Investigating Cannabis-Use Among Students Attending High Schools Within the Cherokee Nation Reservation 2017 and 2019

Oklahoma's medical cannabis is some of the least restrictive in the US. Previous research suggests that American Indian/Alaska Native (AIAN) have higher rates of cannabis use than other racial or ethnic groups. The goals of this paper are, first, to look at cannabis use among high school students living on the Cherokee Nation Reservation before (2017) and after (2019) medical cannabis because legal in Oklahoma (2018) utilizing the Cherokee Nation Youth Risk Behavior Survey (CNYRBS). Second, to describe the socio-demographic characteristics of youth using cannabis in the Cherokee Nation Reservation. Data were retrieved from the 2017 and 2019 CNYRBS. The data for this study included 1,216 high school students who completed the 2017 and 1,476 who completed the 2019 CNYRBS. After removal of incomplete records, there were 2,602 students whose data was analyzed in this study. Data were weighted to be representative of public-school students attending grades 9-12 within Cherokee Nation Reservation. Despite the legalization of medical cannabis in Oklahoma in 2018, there was no change in cannabis use among youth between 2017 and 2019. There were variations in cannabis use based on demographic factors and other substance uses. AIAN individuals had higher odds of current cannabis use compared to non-Hispanic White students, but there were no differences based on ethnicity. Additionally, the use of cigarettes, e-cigarettes, alcohol, and illegal drugs were associated with increased odds of cannabis use among both current and former users compared to those who had never used it. There was no spike in use among youth at least immediately after the legalization of cannabis in the Cherokee Nation Reservation. There were socio-demographic as well as substance use disparities in the use of cannabis.

Dietary intake of vitamin C and gastric cancer: a pooled analysis within the Stomach cancer Pooling (StoP) Project

BACKGROUND

Previous studies suggest that dietary vitamin C is inversely associated with gastric cancer (GC), but most of them did not consider intake of fruit and vegetables. Thus, we aimed to evaluate this association within the Stomach cancer Pooling (StoP) Project, a consortium of epidemiological studies on GC.

METHODS

Fourteen case-control studies were included in the analysis (5362 cases, 11,497 controls). We estimated odds ratios (ORs) and corresponding 95% confidence intervals (CIs) for the association between dietary intake of vitamin C and GC, adjusted for relevant confounders and for intake of fruit and vegetables. The dose-response relationship was evaluated using mixed-effects logistic models with second-order fractional polynomials.

RESULTS

Individuals in the highest quartile of dietary vitamin C intake had reduced odds of GC compared with those in the lowest quartile (OR: 0.64; 95% CI: 0.58, 0.72). Additional adjustment for fruit and vegetables intake led to an OR of 0.85 (95% CI: 0.73, 0.98). A significant inverse association was observed for noncardia GC, as well as for both intestinal and diffuse types of the disease. The results of the dose-response analysis showed decreasing ORs of GC up to 150-200 mg/day of vitamin C (OR: 0.54; 95% CI: 0.41, 0.71), whereas ORs for higher intakes were close to 1.0.

CONCLUSIONS

The findings of our pooled study suggest that vitamin C is inversely associated with GC, with a potentially beneficial effect also for intakes above the currently recommended daily intake (90 mg for men and 75 mg for women).

Disentangling the relationships of body mass index and circulating sex hormone concentrations in mammographic density using Mendelian randomization

PURPOSE

Mammographic density phenotypes, adjusted for age and body mass index (BMI), are strong predictors of breast cancer risk. BMI is associated with mammographic density measures, but the role of circulating sex hormone concentrations is less clear. We investigated the relationship between BMI, circulating sex hormone concentrations, and mammographic density phenotypes using Mendelian randomization (MR).

METHODS

We applied two-sample MR approaches to assess the association between genetically predicted circulating concentrations of sex hormones [estradiol, testosterone, sex hormone-binding globulin (SHBG)], BMI, and mammographic density phenotypes (dense and non-dense area). We created instrumental variables from large European ancestry-based genome-wide association studies and applied estimates to mammographic density phenotypes in up to 14,000 women of European ancestry. We performed analyses overall and by menopausal status.

RESULTS

Genetically predicted BMI was positively associated with non-dense area (IVW: β = 1.79; 95% CI = 1.58, 2.00; p = 9.57 × 10-63) and inversely associated with dense area (IVW: β = - 0.37; 95% CI = - 0.51,- 0.23; p = 4.7 × 10-7). We observed weak evidence for an association of circulating sex hormone concentrations with mammographic density phenotypes, specifically inverse associations between genetically predicted testosterone concentration and dense area (β = - 0.22; 95% CI = - 0.38, - 0.053; p = 0.009) and between genetically predicted estradiol concentration and non-dense area (β =  - 3.32; 95% CI = - 5.83, - 0.82; p = 0.009), although results were not consistent across a range of MR approaches.

CONCLUSION

Our findings support a positive causal association between BMI and mammographic non-dense area and an inverse association between BMI and dense area. Evidence was weaker and inconsistent for a causal effect of circulating sex hormone concentrations on mammographic density phenotypes. Based on our findings, associations between circulating sex hormone concentrations and mammographic density phenotypes are weak at best.

Long-Term Survival of Patients With Cancer, Sepsis, and Vasopressor Requirements Based on Lactate Levels

A prospective cohort study was conducted to evaluate the 1-year survival of cancer patients with sepsis and vasopressor requirements. Eligible patients were admitted a Comprehensive Cancer Center's ICU and were compared based on their admission lactate levels. Of the 132 included patients, 87 (66%) had high lactate (HL; > 2.0 mmol/L), and 45 (34%) had normal lactate (NL; ≤ 2.0 mmol/L). The 1-year survival rates of the two groups were similar (HL 16% vs. NL 18%; p = 0.0921). After adjustment for ICU baseline characteristics, HL was not significantly associated with a 1-year survival (Hazards ratio, 1.39; 95% CI, 0.94-2.05). Critically ill cancer patients with sepsis and vasopressor requirements, regardless of the lactate level, had 1-year survival of less than 20%. Large multicenter cancer registries would enable to confirm our findings and better understand the long-term trajectories of sepsis in this vulnerable population.

An Update on Prenatal Diethylstilbestrol Exposure and High-Grade Squamous Intraepithelial Lesions of the Lower Genital Tract

Women with prenatal diethylstilbestrol exposure are excluded from less frequent cervical cancer screening because of their increased neoplasia risk. We report the results of a prospective follow-up study of prenatal diethylstilbestrol exposure and lower genital tract high-grade (grade 2 or higher) squamous intraepithelial lesions (HSIL). The age-adjusted risk of HSIL among diethylstilbestrol-exposed women (n=4,062) was higher than among the diethylstilbestrol unexposed (n=1,837) through age 44 years (hazard ratio 2.03, 95% CI, 1.31-3.14) but not age 45 years or older. Elevated HSIL risk remained higher in diethylstilbestrol-exposed women, after accounting for frequency of cervical cancer screening. Compared with unexposed women, HSIL risk was higher among women with earlier gestational and high-dose diethylstilbestrol exposure. These data confirm the appropriateness of more frequent screening among diethylstilbestrol-exposed women through age 44 years. Whether those aged 45 years or older should continue to have increased screening will require careful weighing of possible risks and benefits.

Prospective analysis of sleep characteristics, chronotype, and risk of breast cancer in the california teachers study

PURPOSE

Poor sleep quality and evening chronotype were associated with increased risk of breast cancer in a previous retrospective study in the California Teachers Study (CTS). The present analysis examines these sleep factors prospectively in the same cohort of women.

METHODS

From the CTS, we included 1,085 incident breast cancer cases and 38,470 cancer-free participants from 2012 through 2019. We calculated time at risk and used Cox proportional hazards regression models to estimate the hazard ratios (HRs) and control for risk factors such as age, race, body mass index, family history of breast cancer, and reproductive history. The sleep factors examined were quality, latency, duration, disturbance, and sleep medication use, based on a shortened version of the Pittsburgh Sleep Quality Index, as well as chronotype (preference for morning or evening activity). This analysis was limited to women who were post-menopausal at the time they answered these sleep-related questions.

RESULTS

Measures of sleep quality did not appear to be associated with subsequent breast cancer risk. The HR for evening chronotypes compared to morning chronotypes was somewhat elevated (HR 1.19, 95% CI 1.04, 1.36).

CONCLUSION

While the measures of sleep quality and duration were not associated with post-menopausal breast cancer risk in this prospective analysis, the modestly elevated risk observed for evening chronotypes was consistent with the prior retrospective analysis.

