Citations

Abstract Background: The increasing volume and diversity of clinical genomic reports pose a significant challenge across healthcare institutions for the interpretation and proper implementation of precision oncology research. Reports from multiple different vendors (e.g., Invitae, Ambry Genetics, Foundation Medicine) are typically PDFs and exhibit substantial heterogeneity in panel design, gene coverage, and reporting standards, which hinders efficient retrospective data mining and patient cohort identification within the electronic medical records. We sought to develop a framework to interrogate all of these reports. Methods: We extracted genomic reports from patients with breast cancer treated with neoadjuvant chemotherapy and developed MolHarmonizer, a novel, scalable framework leveraging Python and Gemini LLMs, designed to process and harmonize genomic data from disparate multi-vendor reports. Gemini LLMs are employed explicitly for robust information extraction, normalization, and structuring of key genomic features, transforming unstructured data into a unified, queryable dataset. Results: Our MolHarmonizer framework successfully processed 1,147 genomic reports from 1703 breast cancer patients (2006-2023) from 23 different companies, demonstrating robust capability to extract and standardize critical actionable biomarkers. Data sources included Invitae (n=554), Ambry Genetics (n=189), Natera (n=95), Mayo Clinic (n=88), Tempus (n=63), Guardant Health (n=47), and Foundation Medicine (n=37), with others contributing less than 20 reports. Of the samples, 827/1147 (72.1%) were germline (blood/saliva). A majority of the patients were tested using the panels due to a personal/family history (n=925). Overall, 413/1147 (36.0%) reports identified at least one mutation. For breast cancer, 75 reports showed BRCA1/2 mutations (37 BRCA1, 37 BRCA2, and one patient with both BRCA1 and 2). Other mutations identified included: PIK3CA (n=40), TP53 (n=96), PTEN (n=21), ESR1 (n=13) and AKT1/2 (n=8). Conclusion: MolHarmonizer, a powerful framework leveraging Gemini LLMs, effectively addresses genomic data heterogeneity by automating biomarker extraction and harmonization. This enables rapid cohort identification and deep retrospective analyses for clinical insights, biomarker discovery, understanding disease history, facilitating novel pattern discovery, e.g., predicting BRCA1 mutations from WSI, and accelerating research within our neoadjuvant BC cohort. Future plans include expanding to include over 20,000 breast cancer patients, developing a user-friendly chatbot, and ensuring inter-institutional adaptability for a variety of complex diseases. Citation Format: Krishna Rani Kalari, Xiaojia Tang, Thanmayee Boyapati, Tanya L. Hoskin, Sumathilatha Myla, Sumedha G. Penheiter, Richard M. Weinshilboum, Liewei Wang, Hamid R. Tizhoosh, Karthik Vikram Giridhar, Matthew P. Goetz, Judy C. Boughey. Development of an LLM framework for analysis of heterogeneous breast cancer patients genomic reports [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 2756.

