The roles and regulation of MDM2 and MDMX: it is not just about p53.

Most well studied as proteins that restrain the p53 tumor suppressor protein, MDM2 and MDMX have rich lives outside of their relationship to p53. There is much to learn about how these two proteins are regulated and how they can function in cells that lack p53. Regulation of MDM2 and MDMX, which takes place at the level of transcription, post-transcription, and protein modification, can be very intricate and is context-dependent. Equally complex are the myriad roles that these two proteins play in cells that lack wild-type p53; while many of these independent outcomes are consistent with oncogenic transformation, in some settings their functions could also be tumor suppressive. Since numerous small molecules that affect MDM2 and MDMX have been developed for therapeutic outcomes, most if not all designed to prevent their restraint of p53, it will be essential to understand how these diverse molecules might affect the p53-independent activities of MDM2 and MDMX.

MDM2 and MDMX promote ferroptosis by PPARα-mediated lipid remodeling.

MDM2 and MDMX, negative regulators of the tumor suppressor p53, can work separately and as a heteromeric complex to restrain p53's functions. MDM2 also has pro-oncogenic roles in cells, tissues, and animals that are independent of p53. There is less information available about p53-independent roles of MDMX or the MDM2-MDMX complex. We found that MDM2 and MDMX facilitate ferroptosis in cells with or without p53. Using small molecules, RNA interference reagents, and mutant forms of MDMX, we found that MDM2 and MDMX, likely working in part as a complex, normally facilitate ferroptotic death. We observed that MDM2 and MDMX alter the lipid profile of cells to favor ferroptosis. Inhibition of MDM2 or MDMX leads to increased levels of FSP1 protein and a consequent increase in the levels of coenzyme Q10, an endogenous lipophilic antioxidant. This suggests that MDM2 and MDMX normally prevent cells from mounting an adequate defense against lipid peroxidation and thereby promote ferroptosis. Moreover, we found that PPARα activity is essential for MDM2 and MDMX to promote ferroptosis, suggesting that the MDM2-MDMX complex regulates lipids through altering PPARα activity. These findings reveal the complexity of cellular responses to MDM2 and MDMX and suggest that MDM2-MDMX inhibition might be useful for preventing degenerative diseases involving ferroptosis. Furthermore, they suggest that MDM2/MDMX amplification may predict sensitivity of some cancers to ferroptosis inducers.

MDM2, MDMX, and p73 regulate cell-cycle progression in the absence of wild-type p53.

The p53 tumor suppressor protein, known to be critically important in several processes including cell-cycle arrest and apoptosis, is highly regulated by multiple mechanisms, most certifiably the Murine Double Minute 2-Murine Double Minute X (MDM2-MDMX) heterodimer. The role of MDM2-MDMX in cell-cycle regulation through inhibition of p53 has been well established. Here we report that in cells either lacking p53 or expressing certain tumor-derived mutant forms of p53, loss of endogenous MDM2 or MDMX, or inhibition of E3 ligase activity of the heterocomplex, causes cell-cycle arrest. This arrest is correlated with a reduction in E2F1, E2F3, and p73 levels. Remarkably, direct ablation of endogenous p73 produces a similar effect on the cell cycle and the expression of certain E2F family members at both protein and messenger RNA levels. These data suggest that MDM2 and MDMX, working at least in part as a heterocomplex, may play a p53-independent role in maintaining cell-cycle progression by promoting the activity of E2F family members as well as p73, making them a potential target of interest in cancers lacking wild-type p53.

Host, reproductive, and lifestyle factors in relation to quantitative histologic metrics of the normal breast.

