Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets

Genetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identified 889 kidney genes associated with BP of which 399 were prioritised as contributors to BP regulation. Imputation of kidney proteome and microRNAome uncovered 97 renal proteins and 11 miRNAs associated with BP. Integration with plasma proteomics and metabolomics illuminated circulating levels of myo-inositol, 4-guanidinobutanoate and angiotensinogen as downstream effectors of several kidney BP genes (SLC5A11, AGMAT, AGT, respectively). We showed that genetically determined reduction in renal expression may mimic the effects of rare loss-of-function variants on kidney mRNA/protein and lead to an increase in BP (e.g., ENPEP). We demonstrated a strong correlation (r = 0.81) in expression of protein-coding genes between cells harvested from urine and the kidney highlighting a diagnostic potential of urinary cell transcriptomics. We uncovered adenylyl cyclase activators as a repurposing opportunity for hypertension and illustrated examples of BP-elevating effects of anticancer drugs (e.g. tubulin polymerisation inhibitors). Collectively, our studies provide new biological insights into genetic regulation of BP with potential to drive clinical translation in hypertension.

Analysis of anemia and iron supplementation among glioblastoma patients reveals sex-biased association between anemia and survival

The association between anemia and outcomes in glioblastoma patients is unclear. We analyzed data from 1346 histologically confirmed adult glioblastoma patients in the TriNetX Research Network. Median hemoglobin and hematocrit levels were quantified for 6 months following diagnosis and used to classify patients as anemic or non-anemic. Associations of anemia and iron supplementation of anemic patients with median overall survival (median-OS) were then studied. Among 1346 glioblastoma patients, 35.9% of male and 40.5% of female patients were classified as anemic using hemoglobin-based WHO guidelines. Among males, anemia was associated with reduced median-OS compared to matched non-anemic males using hemoglobin (HR 1.24; 95% CI 1.00-1.53) or hematocrit-based cutoffs (HR 1.28; 95% CI 1.03-1.59). Among females, anemia was not associated with median-OS using hemoglobin (HR 1.00; 95% CI 0.78-1.27) or hematocrit-based cutoffs (HR: 1.10; 95% CI 0.85-1.41). Iron supplementation of anemic females trended toward increased median-OS (HR 0.61; 95% CI 0.32-1.19) although failing to reach statistical significance whereas no significant association was found in anemic males (HR 0.85; 95% CI 0.41-1.75). Functional transferrin-binding assays confirmed sexually dimorphic binding in resected patient samples indicating underlying differences in iron biology. Anemia among glioblastoma patients exhibits a sex-specific association with survival.

Iron inhibits glioblastoma cell migration and polarization

Glioblastoma is one of the deadliest malignancies facing modern oncology today. The ability of glioblastoma cells to diffusely spread into neighboring healthy brain makes complete surgical resection nearly impossible and contributes to the recurrent disease faced by most patients. Although research into the impact of iron on glioblastoma has addressed proliferation, there has been little investigation into how cellular iron impacts the ability of glioblastoma cells to migrate-a key question, especially in the context of the diffuse spread observed in these tumors. Herein, we show that increasing cellular iron content results in decreased migratory capacity of human glioblastoma cells. The decrease in migratory capacity was accompanied by a decrease in cellular polarization in the direction of movement. Expression of CDC42, a Rho GTPase that is essential for both cellular migration and establishment of polarity in the direction of cell movement, was reduced upon iron treatment. We then analyzed a single-cell RNA-seq dataset of human glioblastoma samples and found that cells at the tumor periphery had a gene signature that is consistent with having lower levels of cellular iron. Altogether, our results suggest that cellular iron content is impacting glioblastoma cell migratory capacity and that cells with higher iron levels exhibit reduced motility.