COVID-19 perceptions, impacts, and experiences: a cross-sectional analysis among New Jersey cancer survivors

BACKGROUND

Cancer survivors are particularly vulnerable to adverse COVID-19-related outcomes, but limited data exist on perceptions about the pandemic and related experiences in this group.

METHODS

In a cross-sectional analysis of 494 survivors of genitourinary, breast, gynecologic, colorectal, lung, melanoma, or thyroid cancer, from a larger study of cancer survivors in New Jersey, we assessed perceptions about COVID-19 threat, impacts, and experiences using three validated instruments. Responses were coded on a 7-point Likert scale, and subscales were averaged across included items, with higher scores indicating greater perceptions of COVID-19 threat and greater impacts and experiences because of the pandemic. Multivariable linear regression models were used to determine factors associated with higher scores, with Bonferroni correction for multiple comparisons.

RESULTS

In general, cancer survivors reported moderate perceived COVID-19 threat (3 items, mean score = 3.71 ± 1.97), minimal COVID-19-related impacts (6 items, mean score = 2.23 ± 1.34), and COVID-19-related experiences (7 items, mean score = 2.17 ± 1.00). COVID-19 impact subscale scores varied little (mean subscale score range = 2.09 to 2.29), while COVID-19 experiences subscale scores were quite variable (mean subscale score range = 1.52 to 3.39). Asian American/Pacific Islander race, Black race, female sex, and having more cardiovascular and metabolic and other comorbidities were associated with higher scores on the perceived coronavirus threat questionnaire. Having completed the COVID-19 questionnaires earlier in the pandemic, younger age, American/Pacific Islander race, Hispanic ethnicity, and having more comorbidities were associated with higher scores on the COVID-19 impact questionnaire. Younger age, racial minority status, and having more cardiovascular and metabolic comorbidities were associated with higher scores on the COVID-19 experience questionnaire.

CONCLUSION

Among cancer survivors in New Jersey-a state that experienced high rates of COVID-19 infection-sociodemographic and health-related factors (e.g., race and ethnicity, sex, and multimorbidity) correlate with greater perceptions of COVID-19 threat, impacts, and experiences.

IMPLICATIONS FOR CANCER SURVIVORS

Studies are needed to examine the influence of vaccination status on COVID-19 perceptions and identify inequities in clinical outcomes due to pandemic-related disruptions to cancer care.

Germline pathogenic variants associated with triple-negative breast cancer in US Hispanic and Guatemalan women using hospital and community-based recruitment strategies

PURPOSE

Recruit and sequence breast cancer subjects in Guatemalan and US Hispanic populations. Identify optimum strategies to recruit Latin American and Hispanic women into genetic studies of breast cancer.

METHODS

We used targeted gene sequencing to identify pathogenic variants in 19 familial breast cancer susceptibility genes in DNA from unselected Hispanic breast cancer cases in the US and Guatemala. Recruitment across the US was achieved through community-based strategies. In addition, we obtained patients receiving cancer treatment at major hospitals in Texas and Guatemala.

RESULTS

We recruited 287 Hispanic US women, 38 (13%) from community-based and 249 (87%) from hospital-based strategies. In addition, we ascertained 801 Guatemalan women using hospital-based recruitment. In our experience, a hospital-based approach was more efficient than community-based recruitment. In this study, we sequenced 103 US and 137 Guatemalan women and found 11 and 10 pathogenic variants, respectively. The most frequently mutated genes were BRCA1, BRCA2, CHEK2, and ATM. In addition, an analysis of 287 US Hispanic patients with pathology reports showed a significantly higher percentage of triple-negative disease in patients with pathogenic variants (41% vs. 15%). Finally, an analysis of mammography usage in 801 Guatemalan patients found reduced screening in women with a lower socioeconomic status (p < 0.001).

CONCLUSION

Guatemalan and US Hispanic women have rates of hereditary breast cancer pathogenic variants similar to other populations and are more likely to have early age at diagnosis, a family history, and a more aggressive disease. Patient recruitment was higher using hospital-based versus community enrollment. This data supports genetic testing in breast cancer patients to reduce breast cancer mortality in Hispanic women.

A generalisation of the method of regression calibration and comparison with Bayesian and frequentist model averaging methods

For many cancer sites low-dose risks are not known and must be extrapolated from those observed in groups exposed at much higher levels of dose. Measurement error can substantially alter the dose-response shape and hence the extrapolated risk. Even in studies with direct measurement of low-dose exposures measurement error could be substantial in relation to the size of the dose estimates and thereby distort population risk estimates. Recently, there has been considerable attention paid to methods of dealing with shared errors, which are common in many datasets, and particularly important in occupational and environmental settings. In this paper we test Bayesian model averaging (BMA) and frequentist model averaging (FMA) methods, the first of these similar to the so-called Bayesian two-dimensional Monte Carlo (2DMC) method, and both fairly recently proposed, against a very newly proposed modification of the regression calibration method, the extended regression calibration (ERC) method, which is particularly suited to studies in which there is a substantial amount of shared error, and in which there may also be curvature in the true dose response. The quasi-2DMC with BMA method performs well when a linear model is assumed, but very poorly when a linear-quadratic model is assumed, with coverage probabilities both for the linear and quadratic dose coefficients that are under 5% when the magnitude of shared Berkson error is large (50%). For the linear model the bias is generally under 10%. However, using a linear-quadratic model it produces substantially biased (by a factor of 10) estimates of both the linear and quadratic coefficients, with the linear coefficient overestimated and the quadratic coefficient underestimated. FMA performs as well as quasi-2DMC with BMA when a linear model is assumed, and generally much better with a linear-quadratic model, although the coverage probability for the quadratic coefficient is uniformly too high. However both linear and quadratic coefficients have pronounced upward bias, particularly when Berkson error is large. By comparison ERC yields coverage probabilities that are too low when shared and unshared Berkson errors are both large (50%), although otherwise it performs well, and coverage is generally better than the quasi-2DMC with BMA or FMA methods, particularly for the linear-quadratic model. The bias of the predicted relative risk at a variety of doses is generally smallest for ERC, and largest for the quasi-2DMC with BMA and FMA methods (apart from unadjusted regression), with standard regression calibration and Monte Carlo maximum likelihood exhibiting bias in predicted relative risk generally somewhat intermediate between ERC and the other two methods. In general ERC performs best in the scenarios presented, and should be the method of choice in situations where there may be substantial shared error, or suspected curvature in the dose response.

Prediagnostic serum concentrations of per- and polyfluoroalkyl substances and risk of papillary thyroid cancer in the Finnish Maternity Cohort

Human exposure to per- and polyfluoroalkyl substances (PFAS) occurs globally through contaminated food, dust, and drinking water. Studies of PFAS and thyroid cancer have been limited. We conducted a nested case-control study of prediagnostic serum levels of 19 PFAS and papillary thyroid cancer (400 cases, 400 controls) in the Finnish Maternity Cohort (pregnancies 1986-2010; follow-up through 2016), individually matched on sample year and age. We used conditional logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for log2 transformed and categorical exposures, overall and stratified by calendar period, birth cohort, and median age at diagnosis. We adjusted for other PFAS with Spearman correlation rho = 0.3-0.6. Seven PFAS, including perfluoroctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), N-ethyl-perfluorooctane sulfonamidoacetic acid (EtFOSAA), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), and perfluorohexane sulfonic acid (PFHxS) were detected in >50% of women. These PFAS were not associated with risk of thyroid cancer, except for PFHxS, which was inversely associated (OR log2  = 0.82, 95% CI: 0.70-0.97). We observed suggestive but imprecise increased risks associated with PFOA, PFOS, and EtFOSAA for those diagnosed at ages <40 years, whereas associations were null or inverse among those diagnosed at 40+ years (P-interaction: .02, .08, .13, respectively). There was little evidence of other interactions. These results show no clear association between PFAS and papillary thyroid cancer risk. Future work would benefit from evaluation of these relationships among those with higher exposure levels and during periods of early development when the thyroid gland may be more susceptible to environmental harms.