Abstract Background: In metastatic cancer, Circulating Tumor cells (CTCs) are established prognostic indictors of patients (pts) less likely to respond to new lines of systemic therapy, with poor clinical outcomes, such as shorter progression free survival (PFS) and overall survival (OS). However, CTCs are typically found in specific malignancies (breast, prostate & colon), often in <20% of pts with metastatic disease, and pts without CTCs may also rapidly progress. Recently, an inflammatory pro-tumorigenic macrophage emanating from tumor stroma (i.e. Cancer associated macrophage-like cell [CAML]) was found in >90% of metastatic cancer pts, and whose phagocytic engorgement appears to correlate with poor outcomes, independent of CTCs. As CTCs and CAMLs are isolated in conjunction from a single blood sample, and both are prognostic for outcomes, we evaluated their utilization prior to induction of new systemic therapy in 6 types of metastatic cancer to model pt risk stratification based on 2 year outcomes. Methods: A prospective 2 year blind multi-institutional study was undertaken to model CTCs and CAMLs in prognosticating outcomes prior to induction of a new line of systemic therapy (n=233) in metastatic: Breast (n=60), Prostate (n=40), Pancreas (n=25), Colon (n=28), Renal Cell Carcinoma (RCC) (n=39), and Lung (n=40). Blood was filtered by CellSieveTM filters with subtypes of CTCs & hyper-enlarged CAMLs (≥100µm) enumerated. A machine learning algorithm was trained on this initial data set to develop predictive models which could stratify pt populations by risk for likelihood of PFS & OS over 2 years, including known clinical variables. Results: CTCs were absent in 80% (n=185/233) of pts, and their absence was prognostic for better PFS (HR=1.6, p=0.046), but not OS (HR=1.3, p=0.2045). In parallel, enlarged CAMLs (≥100µm) were found in 28% (n=51/185) of pts without CTCs, and were also prognostic for worse PFS (HR=2.0, p=0.0082) and OS (HR=1.9, p=0.0412). Specifically, CTCs were found in 55% (n=33) breast, 20% (n=8) prostate, 12% (n=3) pancreas, 11% (n=3) colon, 0% (n=0) RCC, and 0% (n=0) lung pts. Enlarged CAMLs were found in 45% (n=27) breast, 20% (n=8) prostate, 44% (n=11) pancreas, 44% (n=17) colon, 18% (n=7) RCC and 20% (n=8) lung pts. Overall, models indicated that ≥1 CTC (n=47) had mPFS=3.9 & mOS=14.9, while pts with 0 CTCs and ≥100µm CAMLs (n=51) had a mPFS=6.9 & mOS=13.8, and pts with 0 CTCs and <100µm CAMLs (n=134) had a mPFS=10.7 & mOS>24 months. Conclusions: These initial models confirm that both CTCs and enlarged CAMLs are prognostic indicators of worse PFS & OS. The simultaneous quantification both CTCs and CAMLs allows for more accurate pan-cancer risk stratification in an array of cancer pt populations. Additional clinical variables incorporated into the models may allow better risk subtyping and possibly forecast optimal treatment regimens. Citation Format: Daniel L. Adams, Steven H. Lin, Massimo Cristofanilli, Carolina Reduzzi, Saranya Chumsri, Martin J. Edelman, Susan Tsai, Raymond C. Bergan, Mohammed Aldakkak, Thai H. Ho, Cha-Mei Tang. Combining circulating tumor cells and cancer associated macrophage-like cells enhances risk stratification models in pan-cancer metastatic disease [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 1068.

ABSTRACT The epidemiology of myelodysplastic syndromes/neoplasms (MDS) is challenging to define due to inconsistent reporting, complex diagnostic procedures, and evolving diagnostic criteria. Using the National MDS Natural History Study—a prospective cohort with centrally adjudicated histopathology and genetic variant review—we characterized the landscape of MDS across the United States and identified differences across demographics. Among 2115 participants, 64% (1346) had an MDS spectrum condition, including MDS (24%), MDS/myeloproliferative neoplasm (5%) and precursor conditions—clonal cytopenia of undetermined significance (22%) and idiopathic cytopenia/dysplasia of undetermined significance (13%). The median age was 74 years, and participants were predominantly male (66%), White (91%), and Non‐Hispanic (92%). Myeloid‐associated variants were detected in 68% of participants, most commonly in TET2, DNMT3A, ASXL1, SF3B1, and SRSF2 . Black, compared to White, participants were younger at diagnosis (69 vs. 74 years, p = 0.01), had equal or increased prevalence of higher‐risk MDS, lower hemoglobin, and higher peripheral blood blasts, yet were less likely to receive MDS‐directed therapy (14% vs. 42%, p = 0.008). Black and Hispanic participants had fewer detectable gene mutations than White participants. Females had lower variant allele frequencies and fewer RNA splicing gene mutations than males. After multivariable adjustment, TP53 mutations, MDS diagnosis, and higher‐risk disease were associated with worse progression‐free and overall survival; age was also associated with overall survival. Black race trended toward improved progression‐free survival. These findings highlight the need for enhanced understanding of MDS pathogenesis across patient groups and refined prognostic tools to improve personalized management of MDS spectrum conditions. Trial Registration: ClinicalTrials.gov identifier: NCT02775383

