Abstract BackgroundPreterm birth (PTB), or birth before 37 weeks of gestation, remains a significant public health issue in the United States, particularly in Detroit, Michigan. Growing evidence suggests that volatile organic compounds (VOCs), aromatic or chlorinated organic compounds that vaporize readily, may influence PTB risk. However, much of this prior work is limited by indirect VOC exposure estimates (eg, assignment based on maternal residential address), single-point or cumulative exposure estimates during pregnancy, or limited consideration of potential mechanistic factors. ObjectiveThe Center for Leadership in Environmental Awareness and Research (CLEAR) birth cohort has been designed to test the hypotheses that prenatal VOC exposures, measured as VOC metabolites in maternal urine, increase the risk of PTB; that VOC exposures are associated with maternal inflammation and placental function measures; that associations between prenatal VOC exposures and PTB may be mediated by these maternal inflammation and placental function measures; and that there are neighborhood-level factors that may increase the risk of VOC exposure during pregnancy. MethodsA prospective cohort of 1075 pregnant patients receiving prenatal care at Henry Ford Health will be recruited. Pregnant patients residing in Detroit or receiving prenatal care at a Detroit-based Henry Ford Health women’s health clinic are eligible. Pregnant patients are followed until delivery. Up to 3 urine and blood samples (collected during early, mid, and late pregnancy) are obtained for measurement of VOC metabolites and inflammatory biomarkers, respectively. The placenta is obtained after delivery for epigenomic and transcriptomic measurement. Surveys are administered to pregnant participants to assess a variety of lifestyle, psychosocial, medical, residential, and other factors. Address information collected from both surveys and electronic medical records across pregnancy will be used to identify potential sources of VOC exposure. The electronic medical record is used to obtain medical and delivery data, including infant sex, date of delivery, and gestational age (GA) at delivery. PTB, the primary study outcome, is defined as GA at delivery <37 weeks. A nested case-control approach (frequency matching PTB cases 1:1 with full-term controls [GA at delivery ≥37 weeks] based on infant sex and maternal race) will be applied. Statistical methods, including logistic regression, linear mixed methods, and geographically weighted regression models, as well as chemical mixture approaches, will be used. ResultsFunding began September 2022 and recruitment commenced November 2023. Through April 22, 2026, a total of 468 pregnant patients have consented to participate in the CLEAR birth cohort, and recruitment is ongoing. ConclusionsThe CLEAR cohort will provide novel data on the role of VOCs during pregnancy in the risk of PTB. Additionally, the role of VOC exposures during pregnancy in maternal inflammation and placental function will be examined. Finally, potential sources of VOC exposures, which could be targets for environmental remediation, will be identified.

DNA methylation (DNAm), capturing biological gestational age (GA) and epigenetic gestational age acceleration (EGAA), can be modified by environmental exposures. The Asthma&Allergy array is a new DNAm array developed with content focused on asthma and allergy loci. The association between content on the Asthma&Allergy array and chronological GA and EGAA has not been evaluated alone or in the context of perinatal exposures. We performed an epigenome wide association study(EWAS) based on chronological GA at single CpG sites and regions. We further constructed a multi-CpG site methylation model to predict chronological GA in cord blood from 391 newborn children from a Detroit-based birth cohort. Associations between perinatal environmental factors with GA, epigenetic gestational age (EGA), and EGAA were assessed. We identified 2,435 CpG sites associated with chronological GA. HLA class II (HLA-DRB1,HLA-DQB1,HLA-DRB6) were the most significantly associated with chronological GA. Our multi-CpG site model attained predictive accuracy (cross-validated Pearson's correlation=0.75) comparable to other EGA methods. Using genes implicated in region-based analyses (n=395 regions), the pathways most significantly enriched with chronological GA-associated CpGs included T helper 1(Th1) and 2(Th2) activation, macrophage classical activation, and IL10 signaling, which were also enriched in at least one of the other published epigenetic clocks. In multi-exposure models, prenatal indoor pet exposure and unplanned C-section were associated with EGA deceleration, while infant's first-born status was associated with EGAA. Our findings highlight enrichment for T cell modulated pathways and antigen presentation as biological processes enriched in chronological GA, as well as novel perinatal factors that may impact EGAA.