D-dimer and sinusoidal obstructive syndrome-novel poor prognostic features of thrombotic microangiopathy in children after hematopoietic cellular therapy in a single institution prospective cohort study

Transplant-associated thrombotic microangiopathy (TA-TMA) is a common, severe complication of allogeneic hematopoietic cellular therapy (HCT). Even when treated in many studies, morbidity and mortality rates are high. This prospective single-institution cohort study serially enrolled all allogeneic HCT recipients from August 2019-August 2022. Patients were universally screened for TA-TMA and intermediate and high-risk patients were immediately treated with eculizumab. Sub-distribution cox-proportional hazards models were used to identify sub-distribution hazard ratios (sHR)  for multi-organ dysfunction (MOD) and non-relapse-related mortality (NRM). Of 136 patients, 36 (26%) were diagnosed with TA-TMA and 21/36 (58%) developed MOD, significantly more than those without TA-TMA, (p < .0001). Of those with TA-TMA, 18 (50%) had high-risk TA-TMA (HR-TA-TMA), 11 (31%) had intermediate-risk TA-TMA (IR-TA-TMA), and 8 (22%) had standard risk (SR-TA-TMA). Twenty-six were treated with eculizumab (1/8 SR, 7/11 IR, and 18/18 HR). Elevated D-dimer predicted the development of MOD (sHR 7.6, 95% confidence interval [CI] 1.8-32.3). Children with concurrent sinusoidal obstructive syndrome (SOS) and TA-TMA had an excess risk of MOD of 34% and data supported a biologic interaction. The adjusted NRM risk was significantly higher in the TA-TMA patients (sHR 10.54, 95% CI 3.8-29.2, p < .0001), despite prompt treatment with eculizumab. Significant RF for NRM in TA-TMA patients included SOS (HR 2.89, 95% 1.07-7.80) and elevated D-dimer (HR 3.82, 95% CI 1.14-12.84). An unrelated donor source and random urine protein to creatine ratio ≥2 mg/mg were significantly associated with no response to eculizumab (odds ratio 15, 95% CI 2.0-113.6 and OR 6.5, 95% CI 1.1-38.6 respectively). TA-TMA was independently associated with NRM despite early diagnosis and treatment with eculizumab in this large pediatric transplant cohort. Prognostic implications of D-dimer in TA-TMA merit further investigation as this is a readily accessible biomarker. Concurrent SOS is an exclusion criterion of many ongoing clinical trials, but these data highlight these patients could benefit from novel therapeutic approaches. Multi-institutional clinical trials are needed to understand the impact of TA-TMA-targeted therapies.

Atypical Spitz tumor with SQSTM1::NTRK2 fusion: Report of a case with unique spindled cell features

A host of signature genetic alterations have been demonstrated in Spitz neoplasms, most notably fusions of kinase genes (including BRAF, ALK, ROS1, NTRK1, NTRK3, RET, MET, MAP3K8) or variants in HRAS. While there are multiple reports of rearrangements involving NTRK1 and NTRK3 in Spitz tumors, there are very few reports of NTRK2-rearranged Spitz nevi in the literature. This report presents an NTRK2-rearranged atypical Spitz tumor with spindled cell features. The patient was a 6-year-old female with a growing pigmented papule on the back. Histopathological evaluation revealed an asymmetric, biphasic, compound proliferation of melanocytes featuring an epithelioid cell population arranged as variably sized nests and single cells along the basal layer with extension down adnexa, as well as a population of spindled melanocytes with desmoplastic features and loss of Melan-A expression in the dermis. There was partial loss of p16 expression in the epidermal component and diffuse loss in the dermal component. Immunohistochemistry for PRAME, ALK, NTRK1, HRAS Q61R, p53, and BRAF V600E were negative. A SQSTM1::NTRK2 fusion was identified by RNA sequencing. No TERT promoter hotspot variants were detected. This case report expands the known histopathologic spectrum of genetic alterations in Spitz neoplasms.

The Time-Dependent Association Between Irritable Bowel Syndrome and All-Cause and Cause-Specific Mortality: A Prospective Cohort Study Within the UK Biobank

INTRODUCTION

Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders, but few studies have evaluated mortality risks among individuals with IBS. We explored the association between IBS and all-cause and cause-specific mortality in the UK Biobank.

METHODS

We included 502,369 participants from the UK Biobank with mortality data through 2022. IBS was defined using baseline self-report and linkage to primary care or hospital admission data. We estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for all-cause and cause-specific mortality using multivariable Cox proportional hazards regression models within partitioned follow-up time categories (0-5, >5-10, and >10 years).

RESULTS

A total of 25,697 participants (5.1%) had a history of IBS at baseline. After a median follow-up of 13.7 years, a total of 44,499 deaths occurred. Having an IBS diagnosis was strongly associated with lower risks of all-cause (HR = 0.70, 95% CI = 0.62-0.78) and all-cancer (HR = 0.69, 95% CI = 0.60-0.79) mortality in the first 5 years of follow-up. These associations were attenuated over follow-up, but even after 10 years of follow-up, associations remained inverse (all-cause: HR = 0.89, 95% CI = 0.84-0.96; all-cancer: HR = 0.87, 95% CI = 0.78-0.97) after full adjustment. Individuals with IBS had decreased risk of mortality from breast, prostate, and colorectal cancers in some of the follow-up time categories.

DISCUSSION

We found that earlier during follow-up, having diagnosed IBS was associated with lower mortality risk, and the association attenuated over time. Additional studies to understand whether specific factors, such as lifestyle and healthcare access, explain the inverse association between IBS and mortality are needed.

Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus

High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant's allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.

A rapid HPV typing assay to support global cervical cancer screening and risk-based management: A cross-sectional study

The World Health Organization recommends human papillomavirus (HPV) testing for cervical screening. Extended genotyping can identify the highest-risk HPV-positive women. An inexpensive, rapid, mobile isothermal amplification assay (ScreenFire HPV RS test) was recently redesigned to yield four channels ordered by cancer risk (ie, hierarchical approach): HPV16, HPV18/45, HPV31/33/35/52/58 and HPV39/51/56/59/68. Stored specimens from 2076 women (mean age 30.9) enrolled in a colposcopy clinic, with high HPV prevalence, were tested with ScreenFire. We calculated hierarchical channel positivity and non-hierarchical channel and type positivity, according to histologic diagnosis (256 cancer, 350 cervical intraepithelial neoplasia [CIN]3, 409 CIN2, 1020 < CIN2) and known virologic reference results (Linear Array and TypeSeq). Additionally, we analyzed ScreenFire time-to-positive up to 60 min by channel and histology. Overall clinical sensitivity for CIN3+ was 94.7% (95% confidence interval 92.6-96.4), similar to Linear Array (92.3, 89.7-94.3) and TypeSeq (96.0, 93.9-97.6). Sensitivity was high for all types and channels. The hierarchical approach was well in line with HPV typing and histologic diagnosis, prioritizing higher risk women having HPV16 and precancer. For HPV16, time-to-positive was shorter in women with precancer. ScreenFire showed excellent agreement with research reference typing tests and detection of CIN2+. Risk-based type results could help guide clinical management of HPV-positive women. Time-to-positive combined with genotyping might be useful. ScreenFire is rapid, mobile, relatively inexpensive and designed for implementation of HPV-based screening and management, including in lower-resource settings. Further validation in screening by self-sampling and practical effectiveness merit evaluation.

Dental health and lung cancer risk in the Golestan Cohort Study

BACKGROUND

Poor oral health has been linked to various systemic diseases, including multiple cancer types, but studies of its association with lung cancer have been inconclusive.

METHODS

We examined the relationship between dental status and lung cancer incidence and mortality in the Golestan Cohort Study, a large, prospective cohort of 50,045 adults in northeastern Iran. Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for associations between three dental health measures (i.e., number of missing teeth; the sum of decayed, missing, or filled teeth (DMFT); and toothbrushing frequency) and lung cancer incidence or mortality with adjustment for multiple potential confounders, including cigarette smoking and opium use. We created tertiles of the number of lost teeth/DMFT score in excess of the loess adjusted, age- and sex-specific predicted numbers, with subjects with the expected number of lost teeth/DMFT or fewer as the reference group.

RESULTS

During a median follow-up of 14 years, there were 119 incident lung cancer cases and 98 lung cancer deaths. Higher DMFT scores were associated with a progressively increased risk of lung cancer (linear trend, p = 0.011). Compared with individuals with the expected DMFT score or less, the HRs were 1.27 (95% CI: 0.73, 2.22), 2.15 (95% CI: 1.34, 3.43), and 1.52 (95% CI: 0.81, 2.84) for the first to the third tertiles of DMFT, respectively. The highest tertile of tooth loss also had an increased risk of lung cancer, with a HR of 1.68 (95% CI: 1.04, 2.70) compared with subjects with the expected number of lost teeth or fewer (linear trend, p = 0.043). The results were similar for lung cancer mortality and did not change substantially when the analysis was restricted to never users of cigarettes or opium. We found no associations between toothbrushing frequency and lung cancer incidence or mortality.

CONCLUSION

Poor dental health indicated by tooth loss or DMFT, but not lack of toothbrushing, was associated with increased lung cancer incidence and mortality in this rural Middle Eastern population.

mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T-cell responses in patients with lung cancer

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is highly transmissible and evades pre-established immunity. Messenger RNA (mRNA) vaccination against ancestral strain spike protein can induce intact T-cell immunity against the Omicron variant, but efficacy of booster vaccination in patients with late-stage lung cancer on immune-modulating agents including anti-programmed cell death protein 1(PD-1)/programmed death-ligand 1 (PD-L1) has not yet been elucidated.