Abstract Purpose: Standard care for high-grade gliomas (HGG) involves maximal surgical resection followed by radiation and temozolomide. Postoperative adjuvant therapy frequently causes lymphopenia, which is associated with poor prognosis. Interleukin 7 (IL7) is essential for lymphocyte development, homeostasis, and survival. NT-I7 (efineptakin alfa), a long-acting recombinant IL7, reverses lymphopenia and improves survival in murine glioma models. However, the safety, maximum tolerated dose (MTD), and impact of NT-I7 on immune cells in patients with HGG remain unknown. Patients and Methods: We conducted a phase I trial (NCT03687957) examining the MTD and effect of NT-I7 on lymphocytes in patients with newly diagnosed HGG. The primary endpoint was dose-limiting toxicity; secondary endpoints included absolute lymphocyte count (ALC) changes over time, overall response, progression-free survival, and overall survival. Exploratory endpoints included immune profiling at different time points using single-cell RNA sequencing (scRNA-seq) in a subset of patients. Results: NT-I7 was well tolerated with a MTD of 720 µg/kg. Moreover, NT-I7 significantly increased ALCs for more than 12 weeks in duration. Early elevations in CD4+, CD8+ T cells and NK cells further coincided with increased TNF and CXCL9 cytokine levels. Comprehensive immune profiling of peripheral blood T cells revealed selective clonotype expansion within CD8+, but not CD4+, T cells following NT-I7 administration. Finally, a subset of our patients with MGMT promoter–unmethylated glioblastoma, which are typically associated with a poorer prognosis, demonstrated promising clinical responses. Conclusions: NT-I7 has the potential to maintain and increase lymphocyte counts in patients with HGG and warrants further investigation, particularly in combination with immune-based therapies.

Cellular and molecular heterogeneity in the liver has been increasingly recognized to drive liver fibrosis progression, but the particular events that occur initially in response to liver injury and trigger immune cell recruitment remain unclear. Here, we identify epigenetically aberrant liver sinusoidal endothelial cells (LSECs) as key players in this process. Mechanistically, the epigenetic readers like bromodomain-containing protein 4–dependent (BRD4-dependent) super enhancers (SEs) activate proinflammatory genes, including promyelocytic leukemia (PML). The PML protein, in turn, binds BRD4 and amplifies proinflammatory angiocrine signaling through phase separation–dependent SE activation via PML/BRD4 condensate formation. In mouse models, LSEC-specific depletion of the PML/BRD4 complex mitigates liver inflammation and fibrosis. Single-cell RNA-seq reveals that epigenetically aberrant LSECs exhibit a reprogrammed proinflammatory angiocrine landscape in mouse fibrotic livers. TIMP1 + LSECs promote the recruitment of CD63 + monocyte–derived macrophages (MoMFs) during liver fibrosis progression. Thereby, PML/BRD4 in LSECs governs inflammatory immune cell recruitment in liver fibrosis. Pharmacological BRD4 inhibition or epigenetic PML-SE repression alleviates liver inflammation and fibrosis. In conclusion, PML/BRD4-mediated SE activation via phase separation drives proinflammatory angiocrine signaling in LSECs, initiating the inflammatory cascade and subsequent immune cell recruitment during liver fibrosis.

Aging is a major risk factor for increased morbidity and mortality following acute respiratory virus infections. To elucidate the immune determinants underlying viral pathogenesis and delayed lung repair in the aged lung, a comprehensive time-course study was conducted. Single-cell RNA sequencing (scRNAseq) and high-dimensional flow cytometry were utilized to compare lungs from young and aged mice infected with influenza A virus (IAV). Aged hosts displayed diminished alveolar macrophage (AM) and dendritic cell (DC) but elevated monocyte-derived macrophage (MoM) and interstitial macrophage (IM) presence following infection. Additionally, enhanced accumulation of adaptive immune cells, including CD4+ tissue-resident helper (TRH) cells, CD8+ tissue-resident memory (TRM) cells, and a B cell subset resembling age-associated B cells, was observed in the memory phase. Pathway analysis revealed that elevated type I and II interferon (IFNα/γ) signaling, especially in MoM/IM subsets, distinguished the aged hosts from the young. Inhibition of IFNα/γ signaling after viral clearance improved long-term respiratory outcomes and reduced both IM and TRH populations in aged mice. These findings highlight the pivotal role of IFNα/γ signaling, likely within MoM/IM subsets, in driving the exuberant persistence of adaptive immune cells and chronic immunopathology in the aged lung following acute viral infection.

Aging is a major risk factor for increased morbidity and mortality following acute respiratory virus infections. To elucidate the immune determinants underlying viral pathogenesis and delayed lung repair in the aged lung, a comprehensive time-course study was conducted. Single-cell RNA sequencing (scRNAseq) and high-dimensional flow cytometry were utilized to compare lungs from young and aged mice infected with influenza A virus (IAV). Aged hosts displayed diminished alveolar macrophage (AM) and dendritic cell (DC) but elevated monocyte-derived macrophage (MoM) and interstitial macrophage (IM) presence following infection. Additionally, enhanced accumulation of adaptive immune cells, including CD4+ tissue-resident helper (TRH) cells, CD8+ tissue-resident memory (TRM) cells, and a B cell subset resembling age-associated B cells, was observed in the memory phase. Pathway analysis revealed that elevated type I and II interferon (IFNα/γ) signaling, especially in MoM/IM subsets, distinguished the aged hosts from the young. Inhibition of IFNα/γ signaling after viral clearance improved long-term respiratory outcomes and reduced both IM and TRH populations in aged mice. These findings highlight the pivotal role of IFNα/γ signaling, likely within MoM/IM subsets, in driving the exuberant persistence of adaptive immune cells and chronic immunopathology in the aged lung following acute viral infection.