Lung mucosal immunity must balance effective antimicrobial defense with tightly controlled inflammatory responses to maintain pulmonary homeostasis. Although sex differences in respiratory disease susceptibility are well documented, the developmental origins of these differences and their modulation by prenatal environmental exposures remain poorly defined. Here, we tested the hypothesis that prenatal benzene exposure establishes sex-specific reprogramming of lung mucosal immunity during fetal development. Using a controlled inhalation exposure model in pregnant C57BL/6 mice, we characterized immune responses in fetal and postnatal lungs under baseline conditions and following viral challenge. We found that female offspring displayed heightened type I interferon signaling and enhanced viral clearance, accompanied by exaggerated inflammatory pathology and altered expressions of DREAM and A20. In contrast, male offspring exhibited augmented proinflammatory cytokine production following lipopolysaccharide challenge. Alveolar macrophages from prenatally benzene exposed offspring demonstrated persistent inflammatory priming, indicating durable alteration of innate immune populations. These findings demonstrate that lung mucosal immune development is intrinsically sex-dependent and that prenatal environmental pollutants interact with fetal sex to durably reprogram respiratory immunity. Together, our results identify in utero environmental exposure as a critical determinant of sex-specific mucosal immune trajectories that shape postnatal responses to infection.

Identifying microbial features associated with various covariates is a long-standing goal in microbiome research. Modern association studies incorporate an ever-increasing number of microbial features, covariates, and datasets from diverse cohorts. However, the complexity of microbiome data challenges analysis, often leading to poor replication of findings. We introduce PALM, a quasi-Poisson regression framework that enables fast and reliable association discovery in large-scale studies and meta-analyses. Extensive, realistic simulations demonstrate PALM's advantages in controlling false discovery rates, boosting power, improving computational efficiency, and preserving cross-study homogeneity of association effects. Three real-world applications at different scales illustrate PALM's utility, underscoring its potential to advance microbiome research.

ABSTRACT Keloid disease (KD) is a fibroproliferative skin disorder resulting from abnormal scar formation that causes pain, itching, and decreased quality of life. While multiple KD transcriptomic studies exist, the influence of cell type composition on bulk tissue gene expression is unknown. We characterized fibroblast subtype and immune cell enrichment using bulk RNA-Seq of head and neck keloid and matched adjacent normal skin tissue (MANST) from 14 patients (10 African American and 4 European American). Cell type enrichment was calculated by single sample gene set enrichment analysis. Linear mixed-effects models were employed for 1) differential cell type enrichment across tissue, 2) tissue type-specific associations between fibroblast subtypes and immune cells, and 3) differentially expressed genes (DEGs) across tissue. Validation was conducted in an independent cohort of 8 African Americans. Three fibroblast subtypes and 14 immune cell types were differentially enriched across tissue type. Further, 17 tissue type-specific fibroblast subtype-immune cell enrichment associations were identified, with 14 exhibiting decreased association in keloid tissue relative to MANST. After adjustment for cell type enrichment, MIR31HG and NR4A2 were significant DEGs with the largest positive and negative fold-changes, respectively. By considering cell type enrichment, underlying keloid tissue-specific cell type and gene expression associations were revealed.

BACKGROUND:Elevated IgE levels, a higher prevalence of allergic disorders, and a higher incidence of asthma have been reported among Black children compared with White children. Racial classification is a social construct that is partially influenced by genetic ancestry. The factors contributing to racial health disparities remain uncertain but likely reflect complex interactions between genetic susceptibility and environmental exposures. OBJECTIVE:To assess the associations of genetic ancestry with allergic disorders, IgE production, and lung function among Black children. METHODS:Prospective data from the Wayne County Health, Environment, Allergy, and Asthma Longitudinal Study (WHEALS) birth cohort were analyzed. Race was assigned by maternal report, and Black, non-Hispanic/non-Arabic children were identified (n = 345, 53.3% male). Genome-wide continental percent African ancestry (PAA) was estimated. Associations between PAA and longitudinal total IgE trajectory (from birth to age 10), allergic sensitization, allergic disorders, and spirometry at 10 years were examined. Models were adjusted for confounders, including available variables associated with social determinants of health. RESULTS:A total of 102 participants (56%) were sensitized to 1 or more allergens; 47 (27.5%) had asthma. Each 10-percentage-point increase in PAA was associated with a 68% increased risk of asthma (relative risk [RR], 1.68; 95% CI, 1.16-2.45; P = .007), a 30% higher risk of sensitization to common allergens (RR, 1.30; 95% CI, 1.04-1.63; P = .019), and a decrease in forced expiratory volume in 1 second (FEV1%) predicted by 2.67% (β -2.57; 95% CI, -5.19 to 0.06; P = .055). No association was identified between PAA and total IgE trajectory (P = .11). CONCLUSION:Among Black children, PAA is associated with an increased risk of asthma, allergen-specific IgE sensitization, and decreased lung function at 10 years.