METHODS

We assessed T-cell responses using a modified activation-induced marker assay, coupled with high-dimension flow cytometry analyses. Peripheral blood mononuclear cells (PBMCs) were stimulated with various viral peptides and antigen-specific T-cell responses were evaluated using flow cytometry.

RESULTS

Booster vaccines induced CD8+ T-cell response against the ancestral SARS-CoV-2 strain and Omicron variant in both non-cancer subjects and patients with lung cancer, but only a marginal induction was detected for CD4+ T cells. Importantly, antigen-specific T cells from patients with lung cancer showed distinct subpopulation dynamics with varying degrees of differentiation compared with non-cancer subjects, with evidence of dysfunction. Notably, female-biased T-cell responses were observed.

CONCLUSION

We conclude that patients with lung cancer on immunotherapy show a substantial qualitative deviation from non-cancer subjects in their T-cell response to mRNA vaccines, highlighting the need for heightened protective measures for patients with cancer to minimize the risk of breakthrough infection with the Omicron and other future variants.

Association with menopausal hormone therapy and asymptomatic gallstones in US women in the third National Health and Nutrition Examination Study

15% of US adults have gallstones, most of which are clinically "silent". Several studies show that menopausal hormone therapy (MHT) increases symptomatic gallstones and cholecystectomy risk. MHT use may be contraindicated in women with gallstones and population studies may be biased by "confounding by contraindication" while the true association between MHT and gallstones remains underestimated. We sought to examine whether MHT use was associated with asymptomatic gallstones using instrumental variable (IV) analysis to account for confounding by contraindication. We used 2018 postmenopausal women from the Third National Health and Nutrition Examination Survey to estimate associations of MHT use with asymptomatic gallstones. A traditional logistic regression analysis was compared to instrumental variable (IV) analysis to account for confounding by contraindication. 12% of women with asymptomatic gallstones and 25% of women without gallstones were current MHT users (P < 0.001). The traditional analysis suggested a decreased odds of asymptomatic gallstones in current versus never users (OR 0.58, 95% CI 0.37, 0.89), but increased odds (OR 1.51, 95% CI 0.44, 5.16) in the IV analysis. The traditional analysis consistently underestimated the odds of asymptomatic gallstones with MHT use compared to the IV analysis. Accounting for confounding by contraindication, we found a suggestive, though imprecise, positive association between MHT use and asymptomatic gallstones among postmenopausal women. Failure to consider contraindication can produce incorrect results.

FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases

The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.cancer.gov/ ; https://forge2.altiusinstitute.org/files/forgedb.html ; and https://doi.org/10.5281/zenodo.10067458 ), a standalone and web-based tool that integrates multiple datasets, delivering information on associated regulatory elements, transcription factor binding sites, and target genes for over 37 million variants. FORGEdb scores provide researchers with a quantitative assessment of the relative importance of each variant for targeted functional experiments.

Financial burdens during the COVID-19 pandemic are related to disrupted healthcare utilization among survivors of adolescent and young adult cancers

PURPOSE

We examined whether financial burdens occurring during the COVID-19 pandemic impacted healthcare utilization among survivors of adolescent and young adult cancers.

METHODS

We surveyed survivors enrolled in a patient navigation program to obtain self-reports of delayed/skipped cancer care or other care, changes to medication obtainment, and changes to medication use since the COVID-19 pandemic began. Reported financial burdens were defined as financial toxicity in the past 4 weeks (COmprehensive Score for financial Toxicity [COST] ≤ median 21) and material hardships (range = 4-11) since March 2020. Adjusted logistic regression models calculated associations and effect modification by gender.

RESULTS

Survivors (n = 341) were mostly female (61.3%) and non-Hispanic White (83.3%). Nearly 20% delayed/skipped cancer care, 35.2% delayed/skipped other care, 19.1% changed medication obtainment, and 12.6% changed medication use. Greater material hardships were associated with delayed/skipped cancer care (odds ratio (OR) = 3.13, 95% CI = 1.44-6.81) and other care (OR = 2.17, 95% CI = 1.18-3.98), and changed medication obtainment (OR = 2.72, 95% CI = 1.43-5.18) or use (OR = 4.49, 95% CI = 2.05-9.80). Financial toxicity was associated with delayed/skipped other care (OR = 2.53, 95% CI = 1.31-4.89) and changed medication obtainment (OR = 1.96, 95% CI = 1.01-3.83) and medication use (OR = 3.73, 95% CI = 1.59-8.73). The association of material hardships and any changes in healthcare utilization was greater among female compared to male survivors.

CONCLUSION

Financial burdens experienced during the pandemic impeded survivors' ability to utilize necessary healthcare, with worse impacts among female survivors.

IMPLICATIONS FOR CANCER SURVIVORS

Delayed or skipped healthcare may lead to an increased cancer mortality or severity of therapy-related conditions. Providing resources that enable survivors experiencing financial burdens to continue critical cancer and preventive care during the COVID-19 pandemic is a priority.

Clinicians' perspectives on barriers and facilitators to sperm banking in adolescent males with cancer: a mixed-methods study

PURPOSE

To examine processes, barriers, and facilitators to sperm banking counseling and decision-making for adolescent males newly diagnosed with cancer from the perspective of clinicians who completed Oncofertility communication training. We also identify opportunities for improvement to inform future interventions and implementation.

METHODS

A survey (N=104) and subsequent focus groups (N=15) were conducted with non-physician clinicians practicing in pediatric oncology who completed Oncofertility communication training.

RESULTS

Most survey participants were confident in communicating about the impact of cancer on fertility (n=87, 83.7%) and fertility preservation options (n=80, 76.9%). Most participants reported never/rarely using a sperm banking decision tool (n=70, 67.3%), although 98.1% (n=102) said a decision tool with a family-centered approach would be beneficial. Primary themes in the subsequent focus groups included variable processes/workflows (inconsistent approaches to consult initiation; involvement of adolescents, caregivers, and various clinician types; assessment of puberty/sexual experience), structural and psychosocial barriers (cost and logistics, developmental, cultural, clinical acuity/prognosis), and facilitators (educational materials, alternative options for banking). Opportunities and strategies for improvement (including fertility preservation in existing research protocols; additional staffing/resources; oncologist education and buy-in; and development of decision tools) were informed by challenges identified in the other themes.

CONCLUSION

Barriers to adolescent sperm banking remain, even among clinicians who have completed Oncofertility training. Although training is one factor necessary to facilitate banking, structural and psychosocial barriers persist. Given the complexities of offering sperm banking to pediatric populations, continued efforts are needed to mitigate structural barriers and develop strategies to facilitate decision-making before childhood cancer treatment.

Adherence to oral endocrine therapy in racial/ethnic minority patients with low socioeconomic status before and during the COVID-19 pandemic

BACKGROUND

Adherence to oral endocrine therapy (OET) is crucial in ensuring its maximum benefit in the prevention and treatment of hormone receptor-positive (HR +) breast cancer (BC). Medication use behavior is suboptimal especially in racial/ethnic minorities with lower socioeconomic status (SES).

AIM

We aimed to assess the impact of the coronavirus disease 2019 (COVID-19) pandemic on OET adherence and identify demographic and/or clinical characteristics associated with nonadherence in racial/ethnic minorities with lower SES.

METHOD

A retrospective study was conducted at the Harris Health System in Houston, Texas. Data were collected during the 6 months before and 6 months after the start of the pandemic. The adherence was assessed using the prescription refill data using the proportion of days covered. A multivariable logistic regression model was used to identify demographic/clinical characteristics associated with nonadherence. Eighteen years or older patients on appropriate doses of OET for prevention or treatment of BC were included.

RESULTS

In 258 patients, adherence was significantly lower during the pandemic (44%) compared to before the pandemic (57%). The demographic/clinical characteristics associated with OET nonadherence before the pandemic were Black/African American, obesity/extreme obesity, prevention setting, tamoxifen therapy, and 4 or more years on OET. During the pandemic, prevention setting and those not using home delivery were more likely to be nonadherent.

CONCLUSION

OET adherence was significantly reduced during the COVID-19 pandemic in racial/ethnic minority patients with low SES. Patient-centered interventions are necessary to improve OET adherence in these patients.