BACKGROUND: Emerging data indicate that variations in quantitative epithelial and stromal tissue composition and their relative abundance in benign breast biopsies independently impact risk of future invasive breast cancer. To gain further insights into breast cancer etiopathogenesis, we investigated associations between epidemiological factors and quantitative tissue composition metrics of the normal breast. METHODS: The study participants were 4108 healthy women ages 18-75 years who voluntarily donated breast tissue to the US-based Susan G. Komen Tissue Bank (KTB; 2008-2019). Using high-accuracy machine learning algorithms, we quantified the percentage of epithelial, stromal, adipose, and fibroglandular tissue, as well as the proportion of fibroglandular tissue that is epithelium relative to stroma (i.e., epithelium-to-stroma proportion, ESP) on digitized hematoxylin and eosin (H&E)-stained normal breast biopsy specimens. Data on epidemiological factors were obtained from participants using a detailed questionnaire administered at the time of tissue donation. Associations between epidemiological factors and square root transformed tissue metrics were investigated using multivariable linear regression models. RESULTS: With increasing age, the amount of stromal, epithelial, and fibroglandular tissue declined and adipose tissue increased, while that of ESP demonstrated a bimodal pattern. Several epidemiological factors were associated with individual tissue composition metrics, impacting ESP as a result. Compared with premenopausal women, postmenopausal women had lower ESP [ß (95% Confidence Interval (CI)) = -0.28 (- 0.43, - 0.13); P < 0.001] with ESP peaks at 30-40 years and 60-70 years among pre- and postmenopausal women, respectively. Pregnancy [ß (95%CI) vs nulligravid = 0.19 (0.08, 0.30); P < 0.001] and increasing number of live births (P-trend < 0.001) were positively associated with ESP, while breastfeeding was inversely associated with ESP [ß (95%CI) vs no breastfeeding = -0.15 (- 0.29, - 0.01); P = 0.036]. A positive family history of breast cancer (FHBC) [ß (95%CI) vs no FHBC = 0.14 (0.02-0.26); P = 0.02], being overweight or obese [ß (95%CI) vs normal weight = 0.18 (0.06-0.30); P = 0.004 and 0.32 (0.21-0.44); P < 0.001, respectively], and Black race [ß (95%CI) vs White = 0.12 (- 0.005, 0.25); P = 0.06] were positively associated with ESP. CONCLUSION: Our findings revealed that cumulative exposure to etiological factors over the lifespan impacts normal breast tissue composition metrics, individually or jointly, to alter their dynamic equilibrium, with potential implications for breast cancer susceptibility and tumor etiologic heterogeneity.

Building the competency of health professionals in the Kyrgyz Republic for the Baby-Friendly Hospital Initiative.

Health professional competency building is one of nine national responsibilities (to achieve universal coverage and sustainability) described in the 2018 World Health Organization/UNICEF implementation guidance for the Baby-Friendly Hospital Initiative (BFHI). Skilled breastfeeding support as a standard of newborn care is critical to the establishment of lactation and exclusive breastfeeding. This qualitative case study describes the Kyrgyz Republic's experience with health professional competency building related to breastfeeding counselling and support. We interviewed 38 key informants and reviewed national policies and international guidelines related to BFHI. The study found that although the country has a new policy reflecting BFHI global standards and guidance, the policy has not been disseminated nationally. Additionally, the policy lacks guidance on competency monitoring and verification and does not mention preservice training, even though preservice training on breastfeeding support exists. To achieve universal coverage for health professional competencies, the Kyrgyz Republic uses preservice, in-service and refresher training. However, the main limitations to aligning with the new guidance are a lack of preservice BFHI- and breastfeeding-specific curricula, experienced trainers and sufficient time and funding to dedicate to practical skill development. Conducted during the COVID-19 pandemic, this study confirmed disruptions to BFHI training and service delivery but also documents the Kyrgyz Republic's resilient strides to mitigate impacts on breastfeeding support through facility-level individual champions and adjustments to training such as going online. Opportunities exist for strengthening the competencies of service providers through strengthened preservice training, comprehensive and consistent in-service training, solutions for overworked service providers and clear and sufficiently funded monitoring guidance.

Implementing two national responsibilities of the revised UNICEF/WHO Baby-Friendly Hospital Initiative: A two-country case study.