Real-World Data: Applications and Relevance to Cancer Clinical Trials

Randomized controlled trials (RCTs) are the gold standard for comparative-effectiveness research (CER). Since the 1980s, there has been a rise in the creation and utilization of large national cancer databases to provide readily accessible "real-world data" (RWD). This review article discusses the role of RCTs in oncology, and the role of RWD from the national cancer database in CER. RCTs remain the preferred study type for CER because they minimize confounding and bias. RCTs have challenges to conduct, including extensive time and resources, but these factors do not impact the internal validity of the result. Generalizability and external validity are potential limitations of RCTs. RWD is ideal for studying cancer epidemiology, patterns of care, disparities in care delivery, quality-of-care evaluation, and applicability of RCT data in specific populations excluded from RCTs. However, retrospective databases with RWD have limitations in CER due to unmeasured confounders and are often suboptimal in identifying causal treatment effects.

Future trends in incidence and long-term survival of metastatic cancer in the United States

BACKGROUND

Previous studies have demonstrated epidemiological trends in individual metastatic cancer subtypes; however, research forecasting long-term incidence trends and projected survivorship of metastatic cancers is lacking. We assess the burden of metastatic cancer to 2040 by (1) characterizing past, current, and forecasted incidence trends, and (2) estimating odds of long-term (5-year) survivorship.

METHODS

This retrospective, serial cross-sectional, population-based study used registry data from the Surveillance, Epidemiology, and End Results (SEER 9) database. Average annual percentage change (AAPC) was calculated to describe cancer incidence trends from 1988 to 2018. Autoregressive integrating moving average (ARIMA) models were used to forecast the distribution of primary metastatic cancer and metastatic cancer to specific sites from 2019 to 2040 and JoinPoint models were fitted to estimate mean projected annual percentage change (APC).

RESULTS

The average annual percent change (AAPC) in incidence of metastatic cancer decreased by 0.80 per 100,000 individuals (1988-2018) and we forecast an APC decrease by 0.70 per 100,000 individuals (2018-2040). Analyses predict a decrease in metastases to liver (APC = -3.40, 95% CI [-3.50, -3.30]), lung (APC (2019-2030) = -1.90, 95% CI [-2.90, -1.00]); (2030-2040) = -3.70, 95% CI [-4.60, -2.80]), bone (APC = -4.00, 95% CI [-4.30, -3.70]), and brain (APC = -2.30, 95% CI [-2.60, -2.00]). By 2040, patients with metastatic cancer are predicted to have 46.7% greater odds of long-term survivorship, driven by increasing plurality of patients with more indolent forms of metastatic disease.

CONCLUSIONS

By 2040, the distribution of metastatic cancer patients is predicted to shift in predominance from invariably fatal to indolent cancers subtypes. Continued research on metastatic cancers is important to guide health policy and clinical intervention efforts, and direct allocations of healthcare resources.

Sympathetic Blocks as a Predictor for Response to Ketamine Infusion in Patients with Complex Regional Pain Syndrome: A Multicenter Study

BACKGROUND

Ketamine infusions are frequently employed for refractory complex regional pain syndrome (CRPS), but there are limited data on factors associated with treatment response. Sympathetic blocks are also commonly employed in CRPS for diagnostic and therapeutic purposes and generally precede ketamine infusions.

OBJECTIVES

We sought to determine whether demographic and clinical factors, and technical and psychophysical characteristics of sympathetic blocks are associated with response to ketamine infusion.

METHODS

In this multi-center retrospective study, 71 patients who underwent sympathetic blocks followed by ketamine infusions at 4 hospitals were evaluated. Sympathetically maintained pain (SMP) was defined as ≥ 50% immediate pain relief after sympathetic block and a positive response to ketamine was defined as ≥ 30% pain relief lasting over 3 weeks.

RESULTS

Factors associated with a positive response to ketamine in univariable analysis were the presence of SMP (61.0% success rate vs 26.7% in those with sympathetically independent pain; P = .009) and post-block temperature increase (5.66 ± 4.20 in ketamine responders vs 3.68 ± 3.85 in non-responders; P = .043). No psychiatric factor was associated with ketamine response. In multivariable analysis, SMP (OR 6.54 [95% CI 1.83, 23.44]) and obesity (OR 8.75 [95% 1.45, 52.73]) were associated with a positive ketamine infusion outcome.

CONCLUSIONS

The response to sympathetic blocks may predict response to ketamine infusion in CRPS patients, with alleviation of the affective component of pain and predilection to a positive placebo effect being possible explanations.

Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus

Systemic lupus erythematosus is a heritable autoimmune disease that predominantly affects young women. To improve our understanding of genetic etiology, we conduct multi-ancestry and multi-trait meta-analysis of genome-wide association studies, encompassing 12 systemic lupus erythematosus cohorts from 3 different ancestries and 10 genetically correlated autoimmune diseases, and identify 16 novel loci. We also perform transcriptome-wide association studies, computational drug repurposing analysis, and cell type enrichment analysis. We discover putative drug classes, including a histone deacetylase inhibitor that could be repurposed to treat lupus. We also identify multiple cell types enriched with putative target genes, such as non-classical monocytes and B cells, which may be targeted for future therapeutics. Using this newly assembled result, we further construct polygenic risk score models and demonstrate that integrating polygenic risk score with clinical lab biomarkers improves the diagnostic accuracy of systemic lupus erythematosus using the Vanderbilt BioVU and Michigan Genomics Initiative biobanks.

Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing

Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction.

Factors associated with pregnancy termination in women of childbearing age in 36 low-and middle-income countries

Lack of access to safe, affordable, timely and adequate pregnancy termination care, and the stigma associated with abortion in low-middle income countries (LMICs), pose a serious risk to women's physical and mental well-being throughout the lifespan. Factors associated with pregnancy termination and their heterogeneity across countries in LMICs previously have not been thoroughly investigated. We aim to determine the relative significance of factors associated with pregnancy termination in LMICs and its variation across countries. Analysis of cross-sectional nationally representative household surveys carried out in 36 LMICs from 2010 through 2018. The weighted population-based sample consisted of 1,236,330 women of childbearing aged 15-49 years from the Demographic and Health Surveys. The outcome of interest was self-report of having ever had a pregnancy terminated. We used multivariable logistic regression models to identify factors associated with pregnancy termination. The average pooled weighted prevalence of pregnancy termination in the present study was 13.3% (95% CI: 13.2%-13.4%), ranging from a low of 7.8 (95% CI: 7.2, 8.4%) in Namibia to 33.4% (95% CI: 32.0, 34.7%) in Pakistan. Being married showed the strongest association with pregnancy termination (adjusted OR, 2.94; 95% CI, 2.84-3.05; P < 0.001) compared to unmarried women. Women who had more than four children had higher odds of pregnancy termination (adjusted OR, 2.45; 95% CI, 2.33-2.56; P < 0.001). Moreover, increased age and having primary and secondary levels of education were associated with higher odds of pregnancy termination compared to no education. In this study, married women, having one or more living children, those of older age, and those with at least primary level of education were associated with pregnancy termination in these 36 LMICs. The findings highlighted the need of targeted public health intervention to reduce unintended pregnancies and unsafe abortions.

Genetic diversity fuels gene discovery for tobacco and alcohol use

Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury1-4. These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries5. Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.

TMIC-34. INVESTIGATING THE EFFECT OF IRON IN GLIOBLASTOMA CELL POLARIZATION AND MIGRATION

Glioblastoma represents one of the most difficult-to-treat malignancies as evidenced by the poor prognosis associated with a diagnosis. The ability of glioblastoma cells to diffusely infiltrate into healthy brain tissue renders complete surgical resection challenging. Consequently, a large majority of glioblastoma patients end up with recurrent disease despite receiving maximally feasible surgical resection and rigorous chemoradiation. This work examined how modulation of cellular iron levels in T98G and LN229 glioblastoma cells impacted migratory capacity. Treatment of T98G or LN229 glioblastoma cells with iron in the form of ferric ammonium citrate (FAC) resulted in significantly reduced migration as assessed by time-lapse phase contrast imaging and wound healing assays. The iron-induced reduction in migration was able to be rescued by the addition of equimolar concentrations of deferoxamine, an iron chelator. Cellular proliferation in response to the iron treatments was quantified using both optical confluence and nucleic-acid-based proliferation assays and it was found that iron treatment at the concentrations used for the migration assays (0 – 300 µM FAC) did not result in reduced proliferation. Mechanistically probing iron’s impact on cell migration revealed that addition of iron resulted in decreased expression of Cdc42, a Rho GTPase that is essential to determining cellular polarity during migration. Functional cellular polarization assays further confirmed that reduced expression of Cdc42 corresponded to reduced cellular polarization. Bioinformatic analysis of CDC42 transcripts revealed the presence of potential iron-responsive-elements that may drive the iron-induced reduction in Cdc42 expression. This work highlights the importance of iron biology in impacting glioblastoma cell phenotype and potentially glioblastoma patient outcomes.