Deep neural network based tissue deconvolution of circulating tumor cell RNA

Prior research has shown that the deconvolution of cell-free RNA can uncover the tissue origin. The conventional deconvolution approaches rely on constructing a reference tissue-specific gene panel, which cannot capture the inherent variation present in actual data. To address this, we have developed a novel method that utilizes a neural network framework to leverage the entire training dataset. Our approach involved training a model that incorporated 15 distinct tissue types. Through one semi-independent and two complete independent validations, including deconvolution using a semi in silico dataset, deconvolution with a custom normal tissue mixture RNA-seq data, and deconvolution of longitudinal circulating tumor cell RNA-seq (ctcRNA) data from a cancer patient with metastatic tumors, we demonstrate the efficacy and advantages of the deep-learning approach which were exerted by effectively capturing the inherent variability present in the dataset, thus leading to enhanced accuracy. Sensitivity analyses reveal that neural network models are less susceptible to the presence of missing data, making them more suitable for real-world applications. Moreover, by leveraging the concept of organotropism, we applied our approach to trace the migration of circulating tumor cell-derived RNA (ctcRNA) in a cancer patient with metastatic tumors, thereby highlighting the potential clinical significance of early detection of cancer metastasis.

Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer

A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.

Exposure to pesticides and risk of Hodgkin lymphoma in an international consortium of agricultural cohorts (AGRICOH)

PURPOSE

Some pesticides may increase the risk of certain lymphoid malignancies, but few studies have examined Hodgkin lymphoma (HL). In this exploratory study, we examined associations between agricultural use of 22 individual active ingredients and 13 chemical groups and HL incidence.

METHODS

We used data from three agricultural cohorts participating in the AGRICOH consortium: the French Agriculture and Cancer Cohort (2005-2009), Cancer in the Norwegian Agricultural Population (1993-2011), and the US Agricultural Health Study (1993-2011). Lifetime pesticide use was estimated from crop-exposure matrices or self-report. Cohort-specific covariate-adjusted overall and age-specific (< 40 or ≥ 40 years) hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox regression and combined using random effects meta-analysis.

RESULTS

Among 316 270 farmers (75% male) accumulating 3 574 815 person-years at risk, 91 incident cases of HL occurred. We did not observe statistically significant associations for any of the active ingredients or chemical groups studied. The highest risks of HL overall were observed for the pyrethroids deltamethrin (meta-HR = 1.86, 95% CI 0.76-4.52) and esfenvalerate (1.86, 0.78-4.43), and inverse associations of similar magnitude were observed for parathion and glyphosate. Risk of HL at ≥ 40 years of age was highest for ever-use of dicamba (2.04, 0.93-4.50) and lowest for glyphosate (0.46, 0.20-1.07).

CONCLUSION

We report the largest prospective investigation of these associations. Nonetheless, low statistical power, a mixture of histological subtypes and a lack of information on tumour EBV status complicate the interpretability of the results. Most HL cases occurred at older ages, thus we could not explore associations with adolescent or young adult HL. Furthermore, estimates may be attenuated due to non-differential exposure misclassification. Future work should aim to extend follow-up and refine both exposure and outcome classification.

Impact of preoperative chemotherapy on perioperative morbidity in combined resection of colon cancer and liver metastases

BACKGROUND

Preoperative chemotherapy, or neoadjuvant therapy (NAC) can be used to improve resectability but can also have hepatotoxic effects on the future liver remnant. The purpose of this study was to investigate the impact of NAC on 30-day morbidity among patients undergoing a resection of primary colon cancer and synchronous liver metastases (sLM).

METHODS

This was a retrospective study using the National Surgical Quality Improvement Program database (2012-2020). The association between NAC and 30-day overall morbidity, the primary outcome, was assessed. Subgroup analyses for low and high-risk procedures were performed.

RESULTS

Among 968 patients who underwent the combined resection, 571 (58.99%) received NAC. There was a lower rate of 30-day overall morbidity among patients who received NAC (34.50% vs. 41.56%, p = 0.026) and no difference in rates of postoperative liver failure, bile leak, need for invasive intervention for hepatic procedure, and anastomotic leak. On adjusted analyses, patients who received NAC had decreased odds of overall morbidity (OR 0.73, 95% CI 0.55-0.97, p = 0.031) compared to patients who did not receive NAC. On subgroup analyses, patients who received NAC prior to a low risk combined resection had lower rates of overall morbidity on both adjusted and unadjusted analyses. Among those undergoing high-risk combined resections, there was no difference in overall morbidity.

DISCUSSION AND CONCLUSION

Patients who are deemed to be candidates for preoperative chemotherapy can proceed with planned neoadjuvant chemotherapy prior to combined resection of primary colon cancer and sLM as preoperative neoadjuvant chemotherapy does not appear to be associated with increased postoperative morbidity.

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

BACKGROUND

Single-cell gene expression profiling provides unique opportunities to understand tumor heterogeneity and the tumor microenvironment. Because of cost and feasibility, profiling bulk tumors remains the primary population-scale analytical strategy. Many algorithms can deconvolve these tumors using single-cell profiles to infer their composition. While experimental choices do not change the true underlying composition of the tumor, they can affect the measurements produced by the assay.

RESULTS

We generated a dataset of high-grade serous ovarian tumors with paired expression profiles from using multiple strategies to examine the extent to which experimental factors impact the results of downstream tumor deconvolution methods. We find that pooling samples for single-cell sequencing and subsequent demultiplexing has a minimal effect. We identify dissociation-induced differences that affect cell composition, leading to changes that may compromise the assumptions underlying some deconvolution algorithms. We also observe differences across mRNA enrichment methods that introduce additional discrepancies between the two data types. We also find that experimental factors change cell composition estimates and that the impact differs by method.

CONCLUSIONS

Previous benchmarks of deconvolution methods have largely ignored experimental factors. We find that methods vary in their robustness to experimental factors. We provide recommendations for methods developers seeking to produce the next generation of deconvolution approaches and for scientists designing experiments using deconvolution to study tumor heterogeneity.

Police Bias and Low Relatability and Diet Quality: Examining the Importance of Psychosocial Factors in Predominantly Black Communities

How police bias and low relatability may contribute to poor dietary quality is poorly understood. In this cross-sectional study, we analyzed data from 2021 from a cohort of n = 724 adults living in predominantly Black communities in Pittsburgh, Pennsylvania; these adults were mostly Black (90.6%), low-income (median household income $17,500), and women (79.3%). We estimated direct and indirect paths between police mistrust and dietary quality (measured by Healthy Eating Index (HEI)-2015) through perceived stress, community connectedness, and subjective social status. Dietary quality was poor (mean HEI-2015 score was 50) and mistrust of police was high: 78% of participants either agreed or strongly agreed that something they say might be interpreted as criminal by the police due to their race/ethnicity. Police bias and low relatability was associated with lower perceived social status [Formula: see text]=  - 0.03 (95% confidence interval [CI]: - 0.05, - 0.01). Police bias and low relatability was marginally associated with low dietary quality β =  - 0.14 (95% CI: - 0.29, 0.02). Nineteen percent of the total association between police bias and low relatability and lower dietary quality β =  - 0.16 (- 0.01, - 0.31) was explained by an indirect association through lower community connectedness, or how close respondents felt with their community [Formula: see text] Police bias and low relatability may play a role in community connection, social status, and ultimately dietary disparities for Black Americans. Addressing police bias and low relatability is a continuing and pressing public health issue.

Unusual phenotypes in patients with a pathogenic germline variant in DICER1

Pathogenic germline DICER1 variants are associated with pleuropulmonary blastoma, multinodular goiter, embryonal rhabdomyosarcoma and other tumour types, while mosaic missense DICER1 variants in the RNase IIIb domain are linked to cause GLOW (global developmental delay, lung cysts, overgrowth, and Wilms' tumor) syndrome. Here, we report four families with germline DICER1 pathogenic variants in which one member in each family had a more complex phenotype, including skeletal findings, facial dysmorphism and developmental abnormalities. The developmental features occur with a variable expressivity and incomplete penetrance as also described for the neoplastic and dysplastic lesions associated with DICER1 variants. Whole exome sequencing (WES) was performed on all four cases and revealed no further pathogenic or likely pathogenic dominant, homozygous or compound heterozygous variants in three of them. Notably, a frameshift variant in ARID1B was detected in one patient explaining part of her phenotype. This series of patients shows that pathogenic DICER1 variants may be associated with a broader phenotypic spectrum than initially assumed, including predisposition to different tumours, skeletal findings, dysmorphism and developmental abnormalities, but genetic work up in syndromic patients should be comprehensive in order not to miss additional underlying /modifying causes.

