Percentage of population with mutations and the variant classifications for TP53 in SchildkrautB (n=1211), TCGAW (n=1272), and SchildkrautW (n=1123).

Flow chart showing inclusion and exclusion criteria for individuals in the SchildkrautB and SchildkrautW study populations.

Mismatch repair deficiency (MMRD) genes sensitivity analyses.

Percentage of the population with mutations in HGSC genes in major HGSC genes identified in TCGA, genes identified by de novo significantly mutated gene analysis in SchildkrautB, or mutated in ≥4% of SchildkrautB, by gene expression subtype

Distributions of allelic changes for single nucleotide variants.

Chromosomal copy number alterations.

Somatic variant filtering for mutation annotation format files (MAF) files from TCGAW samples (n=1272).

Percentage of the population with COSMIC signatures shown in Figure 4A

Differences in sequencing and variant calling methods between Schildkraut datasets and TCGA.

Abstract Background: Tumor-infiltrating lymphocytes are associated with improved ovarian cancer (OC) survival in White women but not Black women despite similar T cell abundance. We evaluated whether exhaustion or localization of T cell infiltration may attenuate the survival advantage among Black women using a spatially informed compartment-specific approach to account for heterogeneity of whole tissue sections (WTS). Methods: Among 221 Black OC cases in the African American Cancer Epidemiology Study, multiplex immunofluorescence and HALO image analysis quantified total (CD3+) and cytotoxic (CD3+CD8+) T cells, along with exhausted (TIM3+) and terminally exhausted (TIM3+PD1+) subsets in FFPE WTS. PANCK-defined tumor and stroma were refined by excluding mixed interface regions detected using point-pattern intensities. Logit-transformed proportions were compared with paired t-tests. Cox proportional hazards estimated associations of compartment features with overall survival, adjusting for clinical factors. Results: Black OC cases were primarily advanced stage (58%) and high-grade serous carcinoma (HGSC; 69%); mean follow-up was 6.4 years. In tumor, 60% were T cell infiltrated (≥2% of tumor cells), and the median proportion of cytotoxic cells was 30%. Stroma contained 50% more T cells (p=9.1x10-12) but lower cytotoxic fractions (ΔT-S = -8%; p=3.9x10-19). Immune-excluded tumors (<2% tumor T cells) displayed strong stromal enrichment of total and cytotoxic T cells. Exhausted T cells were rare (1%) with tumors showing higher exhaustion (ΔT-S=1%, p=1.6x10-3) and terminal fractions (ΔT-S=15%, p=8.8x10-18) than stroma. Neither tumor nor stroma T cell abundance was associated with survival in univariate models. However, in compartment-adjusted models, tumoral cytotoxic T cells were associated with improved survival (hazard ratio [HR]=0.72, 95% confidence interval [CI]=0.53, 0.97), whereas stromal cytotoxic T cells were associated with worse survival (HR=1.65, CI=1.14, 2.37). A larger tumor-stroma gradient in cytotoxic T cells (> tumor) was similarly protective (HR=0.65, CI=0.48, 0.89). In HGSC, that had higher infiltration and exhaustion, infiltrated tumors had improved survival with higher exhaustion (HR=0.83, CI=0.70, 0.98) and terminal exhaustion (HR=0.88, CI=0.79, 0.99), while immune-excluded tumors did not. Conclusion: Distinct compartment-specific T cell and exhaustion patterns with divergent survival implications were observed in Black women with OC. Cytotoxic T cells confer a survival benefit only when tumor-dominant rather than stroma-dominant, highlighting the importance of characterizing an immune-exclusion phenotype. Improved survival with tumor T cell exhaustion likely indicates active antitumor immunity. WTS-based spatial profiling is essential for accurate interpretation of immune-survival relationships in Black women with OC. Citation Format: Brett M. Reid, Alex C. Soupir, Anthony J. Alberg, Elisa V. Bandera, Melissa L. Bondy, Michele L. Cote, Kristin Haller, Theresa Hastert, Carlos Moran Segura, Jonathan V. Nguyen, Edward S. Peters, Paul D. Terry, Andrew B. Lawson, Jeffrey R. Marks, Brooke L. Fridley, Joellen M. Schildkraut, Lauren Cole Peres. Tumor-stroma spatial context of T cell infiltration and exhaustion as determinants of ovarian cancer survival in Black women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6814.