Background:In ∼10% of asthma patients, symptoms remain uncontrolled despite maximal treatment, representing an unmet clinical need. The causal variants, genes and pathways underlying genetic risk factors have not been fully elucidated, and it is unclear whether there are unique genetic risk factors for this asthma subtype. Methods:We used electronic healthcare records linked to UK Biobank to identify asthma patients with high treatment burden and/or worse outcomes. We performed a genome-wide association study (GWAS) with this case population and healthy controls. We sought replication for associated (p≤5×10-6) signals in four independent studies (12 152 cases and 32 316 controls). Replicated signals were fine-mapped and linked to genes and pathways. Results:In total, 7681 participants met our case definition and showed enrichment for adult-onset asthma, female gender and higher body mass index compared to asthma individuals not meeting case criteria. GWAS with 7681 cases and 38 405 controls revealed 21 reproducible association signals that had previously been associated with asthma, but had a larger effect size in our study. Variant-to-gene mapping highlighted 85 candidate genes, five of which were considered high confidence (BACH2, D2HGDH, IL1RL1, RPS26, SMAD3). Conclusion:We present the first use of electronic healthcare records in UK Biobank to identify a subtype of asthma enriched for patients with high treatment burden and/or worse outcomes. Our findings support the role of known asthma genes, highlighting genetic risk variants with stronger effect in these groups of patients. The prioritised genes provide potential therapeutic opportunities for this difficult-to-treat patient population.

BACKGROUND:DNA methylation accurately predicts chronological age, including gestational age (GA). Previous studies have used 5'-C-phosphate-G-3' sites (CpGs) on the EPIC or 450K arrays to generate epigenetic clocks for estimating GA. OBJECTIVE:Using the Asthma&Allergy array, we estimated GA and calculated GA acceleration (GAA) in cord blood DNA from 2451 ancestrally diverse participants from 7 birth cohorts investigating early life risk factors for asthma and allergic diseases and disease onset in childhood. METHODS:Two gestational epigenetic clocks were constructed: one used GA-associated CpGs in an epigenome-wide association study (EWAS) and a second used CpGs associated with GA in specific cell types. For both, we calculated GAA and tested for associations with 6 prenatal variables and 8 allergy-related childhood outcomes. We then conducted pathway analysis of expressed genes correlated with GAA and validated gene expression signatures in peripheral blood at age 2 years. RESULTS:Strong correlations between reported GA and estimated GA were observed using the EWAS and the cell-specific clocks (r = 0.90 and 0.83, respectively). Using the cell-specific clock, GAA was associated with 2 outcomes (higher birthweight, Padj = 1.69 × 10-5; less allergic asthma, Padj = .025), while the EWAS clock was associated with birthweight (Padj = 4.68 × 10-4). A significant sex-by-GAA interaction effect on birthweight, with a larger effect size in females, was observed with both clocks (EWAS, Pint = 5.77 × 10-3; cell-specific, Pint = .021). Cord blood RNA-sequencing analysis revealed upregulated IL6 and TNF and downregulated IL10 signaling pathways associated with GAA, and gene expression in blood at age 2 years further revealed associations with asthma at age 7 years. CONCLUSION:Positive correlations between GAA and inflammatory gene expression and the negative association with allergic asthma suggest that increased expression of inflammatory genes in cord blood and at age 2 years is protective against developing asthma. CpGs on the Asthma&Allergy array are accurate predictors of GA, capturing aging aspects specifically related to inflammatory programs.