A generalisation of the method of regression calibration

There is direct evidence of risks at moderate and high levels of radiation dose for highly radiogenic cancers such as leukaemia and thyroid cancer. For many cancer sites, however, it is necessary to assess risks via extrapolation from groups exposed at moderate and high levels of dose, about which there are substantial uncertainties. Crucial to the resolution of this area of uncertainty is the modelling of the dose-response relationship and the importance of both systematic and random dosimetric errors for analyses in the various exposed groups. It is well recognised that measurement error can alter substantially the shape of this relationship and hence the derived population risk estimates. Particular attention has been devoted to the issue of shared errors, common in many datasets, and particularly important in occupational settings. We propose a modification of the regression calibration method which is particularly suited to studies in which there is a substantial amount of shared error, and in which there may also be curvature in the true dose response. This method can be used in settings where there is a mixture of Berkson and classical error. In fits to synthetic datasets in which there is substantial upward curvature in the true dose response, and varying (and sometimes substantial) amounts of classical and Berkson error, we show that the coverage probabilities of all methods for the linear coefficient [Formula: see text] are near the desired level, irrespective of the magnitudes of assumed Berkson and classical error, whether shared or unshared. However, the coverage probabilities for the quadratic coefficient [Formula: see text] are generally too low for the unadjusted and regression calibration methods, particularly for larger magnitudes of the Berkson error, whether this is shared or unshared. In contrast Monte Carlo maximum likelihood yields coverage probabilities for [Formula: see text] that are uniformly too high. The extended regression calibration method yields coverage probabilities that are too low when shared and unshared Berkson errors are both large, although otherwise it performs well, and coverage is generally better than these other three methods. A notable feature is that for all methods apart from extended regression calibration the estimates of the quadratic coefficient [Formula: see text] are substantially upwardly biased.

Reduced racial disparity in receipt of optimal locoregional treatment for women with early-stage breast cancer

INTRODUCTION

Racial disparities in breast cancer treatment contribute to Black women having the worst breast cancer survival rates in the U.S. We investigated whether differences in receipt of optimal locoregional treatment (OLT), defined as receipt of mastectomy, breast-conserving surgery, or no surgery when contraindicated, existed between Black and White women with early-stage breast cancer from 2008-2018.

METHODS

In this retrospective cohort study, data from the Surveillance, Epidemiology, and End Results (SEER) Program Incidence Database was utilized to identify tumor cases from Black and White women aged 20-64 years old with stage I-II breast cancer. Logistic regression analyses were used to evaluate the associations between race and receipt of OLT as well as potential effect modification by tumor characteristics, and year of diagnosis.

RESULTS

Among 177,234 women diagnosed with early-stage breast tumors, disparities in OLT between Black and White women were present from 2008-2010 (2008: 82.1% Black vs. 85.7% White, p<0.001; 2009: 82.1% Black vs. 85.8% White, p<0.001; 2010: 82.2% Black vs. 87.2% White, p<0.001). This disparity was eliminated between 2010-2011 (86.3% Black vs. 87.5% White, p = 0.15), and did not reoccur during the remainder of the study period. From 2010-2011, more Black women received radiation therapy following breast-conserving surgery (43.4% to 48.9%; p = 0.001), which accounted for an overall increased receipt of OLT.

CONCLUSION

Increased receipt of radiation therapy with breast-conserving surgery appeared to drive a substantial increase in OLT for Black women from 2010-2011 that lasted throughout the study period. Further research on the underlying mechanisms that reduced this disparity is warranted.

Ethnic differences in respiratory disease for Native Hawaiians and Pacific Islanders: Analysis of mediation processes in two community samples

OBJECTIVE

The prevalence of asthma and chronic obstructive pulmonary disorder (COPD) is elevated for Native Hawaiians but the basis for this differential is not well understood. We analyze data on asthma and COPD in two samples including Native Hawaiians Pacific Islanders, and Filipinos to determine how ethnicity is related to respiratory disease outcomes.

METHODS

We analyzed the 2016 and 2018 Behavioral Risk Factor Surveillance Survey (BRFSS), a telephone survey of participants ages 18 and over in the State of Hawaii. Criterion variables were a diagnosis of asthma or COPD by a health professional. Structural equation modeling tested how five hypothesized risk factors (cigarette smoking, e-cigarette use, second-hand smoke exposure, obesity, and financial stress) mediated the ethnic differential in the likelihood of disease. Age, sex, and education were included as covariates.

RESULTS

Structural modeling with 2016 data showed that Native Hawaiian ethnicity was related to higher levels of the five risk factors and each risk factor was related to a higher likelihood of respiratory disease. Indirect effects were statistically significant in almost all cases, with direct effects to asthma and COPD also observed. Mediation effects through comparable pathways were also noted for Pacific Islanders and Filipinos. These findings were replicated with data from the 2018 survey.

CONCLUSIONS

Native Hawaiian and Pacific Islander ethnicity is associated with greater exposure to five risk factors and this accounts in part for the ethnic differential in respiratory disease outcomes. The results support a social-ecological model of health disparities in this population. Implications of the findings for preventive interventions are discussed.

Communication Interactions, Needs, and Preferences During Clinical Encounters of African American Parent-Child Dyads

Human papillomavirus (HPV) vaccination rates remain suboptimal among African American adolescents. Although provider recommendations during clinical encounters are believed to be highly effective in increasing uptake and series completion, little has been reported about parent-child perspectives on the counseling received during these encounters. Among African American parent-child dyads, we sought to explore and compare interactions, needs, and preferences during clinical encounters by child's HPV vaccination status. We applied a qualitative, phenomenological study design to conduct semi-structured interviews with African American parent-child dyads representing children who were unvaccinated (n = 10), had initiated but not completed (n = 11), or had completed the HPV vaccine series (n = 9). Using iterative, inductive-deductive thematic analysis, five themes were generated: (1) parents' attitudes varied about the HPV vaccine but were mostly positive for vaccines in general; (2) patient-parent-provider clinical encounters from the parent perspective; (3) patient-parent-provider clinical encounters from the child perspective; (4) methods of distribution of supplemental HPV information; and (5) communication desired on HPV vaccination by parents and children. Parents stating they received a provider's recommendation increased by vaccination status (unvaccinated: 6 out of 10; initiated: 7 out of 11; completed: 9 out of 9). Most parents and children were not satisfied with provider communication on the HPV vaccine and used supplemental materials to inform decision-making. Ongoing communication on the HPV vaccine was requested even post-vaccination of the child. During clinical encounters, children and parental messaging needs are similar yet dissimilar. We offer communication strategies and messaging that can be used for African American parent-child dyads by child HPV vaccination status during a clinical encounter.

Toward 70% cervical cancer screening coverage: Technical challenges and opportunities to increase access to human papillomavirus (HPV) testing

The World Health Organization (WHO) has called for the elimination of cervical cancer as a public health problem. Cervical cancer screening through human papillomavirus (HPV) testing is a core component of the strategy for elimination, with a set target of screening 70% of women twice in their lifetimes. In this review, we discuss technical barriers and opportunities to increase HPV screening globally.

Circulating 27-hydroxycholesterol, lipids, and steroid hormones in breast cancer risk: a nested case-control study of the Multiethnic Cohort Study

BACKGROUND

Laboratory studies have indicated that a cholesterol metabolite and selective estrogen receptor modulator, 27-hydroxycholesterol (27HC), may be important in breast cancer etiology and explain associations between obesity and postmenopausal breast cancer risk. Epidemiologic evidence for 27HC in breast cancer risk is limited, particularly in multiethnic populations.

METHODS

In a nested case-control study of 1470 breast cancer cases and 1470 matched controls within the Multiethnic Cohort Study, we examined associations of pre-diagnostic circulating 27HC with breast cancer risk among African American, Japanese American, Native Hawaiian, Latino, and non-Latino White postmenopausal females. We used multivariable logistic regression adjusted for age, education, parity, body mass index, and smoking status. Stratified analyses were conducted across racial and ethnic groups, hormone receptor (HR) status, and use of lipid-lowering drugs. We assessed interactions of 27HC with steroid hormones.

RESULTS

27HC levels were inversely related to breast cancer risk (odds ratio [OR] 0.80; 95% confidence interval [CI] 0.58, 1.12), but the association was not statistically significant in the full model. Directions of associations differed by racial and ethnic group. Results suggested an inverse association with HR-negative breast cancer (OR 0.46; 95% CI 0.20, 1.06). 27HC interacted with testosterone, but not estrone, on risk of breast cancer; 27HC was only inversely associated with risk among those with the highest levels of testosterone (OR 0.46; 95% CI 0.24, 0.86).

CONCLUSION

This is the first US study to examine circulating 27HC and breast cancer risk and reports a weak inverse association that varies across racial and ethnic groups and testosterone level.