Deep learning-based computer-aided diagnosis (CAD) systems have shown strong performance in breast cancer diagnosis, particularly for classification tasks in mammography. However, domain shifts across multi-site datasets remain a challenge, especially when models are applied to unseen domains. In this work, we proposed a calcification classification framework to improve malignant versus benign breast disease classification across multi-site mammography datasets. The framework consisted of two components: (1) an unsupervised domain adaptation module based on style transfer models (AdaIN and CycleGAN) to generate vendor-specific and technique-specific training samples without additional annotations, and (2) a supervised classification module using Swin Transformer V2 as the backbone. We evaluated the proposed method on three datasets: cross-validation on OPTIMAM (National Health Service, United Kingdom; n=2994), followed by external validation on EMBED (Emory University; n=125), and Duke Calcification Dataset v1 (n=788). These datasets cover multiple vendors and include both full-field digital mammography and synthetic 2D images derived from digital breast tomosynthesis. The proposed framework improved cross-site performance for both EMBED (AUC 0.68 to 0.72) and the Duke Calcification Dataset (AUC 0.68 to 0.73). These findings indicate that domain adaptation can reduce domain shifts and improve the generalization for calcification classification across multi-site datasets.

Background:Single-cell-based analyses of high-grade serous ovarian carcinoma (HGSOC) survival have largely ignored adipocytes, which are fragile and under-represented in single-cell references. Adipocytes are known active components of the tumor microenvironment in many cancers, and HGSOC tumors frequently metastasize to the omentum, a lining of adipose tissue. Methods:We created a composite reference that combines single-nucleus adipose profiles with published HGSOC single-cell data to deconvolve 588 bulk RNA-seq tumours from the Schildkraut cohorts. We used stage-stratified Cox models to quantify the association between intratumoural adipocyte fractions and overall survival while adjusting for age, body mass index (BMI), race, and residual disease. We also evaluated associations with deconvolved immune, stromal, and epithelial cell groups. Results:A 10% increase in estimated tumor adipocyte content was associated with a 41% increase in the hazard of death (HR = 1.41, 95% CI 1.18-1.70, p = 0.0002) after adjusting for age, BMI and race (n=566). A 10% increase in immune cell proportion was associated with favorable survival (HR = 0.82, 95% CI 0.69-0.97, p = 0.024). Stromal and epithelial macro-fractions were not associated with survival. Associations with adipocyte and immune cell type proportions were unchanged in models additionally controlling the other cell type proportions. Results were similar after additionally adjusting for residual disease after debulking surgery. Conclusions:Adipocytes may be a tumor-intrinsic factor associated with adverse outcomes in HGSOC. Quantifying adipocyte burden using bulk RNA-seq could enhance risk stratification and guide the development of adipocyte-targeted therapies.

Percentage of the study populations with mutations in major HGSC genes identified by TCGA shown in Figure 1.

Abstract Background: Black women experience poor survival from epithelial ovarian cancer (EOC), for all stages at diagnosis and EOC histotypes. We present findings of the contribution of African ancestry and an ancestry-related genotype in the Atypical Chemokine Receptor 1 (ACKR1) gene to EOC survival among a cohort of Black/African American women. We also report associations with tumor molecular features that may explain the potential underlying biology related to the Duffy-null ACKR1 genotypes. Methods: The relationship between global African ancestry and the rs2814778 SNP in the promotor region of the ACKR1 gene and survival was determined in a cohort of 408 Black women with EOC (275 with high grade serous ovarian cancer (HGSC)) who participated in the population-based African American Cancer Epidemiology Study (AACES) using a Bayesian modeling approach adjusting for stage, age at diagnosis, the Yost index for socioeconomic status, education, and ovarian cancer family history. Proportion of global African ancestry and the ACKR1 genotype (Duffy-null (CC) vs. TC/ TT) were determined from germline DNA. Tumor molecular features including gene expression using RNAseq, tumor immunity (i.e., T-cell abundance) measured using multiplex immunofluorescence (mIF), and homologous recombination deficiency (HRD) derived from whole exome sequencing data were generated from HGSC tumors. Results: The Duffy-null genotype was present in 70.6% EOC cases overall, and 72.0% of HGSC. The prevalence was higher among individuals with high African ancestry (African ancestry >83.6%) than those with lower African ancestry (83.2% and 58.3%, respectively). The Duffy-null genotype was associated with improved survival among EOC cases (adjusted Hazard Ratio (HR)=0.59, 95% credible intervals (CI): 0.35-0.96). The corresponding HR for HGSC was 0.61 (95% CI: 0.34-1.12). However, global African ancestry—as indicated by a 1% increase in percent African ancestry on the logit scale—was suggestively associated with worse survival, especially for HGSC, with an HR of 1.31 (95% CI: 0.89-1.90). Additionally, we examined the relationship between the CC vs. TC/ TT genotypes and tumor molecular features in HGSC. The Duffy-null genotype was associated with lower ACKR1 expression, lower cytotoxic T cell abundance, and higher HRD in HGSC. Among EOC subjects, mIF-derived myeloid cells (CD11b+) showed lower abundance in those with high African ancestry, which is consistent with worse survival. Conclusion: The Duffy-null genotype is associated with ∼40% decreased EOC mortality in Black women. Lower T-cell infiltrates may reflect lower immune surveillance and may coincide with higher HRD in HGSC among Duffy-null individuals. The HRD finding, in particular, may explain the improved prognosis observed with the Duffy-null genotype, as our group has previously shown that HRD status was associated with better survival in Black women with HGSC. Citation Format: Joellen M. Schildkraut, Jeffrey R. Marks, Xintian Song, Yao Xin, Anthony J. Alberg, Lauren C. Peres, Katherine Anne Lawson-Michod, Lindsay Jane Collin, Jennifer A. Doherty, Andrew B. Lawson, on behalf of the African American Cancer Epidemiology Study. African ancestry, Duffy-null genotype, and epithelial ovarian cancer in a cohort of Black women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2340.

