Introduction: Young women with estrogen receptor (ER)-positive early-stage breast cancer (EBC) frequently present with larger, higher-grade, more aggressive tumors, with lower ER expression than older women. Post-hoc analyses within the MINDACT and TAILORx cohorts reported that women aged 40-50 with ER+ EBC exhibited a chemotherapy benefit independent of genomic risk compared to women aged > 50, possibly due to chemotherapy-induced ovarian suppression (CIOS). However, women < 40 years, who seldom develop CIOS, are under-represented in clinical trials. Therefore, it is important to distinguish the tumor biological profile within this younger age group. To understand the biological basis underlying why younger women have poorer outcomes than older women, this study aimed to identify genes that distinguish tumors in younger women from older women. Methods: EBC patients enrolled in the FLEX study (NCT03053193) undergo standard of care MammaPrint (MP) and BluePrint (BP) tests, and consent to clinically annotated whole transcriptome data collection. MP categorizes tumors as High Risk (HR) or Low Risk (LR) of recurrence. Together, MP and BP classify molecular subtype as Luminal A, Luminal B, HER2, or Basal. Whole transcriptome gene expression differences were compared among ER+ tumor specimens from three age groups: < 40 years old (n=283), 40-54 years old (n=1535), and ≥ 55 years old (n=4355). Differentially expressed genes (DEGs) were identified from 100 randomized iterations for each comparison; an equal number of LR and HR samples were analyzed in each group. DEGs found in > 20 iterations indicated gene stability within the age group. DEGs were also identified within each age group after correcting for BP subtype, and between pre-menopausal (n=1314) and post-menopausal (n=4859) women. Gene expression data were quantile normalized using R package ‘limma’. DEGs with an adjusted p<0.05 and fold change ≥ 2 were considered significant. Results: Overall, 76.0% of women < 40 years, 53.6% of women aged 40-54, and 48.5% of women ≥ 55 years had MP HR tumors. In addition, women < 40 years had higher frequencies of BP Basal and HER2 tumors (20.5% and 9.2%, respectively) compared with women ≥ 55 years (8.0% and 2.4%, respectively; p<0.0001). In line with unsupervised hierarchical clustering and previous studies, tumors from patients aged 40-54 exhibited limited DEGs in comparison to women ≥ 55 years. In contrast, most gene expression differences were primarily observed between women < 40 and ≥ 55 years (11 DEGs; 10 downregulated and 1 upregulated). We identified limited DEGs within BP Luminal A (n=23), Luminal B (n=10), and Basal (n=7) tumors from women aged < 40 relative to women ≥ 55 years. No DEGs were found in HER2-type tumors. Within Luminal A and Basal tumors, upregulated genes in women < 40 years are important for proliferation and immune responses. Luminal B tumors in women aged < 40 have increased DEGs involved in ER and HER2 signaling. Within all subtypes, DEGs supporting metabolic functions were downregulated in tumors of women < 40 years compared with women ≥ 55 years. Few DEGs were observed between pre-menopausal women and post-menopausal women, though none with > 2-fold change. Conclusion: Tumors from women aged 40-54 had few DEGs, suggesting observed chemotherapy benefit represents differences in host biology rather than intrinsic tumor biology as compared with tumors from women < 40 or ≥ 55, where detected DEGs are associated with proliferation, receptor signaling, and metabolism. Fewer DEGs were observed by menopausal status than age, indicating age is a more relevant cutoff. Future studies will aim to further characterize this high risk young patient population. Citation Format: Shubhada Dhage, Mina Gendy, Nina D'Abreo, Ruth Oratz, Sami G. Diab, VK Gadi, Cathy Graham, Midas Kuilman, Shiyu Wang, Patricia Dauer, Andrea Menicucci, William Audeh, Douglas K. Marks. Deciphering the inferior prognosis of young women with estrogen receptor-positive early-stage breast cancer through full transcriptome analysis: A FLEX database sub-study [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-07-05.