EPID-04. IMPACT OF SEX DIFFERENCES IN IRON SUPPLEMENTATION AND OUTCOMES IN ANEMIC GLIOBLASTOMA PATIENTS

We performed a retrospective sex-stratified analysis on 1750 histologically confirmed surgical glioblastoma patients (737 female, 1013 male) diagnosed between January 1, 2000 – January 1, 2020 in the TriNetX Research Network. Among 737 female glioblastoma patients, 140 (18.99%) were classified as anemic (defined as having mean 5-year-post-diagnosis hemoglobin levels &lt; 12 g/dL). Among 1013 male patients, 177 (17.4%) were classified as anemic (mean 5-year-post-diagnosis hemoglobin levels &lt; 13 g/dL). Of the 140 anemic female patients, 30 (21.4%) received iron supplementation whereas 28 (15.8%) of 177 anemic male patients received iron supplementation. Anemic female patients receiving iron supplementation were on average younger than anemic female patients who did not receive supplementation (mean age at diagnosis (SD): 59.08 vs. 64.87, p = 0.037), however no statistically significant differences in presence of chemotherapy administration, radiation administration, or Charlson comorbidity index (CCI) were detected. Anemic male patients receiving iron supplementation had no significant difference in mean age at diagnosis, chemotherapy administration, radiation administration, or CCI compared to anemic male patients not receiving iron supplementation. Kaplan-Meier analysis revealed that iron supplementation in anemic female patients was associated with prolonged overall median survival (536 vs. 361 days, p = 0.03) whereas iron supplementation in anemic male patients was not associated with any significant increase in overall survival (392 vs. 361 days, p = 0.89). Multivariate analysis using a Cox proportional hazards model adjusted for mean 5-year-post-diagnosis hemoglobin levels, age at diagnosis, chemotherapy administration, radiation administration, and CCI revealed that iron supplementation was associated with improved survival in anemic female patients (HR: 0.53, 95% CI: 0.30 – 0.96) but not in anemic male patients (HR: 0.87, 95% CI: 0.54 – 1.43). These results highlight the importance of iron biology in glioblastoma and provide evidence for further investigation into iron supplementation of anemic glioblastoma patients.

Construction and Application of Polygenic Risk Scores in Autoimmune Diseases

Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with autoimmune diseases and provided unique mechanistic insights and informed novel treatments. These individual genetic variants on their own typically confer a small effect of disease risk with limited predictive power; however, when aggregated (e.g., via polygenic risk score method), they could provide meaningful risk predictions for a myriad of diseases. In this review, we describe the recent advances in GWAS for autoimmune diseases and the practical application of this knowledge to predict an individual’s susceptibility/severity for autoimmune diseases such as systemic lupus erythematosus (SLE) via the polygenic risk score method. We provide an overview of methods for deriving different polygenic risk scores and discuss the strategies to integrate additional information from correlated traits and diverse ancestries. We further advocate for the need to integrate clinical features (e.g., anti-nuclear antibody status) with genetic profiling to better identify patients at high risk of disease susceptibility/severity even before clinical signs or symptoms develop. We conclude by discussing future challenges and opportunities of applying polygenic risk score methods in clinical care.

Abstract 2430: The role of cellular iron and the homeostatic iron regulator (HFE) in high-grade brain tumor cell migration