The 2018 implementation guidance for the Baby-Friendly Hospital Initiative (BFHI) recommends institutionalising the ten Steps through nine national responsibilities for universal coverage and sustainability. As countries adapt BFHI programmes to this paradigm shift away from traditional designation programmes, documenting and sharing policy and programme experience are critical and currently sparse. This qualitative case study included desk reviews of published and grey literature on BFHI programming, national plans and policy documents specific to the selected national responsibilities for universal coverage and key informant (KI) interviews across a range of actors. In the Kyrgyz Republic, the case study explored responsibility 5, development and implementation of incentives and/or sanctions, and responsibility 6 in Malawi, providing technical assistance (TA). In both countries, the three sustainability responsibilities (national monitoring [7] communication and advocacy [8] and financing [9]) as they relate to the universal coverage of the targeted responsibilities were also explored. Thirty-eight respondents in the Kyrgyz Republic described approaches that were used in the health system, including BFHI designation plaques, performance-based financing and financial sanctions. However, currently, there are no formal incentives and sanctions. In Malawi, TA was utilised for national planning and to introduce quality improvement processes. Forty-seven respondents mostly described provisions of TA in building and strengthening the capacity of providers. More programmatic evidence to demonstrate which types of incentives or sanctions can be effective and sustained and more documentation of how TA is provided across multiple aspects of implementation are needed as countries institutionalise BFHI.

Anesthetic techniques used for pulsed dye laser (PDL) in the treatment of port-wine birthmarks: An exploratory assessment of current attitudes and practice patterns among pediatric dermatologists in the United States.

BACKGROUND/OBJECTIVES: Pulsed dye laser (PDL) is the gold standard for treating port-wine birthmarks (PWBs), but no consensus exists regarding anesthetic techniques when performing PDL for PWB. Given potential adverse neurocognitive effects from general anesthesia (GA) exposure in early childhood, we sought to establish current attitudes and practice patterns regarding anesthesia when treating PWB with PDL. METHODS: An electronic REDCap survey was distributed to members of the Pediatric Dermatology Research Alliance (PeDRA) and the Society for Pediatric Dermatology (SPD) via email. Aggregate, anonymized results were reported. RESULTS: Among 47 respondents, the majority (83%) identified as board-certified pediatric dermatologists. When treating children <4 years old, 70% endorsed some use of topical anesthesia. Although 87% reported concerns about long-term side effects on development and school performance affecting their pursuit of GA, 61% reported use of GA for PDL in children <4 years old. All 4 (100%) respondents whose PDL was located in the operating room (OR) setting reported use of GA, compared to 6 of 17 (35%) respondents whose PDL machine was not located in the OR. Providers were more likely to use GA in patients between 1 and 4 years old (70%) compared to those <1 year old (2%). CONCLUSIONS: Diverse practice patterns reiterate the need for a standardized anesthetic approach for PDL in young children and continued research on other factors (ie, location/accessibility of PDL, lesion size) impacting anesthesia choices. Given potential neurodevelopmental risks associated with GA, specific guidance to effectively minimize its use in favor of topical anesthetics should be provided.

Direct measurement of local oxygen concentration in the bone marrow of live animals.

Characterization of how the microenvironment, or niche, regulates stem cell activity is central to understanding stem cell biology and to developing strategies for the therapeutic manipulation of stem cells. Low oxygen tension (hypoxia) is commonly thought to be a shared niche characteristic in maintaining quiescence in multiple stem cell types. However, support for the existence of a hypoxic niche has largely come from indirect evidence such as proteomic analysis, expression of hypoxia inducible factor-1α (Hif-1α) and related genes, and staining with surrogate hypoxic markers (for example, pimonidazole). Here we perform direct in vivo measurements of local oxygen tension (pO2) in the bone marrow of live mice. Using two-photon phosphorescence lifetime microscopy, we determined the absolute pO2 of the bone marrow to be quite low (<32 mm Hg) despite very high vascular density. We further uncovered heterogeneities in local pO2, with the lowest pO2 (∼9.9 mm Hg, or 1.3%) found in deeper peri-sinusoidal regions. The endosteal region, by contrast, is less hypoxic as it is perfused with small arteries that are often positive for the marker nestin. These pO2 values change markedly after radiation and chemotherapy, pointing to the role of stress in altering the stem cell metabolic microenvironment.