Using a smartphone application to capture daily work activities: a longitudinal pilot study in a farming population

OBJECTIVES

Smartphones are increasingly used to collect real-time information on time-varying exposures. We developed and deployed an application (app) to evaluate the feasibility of using smartphones to collect real-time information on intermittent agricultural activities and to characterize agricultural task variability in a longitudinal study of farmers.

METHODS

We recruited 19 male farmers, aged 50-60 years, to report their farming activities on 24 randomly selected days over 6 months using the Life in a Day app. Eligibility criteria include personal use of an iOS or Android smartphone and >4 h of farming activities at least two days per week. We developed a study-specific database of 350 farming tasks that were provided in the app; 152 were linked to questions that were asked when the activity ended. We report eligibility, study compliance, number of activities, duration of activities by day and task, and responses to the follow-up questions.

RESULTS

Of the 143 farmers we reached out to for this study, 16 were not reached by phone or refused to answer eligibility questions, 69 were ineligible (limited smartphone use and/or farming time), 58 met study criteria, and 19 agreed to participate. Refusals were mostly related to uneasiness with the app and/or time commitment (32 of 39). Participation declined gradually over time, with 11 farmers reporting activities through the 24-week study period. We obtained data on 279 days (median 554 min/day; median 18 days per farmer) and 1,321 activities (median 61 min/activity; median 3 activities per day per farmer). The activities were predominantly related to animals (36%), transportation (12%), and equipment (10%). Planting crops and yard work had the longest median durations; short-duration tasks included fueling trucks, collecting/storing eggs, and tree work. Time period-specific variability was observed; for example, crop-related activities were reported for an average of 204 min/day during planting but only 28 min/day during pre-planting and 110 min/day during the growing period. We obtained additional information for 485 (37%) activities; the most frequently asked questions were related to "feed animals" (231 activities) and "operate fuel-powered vehicle (transportation)" (120 activities).

CONCLUSIONS

Our study demonstrated feasibility and good compliance in collecting longitudinal activity data over 6 months using smartphones in a relatively homogeneous population of farmers. We captured most of the farming day and observed substantial heterogeneity in activities, highlighting the need for individual activity data when characterizing exposure in farmers. We also identified several areas for improvement. In addition, future evaluations should include more diverse populations.

Examination of two different proteasome inhibitors in reactivating mutant human cystathionine β-synthase in mice

Classic homocystinuria is an inborn error of metabolism caused mainly by missense mutations leading to misfolded and/or unstable human cystathionine β-synthase (CBS) protein, causing the accumulation of excess total homocysteine (tHcy) in tissues. Previously, it has been shown that certain missense containing human CBS proteins can be functionally rescued in mouse models of CBS deficiency by treatment with proteasome inhibitors. The rescue by proteasome inhibitors is thought to work both by inhibiting the degradation of misfolded CBS protein and by inducing the levels of heat-shock chaperone proteins in the liver. Here we examine the effectiveness of two FDA approved protease inhibitors, carfilzomib and bortezomib, on various transgenic mouse models of human CBS deficiency. Our results show that although both drugs are effective in inducing the liver chaperone proteins Hsp70 and Hsp27, and are effective in inhibiting proteasome function, bortezomib was somewhat more robust in restoring the mutant CBS function. Moreover, there was no significant correlation between proteasome inhibition and CBS activity, suggesting that some of bortezomib's effects are via other mechanisms. We also test the use of low-doses of bortezomib and carfilzomib on various mouse models for extended periods of time and find that while low-doses are less toxic, they are also less effective at restoring CBS function. Overall, these results show that while restoration of mutant CBS function is possible with proteasome inhibitors, the exact mechanism is complicated and it will likely be too toxic for long-term patient treatment.

The relationship between unmet cancer care needs and self-rated health among adolescents and young adults with cancer

BACKGROUND

Adolescents and young adults (AYA) with cancer face unique psychosocial challenges that often impact their outcomes, including self-rated health. To date, few studies have focused on AYA cancer survivors' multidimensional unmet needs of cancer care in relation to their health status.

METHODS/PROCEDURE

This study surveyed 324 AYA cancer survivors in a cross-sectional design using the Cancer Needs Questionnaire - Young People (CNQ-YP). In addition to descriptive statistics and bivariate correlations, multinomial logistic regressions were used for analysis.

RESULTS

AYA cancer survivors' daily life needs were found to be significantly and negatively associated with self-rated health, OR = 0.910, 95% CI 0.843, 0.983, p < 0.01, and OR = 0.888, 95% CI 0.818, 0.966, p < 0.01. In addition, the unmet work needs were significantly and positively associated with participants' self-rated health, OR = 1.207, 95% CI 1.003, 1.452, p < 0.05.

CONCLUSIONS

Moving beyond simply describing the unique psychosocial needs confronting AYA cancer survivors, this study empirically identified two specific dimensions of unmet needs of AYA cancer survivors that were significantly correlated to their SRH, both of which should be considered in future service and intervention research to support AYAs with cancer.

JBrowse 2: a modular genome browser with views of synteny and structural variation

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

A need to tailor surveillance based on family history: describing a highly penetrant familial paraganglioma kindred with an SDHD pathogenic variant

Pathogenic variants (PVs) in the SDHD gene increase risk for paragangliomas (PGL)/pheochromocytomas, renal cell carcinomas, and gastrointestinal stromal tumors. Penetrance in individuals with SDHD PVs varies in reported research from 40-70%, and there is limited evidence of specific genotype risks. This study aims to characterize a multi-generational family with SDHD p.Trp43* PVs and potential genotype-phenotype considerations for surveillance. Individuals with a paternally inherited SDHD p.Trp43*(c.129G > A) PV were identified. Genetic, medical and family histories were abstracted, including clinical characteristics, tumor histories, and treatment approaches. Eleven individuals with the SDHD PV in the same kindred were diagnosed with 41 SDHx-related tumors across all family members. Eight individuals developed 27 head and neck PGL of varying origins, and seven individuals developed tumors outside of the head and neck region. Many individuals had multiple tumors, and age of first tumor diagnosis ranged from age 10 to age 45 years old. Individuals with SDHD p.Trp43* variants may have higher risks for SDHx related tumors than other SDHD variants. Prioritizing identification of at-risk individuals and initiating surveillance tailored to family history is recommended given the rate of multiple tumors found in one familial branch of individuals under 18 years old. Individuals with strong family histories of PGL at young ages with this PV will benefit from tailored surveillance recommendations.

Risk stratification for hepatocellular cancer among patients with cirrhosis using a hepatic fat polygenic risk score

BACKGROUND

Polygenic risk scores (PRS) hold the promise to refine prognostication in hepatocellular cancer (HCC). The few available HCC PRS include germline risk variants identified among individuals of mostly European ancestry, but data are lacking on the transportability of these PRS in multiethnic U.S patients with cirrhosis from multiple etiologies.

METHODS

We used data from 1644 patients with cirrhosis enrolled in two prospective cohort studies in the U.S. Patients were followed until HCC diagnosis, death, liver transplantation, or last study visit through June 30, 2021. The high-risk variants in PNPLA3-MBOAT7-TM6SF2-GCKR were combined in a PRS and we evaluated its association with HCC. Discriminatory accuracy was assessed using the C-statistic.

RESULTS

During 4,759 person-years of follow-up, 93 patients developed HCC. Mean age was 59.8 years, 68.6% were male, 27.2% Hispanic, 25.1% non-Hispanic Black, 25.7% had NAFLD, 42.1% had heavy alcohol use, and 19.5% had active HCV. HCC risk increased by 134% per unit increase in PRS (HR = 2.30; 95% CI, 1.35-3.92). Compared to cirrhosis patients in the lowest tertile of the PRS, those in the highest tertile had 2-fold higher risk of HCC (HR = 2.05; 95% CI, 1.22-3.44). The PRS alone had modest discriminatory ability (C-statistic = 0.58; 95% CI, 0.52-0.63); however, adding PRS to a predictive model with traditional HCC risk factors had a C-statistic of 0.70 (95% CI, 0.64-0.76), increasing from 0.68 without the PRS (p = 0.0012).

CONCLUSIONS

Our findings suggest that PRS may enhance risk prediction for HCC in contemporary U.S. cirrhosis patients.

Comparing the gut microbiome of obese, African American, older adults with and without mild cognitive impairment

Those with mild cognitive impairment (MCI), a precursor to dementia, have a gut microbiome distinct from healthy individuals, but this has only been shown in healthy individuals, not in those exhibiting several risk factors for dementia. Using amplicon 16S rRNA gene sequencing in a case-control study of 60 older (ages 55-76), obese, predominately female, African American adults, those with MCI (cases) had different gut microbiota profiles than controls. While microbial community diversity was similar between cases and controls, the abundances of specific microbial taxa weren't, such as Parabacteroides distasonis (lower in cases) and Dialister invisus (higher in cases). These differences disappeared after adjusting for markers of oxidative stress and systemic inflammation. Cognitive scores were positively correlated with levels of Akkermansia muciniphila, a bacterium associated with reduced inflammation. Our study shows that gut microbial composition may be associated with inflammation, oxidative stress, and MCI in those at high risk for dementia.