Somatic mutational prevalences in PDAC patients stratified by their sex and race.

The human leukocyte antigen (HLA) region is highly diverse and plays a crucial role in immune regulation and antigen presentation. Accurate HLA typing is essential for understanding disease susceptibility, transplantation compatibility, and pharmacogenetics. However, its application in African descent populations is challenging due to complex linkage disequilibrium patterns and the lack of ancestry-matched populations in HLA reference panels. Here, we leveraged the latest whole-genome sequencing (WGS) data from UK Biobank African individuals to perform better HLA genotyping, and further utilized allelic and haplotypic data to explore population genetics patterns of this region. With WGS-inferred HLA alleles, we identified specific admixture patterns (predominant West and East African and minor European ancestries) within British African population, revealing their complex evolutionary history. Not only did we reveal the genetic diversity within this population, but also highlighted its differences from African Americans, ancestral Africans, and other global populations. We further identified regional ancestry differences in the HLA genomic region, highlighting discordance between global and local admixture estimates. British Africans also presented unique HLA frequency distributions for both typical and disease-associated alleles or haplotypes. These findings emphasize the need for expanding African-specific HLA reference panel and prove better HLA typing can be achieved by coupling sequencing technologies with computational approaches. The HLA genetic characteristics observed in British Africans provide valuable insights into population-specific immune responses and susceptibility. Overall, this study advances our understanding of HLA diversity and genetic admixture in British African population, with important implications for both disease mechanism and clinical utility.

Purpose: Pancreatic ductal adenocarcinoma (PDAC) patients with tumors enriched for the basal-like molecular subtype exhibit enhanced resistance to standard-of-care treatments and have significantly worse overall survival compared with patients with classic subtype-enriched tumors. It is important to develop genomic resources, enabling identification of novel putative targets in a statistically rigorous manner.Experimental Design: We compiled a single-cell RNA sequencing (scRNA-seq) atlas of the human pancreas with 229 patient samples aggregated from publicly available raw data. We mapped cell type-specific scRNA-seq gene signatures in bulk RNA-seq (n = 744) and spatial transcriptomics (ST; n = 22) and performed validation using multiplex immunostaining.Results: Analysis of tumor cells from our scRNA-seq atlas revealed nine distinct populations, two of which aligned with the basal subtype, correlating with worse overall survival in bulk RNA-seq. Deconvolution identified one of the basal populations to be the predominant tumor subtype in nondissociated ST tissues and in vitro tumor cell and patient-derived organoid lines. We discovered a novel enrichment and spatial association of CXCL10+ cancer-associated fibroblasts with basal tumor cells. We identified that besides immune cells, ductal cells also express CXCR3, the receptor for CXCL10, suggesting a relationship between these cell types in the PDAC tumor microenvironment.Conclusions: We show that our scRNA-seq atlas (700,000 cells), integrated with ST data, has increased statistical power and is a powerful resource, allowing for expansion of current subtyping paradigms in PDAC. We uncovered a novel signaling niche marked by CXCL10+ cancer-associated fibroblasts and basal tumor cells that could be explored for future targeted therapies.

ABSTRACT:Pancreatic cancer is the third leading cause of cancer-related death in the United States. Black or African American patients have a higher incidence of pancreatic cancer compared with other racial groups. It is unclear whether distinct molecular mechanisms are involved in the development of pancreatic cancer in different racial groups. To identify tumor molecular features that are distinctly associated with race in Black or African American and White patients with pancreatic ductal adenocarcinoma (the main subtype of pancreatic cancer), we analyzed deidentified patient records, including tumor sequencing data and expression of PD-L1, from the Tempus multimodal database. Patients with a primary diagnosis of pancreatic ductal adenocarcinoma and who received molecular testing between November 2017 and March 2023 were included in analyses. Among 4,249 patients analyzed in this study, 452 (10.6%) were Black or African American, and 3,797 (89.4%) were White. Black patients had a higher prevalence of TP53 mutations compared with White patients (P < 0.001). KRASG12R mutations occurred more frequently in female patients in the Black versus White group (P = 0.007). Compared with White patients, Black patients had a higher tumor mutational burden (P < 0.001) and PD-L1 overexpression (P = 0.047). In a separate analysis of recent clinical trials testing immunotherapies for pancreatic cancer, we found that Black patients and other minorities were underrepresented in most trials. These findings suggest race-associated molecular differences in tumors that may impact patient responses to immunotherapies. Our study also supports the importance of improving patient diversity in clinical trials on pancreatic cancer treatments. SIGNIFICANCE:By analyzing the records of patients with pancreatic cancer in the Tempus multimodal database, we identified genomic mutations and PD-L1 overexpression occurred more frequently in Black patients compared with their White counterparts. These molecular features may contribute to racial disparities in pancreatic cancer.

