Yasmine Baca

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy 20% more likely to develop in Black African Americans (BAA) compared to Non-African Americans (NAA). Large-scale gene expression analysis of tumor subtypes and cellular microenvironments in a diverse PDAC cohort could help provide insights into cell and molecular differences in BAA cancer cells. Here, we conducted a multi-omics interrogation of BAA versus NAA PDAC using whole exome sequencing, spatial transcriptomics (ST), and spatial proteomics. Whole exome sequencing confirmed patient ancestry and showed no significant differences in driver mutations between race groups. BAA PDAC tumors had significantly fewer classical molecular subtype cells with no change in more aggressive basal-like cells. Instead, BAA patients showed a significant enrichment of the intermediate/hybrid subtype compared to NAA patients. BAA tumors also displayed increased B cell and reduced myeloid cell interactions compared to NAA tumors. Analysis of tertiary lymphoid structures in a validation cohort revealed that tumors in BAA patients displayed larger TLS size and number compared to NAA. In conclusion, these findings identify an increased intermediate molecular subtype signature in BAA tumors at the expense of cells with a classical subtype, accompanied by a distinct immune cell composition and spatial distribution. This study highlights that health disparities in patients of different ancestries may have a molecular basis that influences tumor aggressiveness and the immune response, which may inform therapeutic strategies.

Background: Intraductal carcinoma of the prostate (IDC‐P) is an intra‐acinar and/or intraductal neoplastic epithelial proliferation that is a distinct histological entity according to the 2016 World Health Organization (WHO) classification system. Clinically, it is associated with higher grade tumors and a more aggressive disease course. However, the molecular underpinnings of IDC‐P are not well elucidated. Methods: This study identified radical prostatectomy (RP) cases from the Caris Life Sciences database, classified as prostatic adenocarcinoma with grade group 4/5 or with the words “cribriform,” “necrosis,” or “intraductal” in the pathology report. Digitized hematoxylin–eosin slides underwent central pathology review by a board‐certified genitourinary pathologist to identify the presence of IDC‐P according to the 2022 WHO classification. IDC‐P cases ( n = 175) were compared to non–IDC‐P cases ( n = 5334). Prostatic tumor specimens were sequenced via next‐generation DNA/RNA sequencing. Results: Compared to non–IDC‐P cases, the IDC‐P cohort had significantly more mutations in MUTYH (4.5% vs. 1.4%; p < .01), FANCA (2.7% vs. 0.5%; p < .01), NBN (2.5% vs. 0.6%; p < .05), and MTOR (0.6% vs. 0.1%; p < .05). IDC‐P tumors were enriched for DLL3 and CEACAM5 expression, with lower expression of STEAP1, TROP2, ERBB2, PSCA, and B7‐H3, compared to non–IDC‐P tumors. IDC‐P had significantly higher neuroendocrine prostate cancer signature scores and IFN‐γ signature scores, and similar androgen receptor signature scores, compared to non–IDC‐P. The tumor microenvironment of IDC‐P had significantly higher cell fractions of M2 macrophages and fewer dendritic cells. Conclusions: IDC‐P possesses a distinct molecular and immunological profile. Understanding these molecular underpinnings is crucial for the development of personalized treatment strategies for histologically distinct prostate cancer subsets.

An emerging challenge in prostate cancer (PCa) treatment is the development of drug cross-resistance, wherein resistance to enzalutamide (ENZ), an androgen receptor signaling inhibitor (ARSI), also confers resistance to subsequent ARSI and docetaxel (DTX) treatments. The mechanisms underlying this drug cross-resistance remain unclear. Through RNA sequencing, we identified 93 overlapping differentially expressed genes (DEGs) in ENZ- and DTX-resistant PCa cells. Among the DEGs, HSPB1, which encodes heat shock protein 27 (HSP27), emerged as a key gene of interest. HSP27 is a known target of lens epithelium-derived growth factor p75 (LEDGF/p75), a transcription coactivator regulated by glucocorticoid receptor (GR). Both GR and LEDGF/p75 are overexpressed in advanced PCa and promote drug resistance. HSP27 was overexpressed in ENZ and DTX cross-resistant PCa cell lines and its expression was decreased upon GR or LEDGF/p75 silencing. ChIP sequencing confirmed GR binding at the HSPB1 promoter. Pharmacological targeting of HSP27 in drug-resistant cells reduced proliferation, clonogenicity, and tumorsphere formation, and restored sensitivity to ENZ and DTX. Notably, high transcript expression of a GR-LEDGF/p75-HSP27 gene panel correlated with worse overall survival in PCa patients (n = 4259). These findings identified this axis as a driver of PCa drug cross-resistance and promising therapeutic target for overcoming treatment failure.

Purpose: Preclinical studies suggest that interleukin-1β (IL-1β) influences tumor behavior in non-small cell lung cancer (NSCLC). While the CANTOS trial demonstrated reduced lung cancer incidence with IL-1β inhibition, the CANOPY trials failed to show survival benefit when combined with chemoimmunotherapy. The role of IL-1β in NSCLC with oncogenic mutations remains unclear. We evaluated the prognostic and predictive significance of IL-1β expression across NSCLC subtypes. Methods: We analyzed 21,698 NSCLC tumors profiled by Caris Life Sciences using DNA and RNA next-generation sequencing. IL-1β expression was stratified into quartiles (Q1: lowest 25%, Q4: highest 25%). Real-world overall survival (OS) and time on treatment (TOT) were obtained from insurance claims. Statistical comparisons used Chi-square, Fisher’s exact, or Mann–Whitney U tests. Survival outcomes were assessed with Cox models. Results: Across unselected NSCLC patients, low IL-1β expression (Q1) was associated with modestly longer OS versus high expression (Q4) (median OS 19.5 vs. 17.4 months; HR 0.94; p < 0.0001). This effect was more pronounced in EGFR-mutant adenocarcinoma (36.7 vs. 27.2 months; HR 0.76; p < 0.001) and ALK fusion-positive NSCLC (53.0 vs. 35.2 months; HR 0.62; p = 0.002). In NSCLC without targetable mutations, IL-1β expression was not prognostic. In KRAS-mutant adenocarcinoma, high IL-1β expression was associated with modestly longer TOT on immunotherapy (7.4 vs. 6.4 months; HR 1.15; p = 0.041), but not OS. High IL-1β expression correlated positively with TP53 mutation, TMB-high, and PD-L1 expression and inversely with EGFR, KRAS, BRAF, ERBB2, KEAP1, and STK11 mutations. Conclusions: IL-1β expression is a potential prognostic and predictive biomarker in NSCLC, associated with survival outcomes in defined molecular subsets. These findings suggest that IL-1β-targeted strategies may be particularly relevant in EGFR- or ALK-altered tumors.

Supplementary Figure S6 and legend

Supplementary Figure S7 and legend

Supplementary Table S1 from XPO1R749Q Mutations Co-occur with POLE Mutations in Cancer and Can Be Targeted to Overcome Chemoresistance

Supplementary Figure S2 and legend

Supplementary Figure S5 and legend

Supplementary Figure S4 and legend