77 Background: The incidence of metastatic hormone-sensitive prostate cancer (mHSPC) is increasing in the US, likely due to a decrease in screening practices. There has also been a rapid increase in recent years in the number of treatment options that can improve progression-free and overall survival (OS) for these patients. The objective of the current study was to evaluate the clinical outcomes among patients with mHSPC treated in contemporary US clinical practice (2020 to 2025). Methods: This retrospective, observational cohort study used data from PRECISION, a harmonized dataset on advanced prostate cancer in patients in the US treated in a range of clinical settings. Patients aged ≥18 years who were diagnosed with mHSPC during 01/01/2020–01/01/2024 and who initiated ≥1 therapy (index date = first-line [1L] treatment initiation) were included. The study period was from 01/01/2010 to 06/30/2025. Patient characteristics at mHSPC diagnosis and treatment utilization were evaluated descriptively. Castration resistance-free survival (CRFS; defined as the time to castration-resistant prostate cancer or death) and OS were evaluated from index using Kaplan–Meier analysis. Results: A total of 27,708 patients were included (median age, 72 years); 20,015 (72%) were treated in community urology, 4994 (18%) in community oncology, and 2669 (10%) in academic oncology centers at index. Almost half of patients (47%) initiated 1L treatment with androgen-deprivation therapy (ADT) monotherapy, 44% initiated a 1L doublet regimen (36% ADT + androgen receptor pathway inhibitor [ARPI], 5% 1L ADT + radiotherapy, 2% 1L ADT + docetaxel), and 5% a 1L triplet regimen (ADT + radiotherapy + ARPI or docetaxel); the remaining patients received other regimens. The 5-year CRFS rate was 41%; this was significantly higher in patients with a 1L doublet (45%) or triplet (58%) regimen compared with patients with 1L ADT monotherapy (31%; p<0.001). Similarly, the 5-year OS rate was 59% overall and was significantly higher in patients with a 1L doublet (61%) or triplet (59%) regimen compared with patients with 1L ADT monotherapy (55%; p<0.001) (Table). Conclusions: Though both CRFS and OS rates appear to be increasing among real-world patients with mHSPC, >40% of patients in this study died within 5 years of initiating 1L treatment. Patients who received guideline-recommended combined systemic treatment regimens experienced improved CRFS and OS, confirming the importance of implementing therapies in practice that prolong survival. CRFS and OS rates from start of 1L therapy, by therapy type. CRFS rate (%) OS rate (%) 1 y 2 y 3 y 4 y 5 y 1 y 2 y 3 y 4 y 5 y Overall 68 58 51 46 41 93 84 76 67 59 ADT monotherapy 59 49 41 36 31 92 83 74 65 55 Doublet therapy 72 62 55 49 45 94 85 76 68 61 Triplet therapy 85 77 70 68 58 94 89 82 74 59

