Metastatic Cohort Research Articles

Treatment approaches and survival outcomes in elderly colorectal cancer patients: a single-center comparative study.

Geriatric patients account for nearly half of new colorectal cancer (CRC) cases. This study compares clinicopathological features, treatments, outcomes, and frailty in elderly (≥ 70) and younger (< 70) CRC patients at our center. Patients diagnosed with non-metastatic or de novo metastatic CRC between January 2015 and April 2024 were included. Demographic, pathological, and survival data were retrospectively collected. Analyses were performed using SPSS version 25, with statistical significance set at P < 0.05. Of the 414 non-metastatic CRC patients, 26.6% were aged ≥ 70. Elderly patients received less perioperative chemotherapy (60% vs. 81.6%, P < 0.001) and had more dose reductions (41.6% vs. 19.2%, P < 0.001). Frailty reduced perioperative chemotherapy in elderly non-metastatic patients (54.5% vs. 92.1%, P < 0.001) but did not affect dose reduction (37.9% vs. 33.3%, P = 0.764) or treatment duration (median 24weeks for both groups, P = 0.909). In metastatic patients, frailty shortened chemotherapy duration (9.5 vs. 15.5weeks, P = 0.129). Elderly patients had lower 5- and 8-year overall survival (OS) rates (64.7%, 60.1% vs. 83.0%, 78.8%, P = 0.004). In the de novo metastatic cohort (135 patients), age did not affect OS (19.4 vs. 17.3months, P = 0.590) or PFS (9.8 vs. 7.5months, P = 0.209). Rectal cancer (HR: 2.751, P = 0.005) and early chemotherapy termination (HR: 4.138, P < 0.001) worsened OS in non-metastatic CRC, while absence of RAS (HR: 2.043, P = 0.047), BRAF mutations (HR: 8.263, P = 0.010), and metastasectomy (HR: 3.650, P = 0.036) improved OS in metastatic CRC. Age does not independently worsen CRC survival, though early chemotherapy discontinuation impacts outcomes. Reduced-dose chemotherapy or monotherapy can help minimize adverse effects in elderly patients.

Circulating Adenoid Cystic Carcinoma associated MYB transcripts enable rapid and sensitive detection of metastatic disease in blood liquid biopsies.

Adenoid cystic carcinoma (ACC) is a rare and lethal malignancy that originates in secretory glands of the head and neck. A prominent molecular feature of ACC is the overexpression of the proto-oncogene MYB. ACC has a poor long-term survival due to its high propensity for recurrence and protracted metastasis. Currently, clinical technologies lack the efficiency to distinguish patient prognosis prior to its redevelopment. We hypothesize that metastatic ACC can be detected by monitoring tumor-specific MYB expression in patients' blood. We developed a quantitative polymerase chain reaction (qPCR) assay for MYB transcripts and screened blood samples from four patient cohorts: no history or evidence of ACC (n=23), past history of ACC and no evidence of disease (NED) for greater than three years (n=15), local ACC (n=6), and metastatic ACC (n=5). Our assay detected significantly elevated levels of MYB transcripts in the metastatic ACC cohort (p < 0.01). Receiver operating characteristic (ROC) curves comparing metastatic to NED and metastatic to local disease were significant, with p values < 0.0001 and 0.0008, respectively. Single-cell RNA sequencing (scRNA-seq) of blood from metastatic ACC identified a cluster of circulating tumor cells (CTCs) expressing MYB. Here, we report a sensitive, cost-effective, and minimally invasive diagnostic test that leverages tumor-specific signatures to screen for metastatic ACC disease, potentially enhancing detection earlier than the current clinical standard.

Plasma-based proteomic and metabolomic characterization of lung and lymph node metastases in cervical cancer patients

Metastasis is the leading cause of mortality in cervical cancer (CC), with a particular prevalence of lymph node and lung metastases. Patients with CC who have developed distant metastases typically face a poor prognosis, and there is a scarcity of non-invasive strategies for predicting CC metastasis. In this study, we utilized label-free proteomics and untargeted metabolomics to analyze plasma samples from 25 non-metastatic, 14 with lung metastasis, and 15 with lymph node metastasis CC patients. Pathway enrichment analysis revealed a shared inflammatory process between the two metastatic groups, while the central carbon metabolism in cancer showed distinct features in the lung metastasis cohort. Additionally, cholesterol metabolism, hypoxia-inducible factor 1, and ferroptosis signaling pathways were specifically altered in the lymph node metastasis group. Utilizing the receiver operating characteristic curve analysis and Random Forest algorithm, we identified two distinct biomarker panels for the prediction of lung metastasis and lymph node metastasis, respectively. The lung metastasis panel includes properdin, neural cell adhesion molecule 1, and keratin 6 A, whereas the lymph node metastasis panel consists of quiescin sulfhydryl oxidase 1, paraoxonase 1, and keratin 6 A. Each panel exhibited significant diagnostic potential, with high area under the curve (AUC) values for lung metastasis (training set: 0.989, testing set: 0.789) and lymph node metastasis (training set: 0.973, testing set: 0.900). This study conducted an integrated proteomic and metabolomic analysis to clarify the factors contributing to lung and lymph node metastases in CC and has successfully established two biomarker panels for their prediction.