Treatment patterns and overall survival in metastatic non-small-cell lung cancer in a real-world, US setting.

Aim: To conduct a retrospective analysis of electronic medical record data to understand real-world treatment patterns and overall survival (OS) in patients with metastatic non-small-cell lung cancer (NSCLC). Materials & methods: We included n = 9656 adults (≥18 years) with metastatic NSCLC and no prior therapy. Data from 1 January 2013 to 31 January 2017 were analyzed. Results: Carboplatin plus paclitaxel was the most common first-line therapy (18.6%), and nivolumab was the most common second- (31.0%) and third-line (38.4%) therapy; 26.7% of all patients were untreated. Median OS from initial metastatic diagnosis was 11.1 months (95% CI: 10.8-11.5). Second-line immunotherapy extended OS by over 3 months versus second-line chemotherapy. Conclusion: Platinum-based therapy was the most common first-line therapy, and immunotherapy was the most common second- and third-line therapy. Median OS of patients with metastatic NSCLC was <1 year.

An examination of the relationship between serum uric acid level, a clinical history of gout, and cardiovascular outcomes among patients with acute coronary syndrome.

BACKGROUND: Studies have suggested a relationship between higher baseline serum uric acid (sUA) levels and an elevated risk of subsequent ischemic cardiovascular outcomes among acute coronary syndrome (ACS) patients; this relationship may be modified by a clinical history of gout and has not been studied in large patient cohorts. We sought to understand the effect of sUA and gout on ACS outcomes. METHODS: Using PLATO and TRACER data on 27,959 ACS patients, we evaluated baseline sUA levels in relation to a composite of cardiovascular death, myocardial infarction (MI), or stroke. We assessed interaction terms to determine if a baseline clinical diagnosis of gout modified this putative relationship; 46% (n=12,882) had sUA levels elevated >6.0 mg/dL. RESULTS: Patients with elevated levels were more often male with a history of prior MI, diabetes, and heart failure compared with those with sUA <6.0 mg/dL. The unadjusted risk of the composite endpoint increased with corresponding elevations in sUA levels (per 1 mg/dL increase) (HR=1.23 [95% CI: 1.20-1.26]) above the statistical inflection point of 5.0 mg/dL. After adjustment, the association between sUA level and the composite outcome remained significant (HR=1.07 [95% CI: 1.04-1.10]), and baseline gout did not modify this relationship. CONCLUSIONS: In patients with ACS, increasing levels of sUA are associated with an elevated risk of cardiovascular events, regardless of a clinical diagnosis of gout. Further investigation is warranted to determine the mechanism behind this relationship and to delineate whether sUA is an appropriate therapeutic target to reduce cardiovascular risk.

In vitro modeling of endothelial interaction with macrophages and pericytes demonstrates Notch signaling function in the vascular microenvironment.

Angiogenesis is regulated by complex interactions between endothelial cells and support cells of the vascular microenvironment, such as tissue myeloid cells and vascular mural cells. Multicellular interactions during angiogenesis are difficult to study in animals and challenging in a reductive setting. We incorporated stromal cells into an established bead-based capillary sprouting assay to develop assays that faithfully reproduce major steps of vessel sprouting and maturation. We observed that macrophages enhance angiogenesis, increasing the number and length of endothelial sprouts, a property we have dubbed "angiotrophism." We found that polarizing macrophages toward a pro-inflammatory profile further increased their angiotrophic stimulation of vessel sprouting, and this increase was dependent on macrophage Notch signaling. To study endothelial/pericyte interactions, we added vascular pericytes directly to the bead-bound endothelial monolayer. These pericytes formed close associations with the endothelial sprouts, causing increased sprout number and vessel caliber. We found that Jagged1 expression and Notch signaling are essential for the growth of both endothelial cells and pericytes and may function in their interaction. We observed that combining endothelial cells with both macrophages and pericytes in the same sprouting assay has multiplicative effects on sprouting. These results significantly improve bead-capillary sprouting assays and provide an enhanced method for modeling interactions between the endothelium and the vascular microenvironment. Achieving this in a reductive in vitro setting represents a significant step toward a better understanding of the cellular elements that contribute to the formation of mature vasculature.

