race/ethnicity and nativity. We examined data from all live births between 1999 and 2014 in New Jersey with a non-missing, plausible value of birthweight (n = 1,609,516). We compared the risk for LBW and macrosomia among non-Hispanic White, non-Hispanic Black, Hispanic, and non-Hispanic Asian mothers, and between the US- and native-born. For Hispanics and Asians, we also examined differences by country of origin. The racial/ethnic patterns for macrosomia mirrored those of LBW, suggesting that the factors underlying LBW shift birthweight distributions. For example, non-Hispanic White mothers had the lowest risk for LBW and the highest risk for macrosomia. Nativity patterns differed by subgroup, however, with unique risks for macrosomia among some origin groups, such as foreign-born Cubans. The racial/ethnic and nativity patterns of macrosomia do not completely mirror those of LBW, suggesting some distinct social risk factors for macrosomia. Our findings raise questions about whether and how racial/ethnic and nativity patterning in both low and excess birthweight is retained in later conditions, such as childhood obesity.