High-grade brain tumors such as grade III astrocytoma and glioblastoma represent among the most difficult to manage malignancies facing oncological practice. Diffuse migration and invasion into adjacent healthy brain tissue yields complete surgical resection of these tumors unfeasible. As a result, despite receiving maximal surgical resection and an aggressive course of chemoradiation, the majority of high-grade brain tumor patients suffer from recurrent disease. Increased expression levels of the homeostatic iron regulator gene (HFE) in high-grade brain tumors have been correlated with poorer outcomes. HFE is known to influence cellular iron metabolism by inhibiting transferrin-mediated iron uptake yet little is known regarding how HFE or iron impact the migratory capabilities of high-grade brain tumor cells. In order to better understand how HFE expression and cellular iron metabolism influence cell migration in high grade brain tumors, we utilized brain tumor cell lines that had been genetically manipulated to express different levels of HFE. We observed that knocking down HFE in KR158 or LN229 glioma cell lines resulted in significantly decreased migratory capacity. Since HFE is known to inhibit transferrin mediated iron uptake, we studied how directly modulating the iron status of glioma cells impacted their ability to migrate. Treatment of a panel of glioma cell lines: LN229, T98G, U87, KR158, with iron in the form of hemin or ferric ammonium citrate resulted in significantly reduced migration. Furthermore, the iron-induced reduction in migration could be rescued by the addition of deferoxamine, an iron chelator. Cell viability in response to the iron treatments was assayed and found to not be significantly altered - suggesting that cellular iron status was influencing migratory capacity independent of cell viability. To gain mechanistic insights into HFE and iron-induced effects on cell migration, we analyzed the Chinese Glioma Genome Atlas (CGGA) for correlations between HFE and the Rho GTPases RHOA, RAC1, and CDC42 – genes which are known to play a crucial role in determining the migratory capacity of cancer cells. Interestingly, we found statistically significant correlations between the Rho GTPases RHOA, RAC1, CDC42 and HFE in both grade III astrocytoma and glioblastoma patient cohorts. Immunoblotting of iron treated glioma cell lines demonstrated that expression of RhoA and Cdc42 was reduced suggesting that alterations in Rho GTPase expression and signaling may play a role in iron-induced effects on cell migration. Our results demonstrate that targeting cancer cell iron metabolism as an addition to existing treatment regimens may be a promising avenue for further investigation.

Citation Format: Ganesh Shenoy, Katie Troike, Kondaiah Palsa, Madison Kuhn, Quinn Wade, Becky Slagle-Webb, Amanda Snyder, Chachrit Khunsriraksakul, Justin D. Lathia, Dhimant Desai, Hong-Gang Wang, Elizabeth Proctor, James R. Connor. The role of cellular iron and the homeostatic iron regulator (HFE) in high-grade brain tumor cell migration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2430.

Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies

Transcriptome-wide association studies (TWAS) are popular approaches to test for association between imputed gene expression levels and traits of interest. Here, we propose an integrative method PUMICE (Prediction Using Models Informed by Chromatin conformations and Epigenomics) to integrate 3D genomic and epigenomic data with expression quantitative trait loci (eQTL) to more accurately predict gene expressions. PUMICE helps define and prioritize regions that harbor cis-regulatory variants, which outperforms competing methods. We further describe an extension to our method PUMICE +, which jointly combines TWAS results from single- and multi-tissue models. Across 79 traits, PUMICE + identifies 22% more independent novel genes and increases median chi-square statistics values at known loci by 35% compared to the second-best method, as well as achieves the narrowest credible interval size. Lastly, we perform computational drug repurposing and confirm that PUMICE + outperforms other TWAS methods.

Association of Spinal Cord Stimulator Implantation With Persistent Opioid Use in Patients With Postlaminectomy Syndrome

IMPORTANCE

The results of studies evaluating spinal cord stimulation (SCS) for postlaminectomy syndrome (PLS) have yielded mixed results. This has led to an increased emphasis on objective outcome measures such as opioid prescribing.

OBJECTIVE

To determine the association between SCS and long-term opioid therapy (LOT) for PLS.

DESIGN, SETTING, AND PARTICIPANTS

In this cohort study, adults with PLS were identified using the TriNetx Diamond Network and separated based on whether they underwent SCS. Patients were stratified according to baseline opioid use (opioid-naive or receiving LOT) and subsequent opioid therapy over the 12-month period ranging from 3 to 15 months post-SCS implantation or post-PLS index date. Statistical analysis was performed from June to December 2021.

EXPOSURE

SCS.

MAIN OUTCOMES AND MEASURES

The main outcome was cessation of opioid use among patients receiving LOT or abstinence from opioids among opioid-naive patients. Opioid-naive patients were defined as those receiving at most 2 opioid prescriptions per year, and patients on LOT were those receiving at least 6 opioid prescriptions per year.