Examining Multilevel Correlates of Geographic Mobility in a Sample of US Young Adults Before and During the COVID-19 Pandemic

Before the COVID-19 pandemic, geographic mobility, previously viewed as an indicator of economic stability, was declining among young adults. Yet, these trends shifted during the COVID-19 pandemic; young adults were more likely to move during COVID-19 for reasons related to reducing disease transmission and fewer educational and job opportunities. Few studies have documented the individual and neighborhood characteristics of young adults who moved before and during the pandemic. We used data from a cohort of young adults aged 18-34 in six metropolitan areas to examine individual- and neighborhood-level predictors of mobility before and during the COVID-19 pandemic. The sample was majority female, white, and educated with a bachelor's degree or more. Residents in neighborhoods they lived in were mostly White, US-born, employed, and lived above the poverty level. Before the pandemic, identifying as a sexual minority was significantly related to mobility. During the pandemic, being younger, single, and non-Hispanic were significantly related to mobility. Higher neighborhood poverty was significantly related to mobility before and during the COVID-19 pandemic. Future studies that examine young adult populations who moved during the pandemic are needed to determine whether COVID-19 related moves increase economic instability and subsequent health-related outcomes.

Inflated expectations: Rare-variant association analysis using public controls

The use of publicly available sequencing datasets as controls (hereafter, "public controls") in studies of rare variant disease associations has great promise but can increase the risk of false-positive discovery. The specific factors that could contribute to inflated distribution of test statistics have not been systematically examined. Here, we leveraged both public controls, gnomAD v2.1 and several datasets sequenced in our laboratory to systematically investigate factors that could contribute to the false-positive discovery, as measured by λΔ95, a measure to quantify the degree of inflation in statistical significance. Analyses of datasets in this investigation found that 1) the significantly inflated distribution of test statistics decreased substantially when the same variant caller and filtering pipelines were employed, 2) differences in library prep kits and sequencers did not affect the false-positive discovery rate and, 3) joint vs. separate variant-calling of cases and controls did not contribute to the inflation of test statistics. Currently available methods do not adequately adjust for the high false-positive discovery. These results, especially if replicated, emphasize the risks of using public controls for rare-variant association tests in which individual-level data and the computational pipeline are not readily accessible, which prevents the use of the same variant-calling and filtering pipelines on both cases and controls. A plausible solution exists with the emergence of cloud-based computing, which can make it possible to bring containerized analytical pipelines to the data (rather than the data to the pipeline) and could avert or minimize these issues. It is suggested that future reports account for this issue and provide this as a limitation in reporting new findings based on studies that cannot practically analyze all data on a single pipeline.

Maternal Periconceptional Folic Acid Supplementation and DNA Methylation Patterns in Adolescent Offspring

BACKGROUND

Folate, including the folic acid form, is a key component of the one-carbon metabolic pathway used for DNA methylation. Changes in DNA methylation patterns during critical development periods are associated with disease outcomes and are associated with changes in nutritional status in pregnancy. The long-term impact of periconceptional folic acid supplementation on DNA methylation patterns is unknown.

OBJECTIVES

To determine the long-term impact of periconceptional folic acid supplementation on DNA methylation patterns, we examined the association of the recommended dosage (400 μg/d) and time period (periconceptional before pregnancy through first trimester) of folic acid supplementation with the DNA methylation patterns in the offspring at age 14-17 y compared with offspring with no supplementation.

METHODS

Two geographic sites in China from the 1993-1995 Community Intervention Program of folic acid supplementation were selected for the follow-up study. DNA methylation at 402,730 CpG sites was assessed using saliva samples from 89 mothers and 179 adolescents (89 male). The mean age at saliva collection was 40 y among mothers (range: 35-54 y) and 15 y among adolescents (range: 14-17 y). Epigenome-wide analyses were conducted to assess the interactions of periconceptional folic acid exposure, the 5,10-methylenetetrahydrofolate reductase (MTHFR)-C677T genotype, and epigenome-wide DNA methylation controlling for offspring sex, geographic region, and background cell composition in the saliva.

RESULTS

In the primary outcome, no significant differences were observed in epigenome-wide methylation patterns between adolescents exposed and those non-exposed to maternal periconceptional folic acid supplementation after adjustment for potential confounders [false discovery rate (FDR) P values < 0.05]. The MTHFR-C677T genotype did not modify this lack of association (FDR P values < 0.05).

CONCLUSIONS

Overall, there were no differences in DNA methylation between adolescents who were exposed during the critical developmental window and those not exposed to the recommended periconceptional/first-trimester dosage of folic acid.

Smoking and pancreatic cancer: a sex-specific analysis in the Multiethnic Cohort study

PURPOSE

To examine whether the detrimental smoking-related association with pancreatic cancer (PC) is the same for women as for men.

METHODS

We analyzed data from 192,035 participants aged 45-75 years, enrolled in the Multiethnic Cohort study (MEC) in 1993-1996. We identified PC cases via linkage to the Hawaii and California Surveillance, Epidemiology, and End Results Program cancer registries through December 2017.

RESULTS

During a mean follow-up of 19.2 years, we identified 1,936 incident PC cases. Women smokers smoked on average less than men smokers. In multivariate Cox regression models, as compared with sex-specific never smokers, current smokers had a similar elevated risk of PC for women, hazard ratio (HR) 1.49 (95% CI 1.24, 1.79) and as for men, HR 1.48 (95% CI 1.22, 1.79) (pheterogeneity: 0.79). Former smokers showed a decrease in risk of PC for men within 5 years, HR 0.74 (95% CI 0.57, 0.97) and for women within 10 years after quitting, HR 0.70 (95% CI 0.50, 0.96), compared with their sex-specific current smokers. Both sexes showed a consistent, strong, positive dose-response association with PC for the four measures (age at initiation, duration, number of cigarettes per day, number of pack-years) of smoking exposure among current smokers and an inverse association for years of quitting and age at smoking cessation among former smokers (all ptrend's < 0.001).

CONCLUSION

Although MEC women smoke on average less than their men counterparts, the smoking-related increase in PC risk and the benefits of cessation seem to be of similar magnitudes for women as for men.

Sparse canonical correlation to identify breast cancer related genes regulated by copy number aberrations

BACKGROUND

Copy number aberrations (CNAs) in cancer affect disease outcomes by regulating molecular phenotypes, such as gene expressions, that drive important biological processes. To gain comprehensive insights into molecular biomarkers for cancer, it is critical to identify key groups of CNAs, the associated gene modules, regulatory modules, and their downstream effect on outcomes.

METHODS

In this paper, we demonstrate an innovative use of sparse canonical correlation analysis (sCCA) to effectively identify the ensemble of CNAs, and gene modules in the context of binary and censored disease endpoints. Our approach detects potentially orthogonal gene expression modules which are highly correlated with sets of CNA and then identifies the genes within these modules that are associated with the outcome.

RESULTS

Analyzing clinical and genomic data on 1,904 breast cancer patients from the METABRIC study, we found 14 gene modules to be regulated by groups of proximally located CNA sites. We validated this finding using an independent set of 1,077 breast invasive carcinoma samples from The Cancer Genome Atlas (TCGA). Our analysis of 7 clinical endpoints identified several novel and interpretable regulatory associations, highlighting the role of CNAs in key biological pathways and processes for breast cancer. Genes significantly associated with the outcomes were enriched for early estrogen response pathway, DNA repair pathways as well as targets of transcription factors such as E2F4, MYC, and ETS1 that have recognized roles in tumor characteristics and survival. Subsequent meta-analysis across the endpoints further identified several genes through the aggregation of weaker associations.

CONCLUSIONS

Our findings suggest that sCCA analysis can aggregate weaker associations to identify interpretable and important genes, modules, and clinically consequential pathways.

Spatial omics technologies at multimodal and single cell/subcellular level

Spatial omics technologies enable a deeper understanding of cellular organizations and interactions within a tissue of interest. These assays can identify specific compartments or regions in a tissue with differential transcript or protein abundance, delineate their interactions, and complement other methods in defining cellular phenotypes. A variety of spatial methodologies are being developed and commercialized; however, these techniques differ in spatial resolution, multiplexing capability, scale/throughput, and coverage. Here, we review the current and prospective landscape of single cell to subcellular resolution spatial omics technologies and analysis tools to provide a comprehensive picture for both research and clinical applications.