Background:Ductal carcinoma in situ (DCIS) is a noninvasive breast lesion with variable risk of progression to invasive breast cancer (IBC). Current transcription and cell marker investigations suggest ECM decreases in later events but are limited in details of ECM proteomic composition, including post-translational modifications. We investigated whether the extracellular matrix (ECM) proteome alters with later breast events of DCIS or IBC. Methods:ECM-targeted mass spectrometry imaging and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were applied to ten tissue microarrays from the Resource of Archival Human Breast Tissue cohort (RAHBT). Primary DCIS specimens (n=136) were analyzed in relation to later events of DCIS (n=40) or IBC(n=30), with a mean follow-up of 192.1 months 95% CI [179.1,205.1]. Statistical modeling, survival analyses, and exploratory machine learning approaches were used to identify ECM peptide signatures associated with later events. Results:Distinct ECM peptide profiles were associated with later events of DCIS or IBC. Fifteen peptides derived from fibrillar collagens (COL1A1, COL1A2, COL3A1) and elastin, showed significantly reduced abundance in patients who developed IBC. Lower expression of specific collagen peptides associated with overall 19.9% 95% CI [17.92, 21.81] decreased disease-free survival for IBC. Lower expression of these peptides was significantly associated with reduced disease-free survival (age-adjusted hazard ratio [HR] = 2.45, 95% CI: 2.33-2.57; P < 0.05). Patient-matched samples of primary DCIS, later DCIS, and later invasive breast cancer further demonstrated reduction in ECM peptide detection. Exploratory predictive modeling from patient-matched samples achieved high performance (AUROC >0.98, accuracy >93%) in distinguishing primary from later events. Following prior work in the RAHBT cohort, reduction of certain collagen peptides was also observed in primary DCIS samples from higher risk patient groups. Conclusions:ECM proteomic remodeling, particularly decreases of specific collagen domains, is strongly associated with later events of DCIS and IBC. These findings highlight ECM proteome as a critical regulator of breast cancer emergence with potential as a prognosticator of risk stratification to guide clinical management of DCIS.

Immune escape during the ductal carcinoma in situ (DCIS)-to-invasive breast cancer (IBC) transition shapes tumor evolution. Through transcriptomic mapping of the immune landscapes of normal breast, DCIS, and IBC from large patient cohorts, we identified T and myeloid cells as the primary distinguishing features between DCIS and IBC. We discovered cycling regulatory T cells (cycTreg) as an orchestrator of immunosuppression in IBC. cycTreg frequency predicts cytotoxic CD8+, TCR diversity, disease-specific survival in IBC, and recurrence in DCIS. In a rat model of breast cancer, we demonstrated that cycTreg act as precursors to mature Treg and are inducible by tumor-localized type 2 dendritic cells. Profiling of tumors subjected to αOX40 and αPD-L1 therapies revealed an IL-33-mediated fibroblast-cycTreg signaling loop, the disruption of which enhances intratumoral antigen-experienced CD8+ effectors and systemic immunosurveillance. Our study defines cycTreg as critical inducers of immune escape and promising immuno-oncology targets in breast cancer.

MutSig2CV significantly mutated gene analysis results for SchildkrautB.