RESULTS

Among 552 937 eligible patients treated between December 2015 and May 2021, 26 179 with PLS received an SCS implant. The median (IQR) patient age was 60 (51-69) years; 305 802 patients (55.3%) were female. Among those reporting racial identify (37.0% [204 758 patients]), 9.3% (18 971 patients) were African American, 0.3% (648 patients) were Asian, and 90.4% (185 139 patients) were White. Compared with those who did not receive an SCS, individuals who received an SCS were more likely to be using opioids preimplantation (mean [SD] prescriptions: 4.3 [8.5] vs 4.1 [9.3]; P < .001) but less likely to be using opioids after SCS implantation (mean [SD] prescriptions: 3.8 [8.2] vs 4.0 [9.4]; P = .006). In the 12-month study period, similar proportions in the SCS and no-SCS groups receiving baseline LOT remained on LOT (70.3% [n = 74 585] vs 69.2% [n = 3882], respectively; P = .10). In opioid-naive patients, SCS was associated with a small decreased likelihood of patients subsequently receiving LOT (7.6% vs 7.0%; difference, -0.6% [95% CI, -1.0% to -0.2%]; P = .003). In multivariable analysis, SCS was associated with an increased likelihood of not being on opioids in both opioid-naive (adjusted odds ratio [OR], 0.90 [95% CI, 0.85-0.96]; P < .001) and LOT patients (adjusted OR, 0.93 [95% CI, 0.88-0.99]; P = .02). White patients were significantly more likely to be diagnosed with PLS (ie, underwent surgery) (90.4% vs 85.2%; difference, 5.2% [95% CI, 5.1%-5.4%]; P < .001) and receive an SCS (93.7% vs 90.3%; difference, 3.4% [95% CI, 2.9% to 4.0%]; P < .001) than patients of other racial identities.

CONCLUSIONS AND RELEVANCE

These findings suggest that under real-life conditions, SCS was associated with small, clinically questionable associations with opioid discontinuation and not starting opioids in the context of PLS.

TAMI-42. THE ROLE OF HFE AND IRON IN CELL ADHESION AND MIGRATION IN GLIOBLASTOMA

Glioblastoma (GBM) remains one of the most difficult to treat malignancies facing modern medicine. The strong migratory and invasive capacity of GBM cells allows for diffuse invasion into neighboring healthy brain which presents a significant hurdle for complete surgical resection of these tumors. Unsurprisingly, even after receiving maximal surgical resection, radiation and chemotherapy, the majority of GBM patients end up with recurrent disease. Increased expression levels of the homeostatic iron regulator gene (HFE) in brain tumors such as GBM have been associated with poorer outcomes. In order to better understand how HFE expression impacts the adhesive and migratory capacity of GBM, we utilized syngeneic mouse glioma models (KR158, CT2A) that have been transfected to either over-express or under-express HFE. We observed that knocking down HFE in the KR158 model resulted in significantly decreased migratory capacity as well as decreased adhesion to fibronectin and artificial basement membrane. Likewise, overexpressing HFE in a CT2A model resulted in increased adhesion to fibronectin or artificial basement membrane. Since HFE is known to regulate iron uptake, we studied how modulating the iron status of GBM cells impacted their ability to migrate and adhere. We found that increasing the iron pool of these mouse glioma models by exposure to exogenous iron compounds decreased migratory capacity. To better understand mechanistically how HFE and iron status impacted migration and adhesion, we probed how expression of integrins and their downstream signaling molecules, the Rho GTPases were altered in response to iron. We found that exposure to iron decreased levels of the Rho GTPases Cdc42 and RhoA. Furthermore, cells that overexpressed HFE were found to have increased expression of integrin β1 and integrin α5 suggesting that HFE and iron may impact integrins and their downstream signaling pathways to alter migration of GBM cells.

Medical Service Use and Charges for Cancer Care in 2018 for Privately Insured Patients Younger Than 65 Years in the US

IMPORTANCE

Currently, there are limited published data regarding resource use and spending on cancer care in the US.