The Epidemiology of Biliary Tract Cancer and Associated Prevalence of MDM2 Amplification: A Targeted Literature Review.

Biliary tract cancer (BTC) is a rare and aggressive malignancy that is anatomically classified as gallbladder cancer (GBC), extra- and intra-hepatic cholangiocarcinoma (eCCA and iCCA) and ampullary cancer (AC). BTC is often diagnosed at an advanced stage when treatment options are limited and patients have a poor prognosis, so the identification of new drug targets is of critical importance. BTC is molecularly diverse and harbours different therapeutically actionable biomarkers, including mouse double minute 2 homolog (MDM2), which is currently being investigated as a drug target. The aim of this targeted review was to evaluate and synthesise evidence on the epidemiology of BTC and its subtypes in different geographic regions and on the frequency of MDM2 amplifications in BTC tumours. Epidemiological studies (N = 33) consistently demonstrated high incidence rates in South and Central Asia for BTC overall (up to 9.00/100,000) and for all subtypes, with much lower rates in Europe and the US. Among the different types of BTC, the highest global incidence was observed for CCA, mainly driven by iCCA (1.4/100,000), followed by GBC (1.2/100,000) and AC (0.18-0.93 per 100,000). Studies of MDM2 in BTC (N = 19) demonstrated variable frequency of MDM2 amplification according to subtype, with consistently high MDM2 amplification rates in GBC (up to 17.5%), and lower rates in CCA (up to 4.4%). The results from this literature review highlight the geographic heterogeneity of BTC and the need for standardised clinicopathologic assessment and reporting to allow cross-study comparisons.

Genomic profiles and clinical presentation of chordoma.

Chordoma is a rare bone cancer with variable clinical outcomes. Here, we recruited 184 sporadic chordoma patients from the US and Canada and collected their clinical and treatment data. The average age at diagnosis was 45.5 years (Range 5-78) and the chordoma site distribution was 49.2% clivus, 26.2% spinal, and 24.0% sacral. Most patients (97.5%) received surgery as the primary treatment, among whom 85.3% also received additional treatment. Except for the most prevalent cancers like prostate, lung, breast, and skin cancer, there was no discernible enrichment for any specific cancer type among patients or their family members. Among a subset of patients (N = 70) with tumor materials, we conducted omics analyses and obtained targeted panel sequencing and SNP array genotyping data for 51 and 49 patients, respectively. The most recurrent somatic driver mutations included PIK3CA (12%), followed by chromatin remodeling genes PBRM1 and SETD2. Amplification of the 6q27 region, containing the chordoma susceptibility gene TBXT, was detected in eight patients (16.3%). Clival patients appeared to be less likely to carry driver gene mutations, chromosome arm level deletion events (e.g., 5p, 5p, and 9p), or 6q27 amplification compared to sacral patients. After adjusting for age, sex, tumor site, and additional treatment, patients with somatic deletions of 14q (OR = 13.73, 95% CI 1.96-96.02, P = 0.008) and 18p (OR = 13.68, 95% CI 1.77-105.89, P = 0.012) were more likely to have persistent chordoma. The study highlights genomic heterogeneity in chordoma, potentially linked to location and clinical progression.

APOBEC shapes tumor evolution and age at onset of lung cancer in smokers.

APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.

Characteristics of venous leg ulcer patients at a tertiary wound care center.

OBJECTIVE: The objective of this study was to assess patient, wound, care, and reflux characteristics of venous leg ulcers (VLUs) to update and improve knowledge of disease etiology, identify barriers to healing, and improve treatment. METHODS: Patients diagnosed with VLUs treated at the Stanford Advanced Wound Care Center between 2018 and 2019 were identified from the Healogics iHeal database. We identified 327 VLU entries, of which 133 were patients who had multiple or recurring wounds. An additional 27 patients were labeled as misdiagnosis, resulting in a final patient sample of 167. Patient demographics, wound, care, and ultrasound data for these patients were extracted from the Stanford electronic medical records regarding characteristics. The initial data analysis suggested possible differences in VLU characteristics depending on patient age and body mass index (BMI), which was then further analyzed. RESULTS: Of the 167 VLU patients assessed, 53.9% were male and 46.1% were female. The mean age was 74.7 years, and the average BMI was 30.2 kg/m2, including 41.1% of patients with a BMI over 30 kg/m2. Approximately 50% of wounds were presented in multiples, had cellulitis, or were recurring, and 39.5% were caused by trauma. Most common venous reflux patterns on duplex ultrasound examination were below-knee great saphenous vein reflux and calf perforator reflux, which was identified in 37.7% and 29.3% of the patients, respectively. Axial great saphenous vein reflux was detected in 14.4% of patients. When looking at the patient sample under 60 years of age, 67.7% were male, 61.3% presented with venous skin changes, and 51.6% had diabetes. In the patients older than 60, only 51.9% were male, 37.6% presented with venous skin changes, and 31.6% had diabetes. BMI was greater in the patients under age 60, with an average of 39.2 kg/m2, compared with 28.2 kg/m2 in those above 60. Of the patients with a BMI ≥30 kg/m2, 64.3% had multiple wounds, 61.4% had recurring wounds, and 56.5% had venous skin changes. In contrast, in patients with BMI <30 kg/m2, 47.4% had multiple wounds, 39.2% had recurring wounds, and 32.0% had venous skin changes. CONCLUSIONS: VLU pathology appears to differ depending on patient demographics and characteristics. Different drivers may influence disease cause, progression, and prognosis, making a standard approach to VLUs difficult. Our findings suggest that identifying different subtypes of VLUs and adapting an algorithm of care with a personalized treatment may help optimize management of these patients.

Nutritional care for children with feeding difficulties and disabilities: A scoping review.

One billion people worldwide have a disability, and 80 percent of them live in low- and middle-income countries (LMICs). The prevalence of feeding difficulties globally ranges from 25-45 percent to 33-80 percent in children without and with disabilities, respectively. The U.S. Agency for International Development's (USAID) flagship multi-sectoral nutrition project, USAID Advancing Nutrition, conducted a scoping review of programs supporting nutritional care of children with disability and non-disability related feeding difficulties. The non-systematic scoping review included a desk review of peer-reviewed and non-peer-reviewed literature and key informant interviews. In all, 127 documents with publication dates ranging from 2003 to 2022 were identified through keyword searches and snowballing and met the inclusion criteria, and 42 experts in nutrition and disability were interviewed. Findings were organized using structured matrices of challenges and opportunities across the universal progressive model of care framework in the identification and management of feeding difficulties and disabilities and support for children with feeding difficulties and disabilities and their families. The review found insufficient policies, programs, and evidence to support children with feeding difficulties and disabilities and their families. While some resources and promising approaches exist, they are not standardized or universally used, staff are not trained to use them, and there is insufficient funding to implement them. The combination of challenges in identifying feeding difficulties and disabilities, a lack of understanding of the link between disabilities and feeding, and weak or nonexistent referral or specialized services puts these children at risk of malnutrition. Additionally, their families face challenges providing the care they need, including coping with high care demands, accessing support, obtaining appropriate foods, and managing stigma. Four areas of recommendations emerged to support children with feeding difficulties and disabilities: (1) Strengthen systems to improve identification and service provision; (2) Provide direct support to families to address determinants that affect nutrition outcomes; (3) Conduct advocacy to raise awareness of the needs and opportunities; and (4) Build the evidence base on effective interventions to identify and support these children and their families.

ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci.

Genome-wide association studies (GWAS) have identified thousands of genomic loci associated with complex diseases and traits, including cancer. The vast majority of common trait-associated variants identified via GWAS fall in non-coding regions of the genome, posing a challenge in elucidating the causal variants, genes, and mechanisms involved. Expression quantitative trait locus (eQTL) and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization methods. While QTL colocalization is becoming a standard analysis in post-GWAS investigation, an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been lacking. Here, we present ezQTL, a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS loci and molecular QTLs under different linkage disequilibrium (LD) patterns (1000 Genomes Project, UK Biobank, or user-provided data). This application allows users to perform data quality control for variants matched between different datasets, LD visualization, and two-trait colocalization analyses using two state-of-the-art methodologies (eCAVIAR and HyPrColoc), including batch processing. ezQTL is a free and publicly available cross-platform web tool, which can be accessed online at https://analysistools.cancer.gov/ezqtl.

Formative Research to Inform Market-Based Interventions to Increase Egg Purchase and Consumption in Tigray, Ethiopia.

Animal source foods (ASFs) have a demonstrated ability to improve child health yet are underutilized by many communities faced with malnutrition. Recognizing that improving knowledge about the benefits of consuming ASFs alone is not adequate to change behavior, the Studying Animal Food Markets in Rural Areas (SAFIRA) pilot project planned to test a market-based intervention to increasing the intake of ASFs by children 6-23 months in rural Tigray, Ethiopia. Our process of designing in-market behavior change strategies involved identifying the project's target ASF, cocreating and testing marketing interventions, and understanding barriers and enablers driving key retailer behaviors. Qualitative research methods including focus group discussions, key informant interviews, trials of improved practices, and transect walks were used throughout 2 rounds of formative research. The first round of formative research led the project to focus on eggs, and the second round resulted in an improved understanding of the Tigrayan local food markets and egg consumption. Consumers were receptive to nutrition messaging from trusted community members and consider eggs to be healthy and affordable relative to other ASFs. Despite a willingness on the part of egg retailers in Tigrayan markets to try new practices to market eggs to consumers, formative research revealed that retailers function primarily as aggregators, moving eggs toward urban markets, correcting a foundational assumption that households routinely purchase eggs at local markets. These findings demonstrate the importance of formative research to inform design-especially in the development of context-specific behavior change interventions situated within local marketplaces.

Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis.

Myelofibrosis is a rare myeloproliferative neoplasm (MPN) with high risk for progression to acute myeloid leukemia. Our integrated genomic analysis of up to 933 myelofibrosis cases identifies 6 germline susceptibility loci, 4 of which overlap with previously identified MPN loci. Virtual karyotyping identifies high frequencies of mosaic chromosomal alterations (mCAs), with enrichment at myelofibrosis GWAS susceptibility loci and recurrently somatically mutated MPN genes (e.g., JAK2). We replicate prior MPN associations showing germline variation at the 9p24.1 risk haplotype confers elevated risk of acquiring JAK2V617F mutations, demonstrating with long-read sequencing that this relationship occurs in cis. We also describe recurrent 9p24.1 large mCAs that selectively retained JAK2V617F mutations. Germline variation associated with longer telomeres is associated with increased myelofibrosis risk. Myelofibrosis cases with high-frequency JAK2 mCAs have marked reductions in measured telomere length - suggesting a relationship between telomere biology and myelofibrosis clonal expansion. Our results advance understanding of the germline-somatic interaction at JAK2 and implicate mCAs involving JAK2 as strong promoters of clonal expansion of those mutated clones.