Background: The close relationships between mental disorders and suicidality are frequently seen in epidemiology. Shared genetic liabilities and brain structure variation may underlie these associations. Therefore, we aimed to investigate the phenotypic and polygenetic associations between multiple mental disorders and different levels of suicidality, as well as mediation by grey morphology and white matter tracts. Methods: Using raw data from the UK Biobank (UKB) European population, we first evaluated the phenotypic and polygenic relationships between 12 mental disorders and gradient scales of suicidality. We then accessed data from the All of Us (AoU) diverse cohort to replicate findings in European and African American populations. Demographic and social factors, including age, sex, BMI, education, deprivation, income, smoking, and chronic pain were included as covariates. Second, we used existing genome-wide association study (GWAS) summary statistics from 12 major mental conditions to estimate genetic correlations and identify pleiotropic genes using a combination of statistical genetics tools. Third, we further explored the potential mediation effects of brain structure on the relationship between mental disorders and suicidality through structural equation modeling and Mendelian randomization analyses. Results: In the UKB European population, 150,861 eligible individuals were retained after standard GWAS quality control. Nine out of 12 mental disorders showed both significant phenotypic and polygenic correlations with gradient suicidality (Pbonferroni <0.05). Using GWAS summary statistics, we also observed positive global and regional genetic correlations between the 12 mental disorders and suicidality (rg ranging from 0.25 to 0.68, Pbonferroni <0.05). Across pairs of suicidality and other mental disorders, we identified 73 out of 136 pleiotropic functional genes (including 58 novel ones associated with suicidality) shared by two or more pairs. These genes were enriched in pathways including regulation of immune system process and DNA, nucleosome and chromatin organization, and phenotypes as common mental disorders and brain morphology. Finally, the association between mental disorders and suicidality was significantly mediated by several structural brain imaging features. Conclusion: This study underscores the urgent need to address the shared and distinct genetic architecture of suicidality and its related mental conditions. Combining longitudinal population-level biobanks with disease-ascertained GWAS data is warranted to further enhance our understanding of this complex phenomenon. Our research findings will guide future suicide prevention and precise treatment among individuals with or without major mental disorders. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was financially supported by the National Nature Science Foundation of China (Grant NO. 82171499 to QW, and Grant NO. 82301683 to ST), Chinese National Programs for Brain Science and Brian-like Intelligence Technology, China Depression Cohort Study (STI2030-Major Projects-2021ZD0200700 to QW), Science and Technology Project of Sichuan Province (Grant NO. 2023YFS0030 to QW), Natural Science Foundation of Sichuan Province (Grant no. 2024NSFSC1560 to ST). HG is supported by Mentored Scientist Grant in Henry Ford Health (A20067), NIH grant R03MH135347, and American Foundation for Suicide Prevention grant SRG-0-061-23. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Institutional Review Board (IRB) of Henry Ford Health gave ethical approval for this work(project No. 16896-01). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data used in the present study are available online at the UK Biobank data Access Management System (https://www.ukbiobank.ac.uk/enable-your-research/apply-for-access) and the researcher workbench of the All of Us Research Program located at https://workbench.researchallofus.org

Summary of race representation in clinical trials evaluating immunotherapies for pancreatic cancer. Numbers in the brackets represent percentages of patients in designated groups

Prevalences of specific mutant alleles in TP53 and GNAS genes in White and BAA patients with PDAC.