75 Background: Although the number of life-prolonging treatment options for pts with mHSPC has increased, initial real-world evidence has demonstrated slow uptake. This study utilized a large, contemporary, real-world dataset to evaluate the characteristics and treatment utilization among US pts with mHSPC in recent years. Methods: This retrospective, observational study used data from PRECISION, a harmonized dataset on pts with advanced prostate cancer. Adult men who were diagnosed with mHSPC during 01/01/2020–01/01/2024 (index date) and who initiated ≥1 therapy were included; the study period was 01/01/2010–06/30/2025. Pt characteristics were described at index. Treatment utilization was evaluated from index until progression to metastatic castration-resistant prostate cancer, death, or last follow-up. If an androgen receptor pathway inhibitor (ARPI), docetaxel, or radiotherapy was started within 4 months of index/androgen-deprivation therapy (ADT) start, it was considered a first-line (1L) combination; if it was started after >4 months, it was considered treatment intensification. All analyses were descriptive. Results: Among the 27,708 pts who met the inclusion criteria in PRECISION, 72%, 18%, and 10% were treated in community urology, community oncology, and academic oncology centers at index, respectively. Median age was 72 years; 62% were White; 43% were from the US South; 53% had synchronous and 54% had metachronous metastases (2% unknown). Median prostate-specific antigen level was 9 ng/mL (mean, 130 ng/mL). Prior to mHSPC diagnosis, 19% of pts had a prostatectomy and 17% had radiotherapy. Almost half of pts (47%) initiated 1L treatment with ADT monotherapy; 36% initiated 1L ADT + ARPI, 5% 1L ADT + radiotherapy, 2% 1L ADT + docetaxel, 5% 1L ADT + radiotherapy + ARPI or docetaxel, and 5% other regimens. From 2020 to 2023, 1L ADT monotherapy use decreased, while 1L combination use increased (Table). In addition, 19% of pts with 1L ADT monotherapy had evidence of subsequent treatment intensification, mainly the addition of an ARPI. Conclusions: In this study, use of 1L ADT monotherapy declined over time, accompanied by an increase in 1L combinations and treatment intensification. Nonetheless, approximately 1/3 of pts still did not receive a combination or intensification. Further research is needed to understand treatment trends in pts with mHSPC. Treatment patterns by index year. Pts, % 2020(n=5278) 2021(n=6203) 2022(n=7701) 2023(n=8526) 1L ADT monotherapy* 54 52 45 40 Subsequent treatment intensification* 18 19 20 18 1L ADT + ARPI* 29 33 38 42 1L ADT + radiotherapy 5 5 5 6 1L ADT + docetaxel* 3 2 2 1 1L ADT + radiotherapy + ARPI or docetaxel* 3 3 5 7 *p<0.001 for trend across years.

382 Background: Androgen receptor signaling drives prostate cancer (PC) progression, and genes involved in androgen production, uptake, and conversion (APUC) are key therapeutic targets. We previously defined a 6-APUC gene set ( HSD3B1, HSD3B2, CYP3A43, CYP11A1, CYP11B1, and CYP17A1 ), that identified metastatic PC with favorable prognosis and predict docetaxel benefit. However, the expression landscape and clinical relevance of APUC genes have not been interrogated in localized PC. Methods: We analyzed the expression of 21 APUC genes in 55,329 radical prostatectomy tumor samples that underwent Decipher prostate genomic classifier (GC) testing (Veracyte Inc) between 2016-2024. Baseline clinical/pathologic factors were retrieved from Decipher GRID database (NCT02609269). Associations between gene expression quartiles with PathoGenomic Risk Factors (PGRF) including Very High Decipher score >0.85 (VHD), Grade Group (GG) 4-5, LNI and SVI were examined. Associations with distant metastatic (DM) outcomes and metastasis free survival (MFS) were evaluated using logistic regression in Mayo545 and Cox regression in Meta855 RP cohorts, respectively. Results: High expression of SRD5A2 was associated with favorable PGRF (lower odds ratio (OR), p<0.0001), lower rate of development of DM (OR 0.36, p<0.05), and longer MFS (Hazard ratio (HR) 0.51, p<0.05). HSD17B6 showed similar results for PGRF (lower OR, p<0.0001), DM (OR 0.58, p<0.05) and longer MFS (HR 0.39, p<0.05) despite being associated with GG4-5 and SVI+ in samples with VHD. In contrast, high expression of SRD5A3 and HSD17B10 had high OR for PGRFs (p<0.0001). High expression of SLCO2B1 , an androgen uptake gene, had the strongest association with GG4-5 and SVI/LNI (p<0.001 for both). We noted that SRD5A2 lacked correlation with SRD5A1 and SRD5A3 , which instead correlated with each other. Compared to all APUC genes, SRD5A2 had limited correlations with almost all APUC genes, including ones that exhibited robust cross correlation with each other . Similar to our prior finding, most APUC genes demonstrated negative correlation with AR expression and AR activity signatures. Key outcomes were validated based on transcriptomic data from 492 samples from TCGA database. Conclusions: Comprehensive analysis of 21 APUC genes in over 55,000 PC identified distinct, context-dependent associations with metastatic outcomes and clinical and molecular risk factors. Notably, high SRD5A2 expression was associated with lower odds of high-risk features and metastatic outcomes, whereas SRD5A1 and SRD5A3 linked to adverse outcomes, suggesting critical yet divergent roles among 5-alpha-reductase family members. These findings underscoring androgen-metabolic heterogeneity and highlighting SRD5A2 as a potential biomarker of indolent biology in localized prostate cancer.