OBJECTIVE

To characterize the most frequent medical services provided and the associated spending for privately insured patients with cancer in the US.

DESIGN, SETTING, AND PARTICIPANTS

This cohort study used data from the MarketScan database for the calendar year 2018 from a sample of 27.1 million privately insured individuals, including patients with a diagnosis of the 15 most prevalent cancers, predominantly from large insurers and self-insured employers. Overall societal health care spending was estimated for each cancer type by multiplying the mean total spending per patient (estimated from MarketScan) by the number of privately insured patients living with that cancer in 2018, as reported by the National Cancer Institute's Surveillance, Epidemiology, and End Results program. Analyses were performed from February 1, 2018, to July 8, 2021.

EXPOSURES

Evaluation and management as prescribed by treating care team.

MAIN OUTCOMES AND MEASURES

Current Procedural Terminology and Healthcare Common Procedure Coding System codes based on cancer diagnosis code.

RESULTS

The estimated cost of cancer care in 2018 for 402 115 patients with the 15 most prevalent cancer types was approximately $156.2 billion for privately insured adults younger than 65 years in the US. There were a total of 38.4 million documented procedure codes for 15 cancers in the MarketScan database, totaling $10.8 billion. Patients with breast cancer contributed the greatest total number of services (10.9 million [28.4%]), followed by those with colorectal cancer (3.9 million [10.2%]) and prostate cancer (3.6 million [9.4%]). Pathology and laboratory tests contributed the highest number of services performed (11.7 million [30.5%]), followed by medical services (6.3 million [16.4%]) and medical supplies and nonphysician services (6.1 million [15.9%]). The costliest cancers were those of the breast ($3.4 billion [31.5%]), followed by lung ($1.1 billion [10.2%]) and colorectum ($1.1 billion [10.2%]). Medical supplies and nonphysician services contributed the highest total spent ($4.0 billion [37.0%]), followed by radiology ($2.1 billion [19.4%]) and surgery ($1.8 billion [16.7%]).

CONCLUSIONS AND RELEVANCE

This analysis suggests that patients with breast, colorectal, and prostate cancers had the greatest number of services performed, particularly for pathology and laboratory tests, whereas patients with breast, lung, lymphoma, and colorectal cancer incurred the greatest costs, particularly for medical supplies and nonphysician services. The cost of cancer care in 2018 for the 15 most prevalent cancer types was estimated to be approximately $156.2 billion for privately insured adults younger than 65 years in the US.

A map of cis-regulatory elements and 3D genome structures in zebrafish

The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species¹. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.

A supervised learning framework for chromatin loop detection in genome-wide contact maps

Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on a genome-wide map. However, given the availability of orthogonal data types such as ChIA-PET, HiChIP, Capture Hi-C, and high-throughput imaging, a supervised learning approach could facilitate the discovery of a comprehensive set of chromatin interactions. Here, we present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide contact maps. We compare Peakachu with current enrichment-based approaches, and find that Peakachu identifies a unique set of short-range interactions. We show that our models perform well in different platforms, across different sequencing depths, and across different species. We apply this framework to predict chromatin loops in 56 Hi-C datasets, and release the results at the 3D Genome Browser.

Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae

We have developed a method for assembling genetic pathways for expression in Saccharomyces cerevisiae. Our pathway assembly method, called VEGAS (Versatile genetic assembly system), exploits the native capacity of S. cerevisiae to perform homologous recombination and efficiently join sequences with terminal homology. In the VEGAS workflow, terminal homology between adjacent pathway genes and the assembly vector is encoded by 'VEGAS adapter' (VA) sequences, which are orthogonal in sequence with respect to the yeast genome. Prior to pathway assembly by VEGAS in S. cerevisiae, each gene is assigned an appropriate pair of VAs and assembled using a previously described technique called yeast Golden Gate (yGG). Here we describe the application of yGG specifically to building transcription units for VEGAS assembly as well as the VEGAS methodology. We demonstrate the assembly of four-, five- and six-gene pathways by VEGAS to generate S. cerevisiae cells synthesizing β-carotene and violacein. Moreover, we demonstrate the capacity of yGG coupled to VEGAS for combinatorial assembly.