PURPOSE:Although KRAS mutations represent the primary oncogenic driver in pancreatic ductal adenocarcinoma (PDAC), the association between codon-specific alterations and patient outcomes remains poorly elucidated, largely because of a lack of data sets coupling genomic profiling with rich clinical annotations across disease stages. MATERIALS AND METHODS:We used American Association for Cancer Research's GENIE Biopharma Consortium Pancreas v1.2 data set to test the association of codon-specific KRAS mutations with clinicogenomic features and patient outcomes in patients with PDAC diagnosed with localized (stages I to III) and advanced disease (stage IV). Overall survival (OS) was compared using Kaplan-Meier and multivariable Cox proportional hazards methods. RESULTS:Among 1,032 eligible patients, 949 (92%) exhibited mutant KRAS. These mutations were predominantly observed at G12D (n = 390, 41%), G12V (n = 305, 32%), and G12R (n = 149, 16%). In the group of patients who presented with localized disease, those with G12V mutation had notably longer survival compared with G12D mutation (P = .03). By contrast, patients with G12V mutation who presented with metastatic disease experienced shorter OS compared with those with G12R (P = .04) and G12D mutations (P = .04). Furthermore, no significant differences were observed in the frequencies of coaltered driver genes, including TP53, CDKN2A, and SMAD4, across the different KRAS mutations. CONCLUSION:These findings demonstrated that codon-specific KRAS mutations affect PDAC outcomes differently based on disease stage at diagnosis. As studies testing KRAS inhibitors continue to emerge and mature, the prognostic variability of individual KRAS mutations must be carefully considered to avoid confounding and ensure accurate evaluation of therapeutic efficacy in early-phase studies.

Somatic variant filtering for tumor WES in SchildkrautB analytic samples (n=211) and SchildkrautW analytic samples (n=123).

Abstract Background: High-grade serous ovarian cancer (HGSC) is a deadly gynecologic cancer and is characterized by widespread copy number alterations (CNA). However, knowledge of racial differences in HGSC CNA is limited. Using methylation-inferred CNA, we defined and characterized CNA-based tumor clusters to assess patterns by self-reported race. Methods: Tumor CNA were calculated using Illumina EPIC v1/v2 methylation data for 678 cohort participants (African American Cancer Epidemiology Study, North Carolina Ovarian Cancer Study, Nurses’ Health Study) compared to 296 blood samples. Probes were binned (≥10; ≥100 kb), segmented using circular binary methods, autocorrected, and filtered (|mean log R ratio|≥0.3; >4 markers), to define cytoband-level copy number states (-1-loss /0-neutral /+1-gain). CNA were clustered with Ward’s method. For each cluster, we computed length-weighted cytoband burden (% genome in gain, loss, or neutral states) and region-level ORs to identify CNA-enriched regions. Models clustered by race were then fit to assess differences. Results: Combined analysis of HGSC samples from 403 White (59%) and 275 Black women (41%), identified three CNA clusters: C1 (27%), C2 (57%), and C3 (15%). Clusters showed distinct genomic burdens (Kruskal-Wallis p<10 −55). C1 showed widespread losses, notably in 4q (∼75% vs 14% in C2/C3, q<10-45), which has been reported in HGSOC, and 17p (71% vs 13% in C2/C3, q<10-46), which includes TP53. C3 exhibited extensive chromosomal gains, including 20p/q (∼82%/72%, q <10-38), 1q/1p (∼64%/39%, q<10-32), and 2p/2q (∼56%/42%, q <10-31). Gains on 2p/q have been linked to advanced stage and poor prognosis, potentially via overexpression of AURKA, GNAS, and TPD52L2. Amplified 1q may enhance DHX9 expression, a regulator of genomic stability, while BARD1 (2q) interacts with BRCA1 in DNA repair; aberrant BARD1 expression correlates with poor outcomes. Cluster membership was similar between Black and White women (C1: 30% vs 26%, C2: 53% vs 59%, C3: 17% vs 15%). However, arm-level copy number racial differences were observed. Overall, 21q loss was more frequent in tumors from Black women (28%) than White women (16%; OR=0.5, 95% CI=0.34-0.73, q=0.02). This difference was most pronounced in C2, where 21q loss occurred in 27% of Black women compared to 10% in White women (OR = 0.31, 95% CI=0.17-0.56, qcluster=0.002). Conclusion: Broad arm-level CNAs define molecularly distinct HGSC subgroups with characteristic gain/loss patterns. Race-associated genomic alterations, including 21q loss among Black women, appear to be cluster-dependent genomic events suggesting underlying biological heterogeneity related to focal genomic instability or selective pressures rather than the result of wide-spread changes in overall copy number burden. Citation Format: Irma M. Vlasac, Brett M. Reid, Courtney Johnson, Alicia R. Richards, Christelle M. Colin Leitzinger, Sean J. Yoder, Dana Roeber, Tania Mesa, Andrew Berchuck, Brooke Fridley, Jing-Yi Chern, Jennifer A. Doherty, Kristin Haller, Shelley Tworoger, Jeffrey R. Marks, Joellen M. Schildkrau, Brock C. Christensen, Lauren Cole Peres, Lucas A. Salas Diaz, on behalf of the African American Cancer Epidemiology Study. Characterization of high-grade serous ovarian cancer copy number alterations in Black and White Women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6813.