Survival analysis of the metastatic cohort of Italian Association of Medical Oncology (AIOM) GARIBALDI survey

This analysis from the GARIBALDI study was aimed to address the role of center self-declared expertise, type and commitment on the overall survival (OS) of patients with metastatic Pancreatic Ductal Adenocarcinoma (mPDAC).Treatment-naïve patients ≥18-year with pathological diagnosis of mPDAC were enrolled. OS was defined as the time from chemotherapy start to death from any cause. The impact of clinical-demographic and centers characteristics on OS was evaluated using Cox models.Between July 2017 and October 2019, 473 patients enrolled in 43 centers were eligible for this analysis. Median age was 69.3 (first-third quartile 61.2–74.5); 46.1 % females; 90.8 % ECOG PS 0–1; 67.4 % had liver metastases; median CA19.9700.5 UI/mL (first-third quartile 77.5-6629.5). For 37.1 % of patients chemotherapy started <4 weeks from diagnosis; 69.9 % of patients received nab-paclitaxel + gemcitabine; 16.9 % gemcitabine alone; 7.6 % FOLFIRINOX. The median follow-up was 51.8 months and 428 patients died. No statistically significant role of the type of institution was observed. Additionally, no statistically significant role of neither the self-declared expertise nor the accrual rate was observed.The GARIBALDI study suggests that the self-declared center expertise and the academic brand are not associated to OS in patients with mPDAC, while center commitment warrants further exploration.

Functional activation of the AKT-mTOR signalling axis in a real-world metastatic breast cancer cohort.

Mutations of the PIK3CA/AKT/mTOR axis are common events in metastatic breast cancers (MBCs). This study was designed to evaluate the extent to which genetic alterations of the PIK3CA/AKT/mTOR can predict protein activation of this signalling axis in MBCs. Molecular profiles were generated by CLIA-certified laboratories from a real-world evidence cohort of 171 MBC patients. Genetic alterations of the PIK3CA pathway were measured using next-generation sequencing. Activation levels of AKT and downstream signalling molecules were quantified using two orthogonal proteomic methods. Protein activity was correlated with underlying genomic profiles and response to CDK4/6 inhibition in combination with endocrine treatment (ET). Oncogenic alterations of the PIK3CA/AKT/PTEN pathway were identified in 49.7% of cases. Genomic profiles emerged as poor predictors of protein activity (AUC:0.69), and AKT phosphorylation levels mimicked those of mutant lesions in 76.9% of wild-type tumours. High phosphorylation levels of the PI3K/AKT/mTOR downstream target p70S6 Kinase (T389) were associated with shorter PFS in patients treated with CDK4/6 inhibitors in combination with ET (HR:4.18 95%CI:1.19-14.63); this association was not seen when patients were classified by mutational status. Phosphoprotein-based measurements of drug targets and downstream substrates should be captured along with genomic information to identify MBCs driven by the PI3K/AKT/mTOR signalling.

Abstract C037: Inflammatory breast cancer by metastatic status: Racial and ethnic and socioeconomic disparities in receipt of treatment

Abstract Background: Inflammatory breast cancer (IBC) is a relatively rare but aggressive type of breast cancer. Racial and ethnic minority patients are disproportionately affected by IBC and often face barriers to accessing cancer care and services. However, racial and ethnic disparities in receipt of treatment are not well defined among patients with IBC by metastatic status. Methods: We analyzed data from patients with IBC in the 2004-2020 U.S. National Cancer Database. Five treatment modalities were assessed: hormone therapy, chemotherapy, radiotherapy, surgery, and trimodal therapy. Metastatic status was dichotomous as “metastatic/non-metastatic.” Racial and ethnic groups included Asian or Pacific Islander, American Indian, Alaska Native, or Other, Black, Hispanic, and White. Separate logistic regression models were fit, adjusting for sociodemographic and clinicopathological characteristics, stratified by metastatic status. Adjusted odds ratios (aOR) and 95% CIs were calculated. Results: Of 33,376 patients with IBC (mean age 58 years [SD=14]), most (70.6%) identified as White, followed by 18.1% as Black, 7.0% as Hispanic, 2.5% as Asian or Pacific Islander, 1.8% as American Indian, Alaska Native, or Other; and 32.5% were metastatic. In the non-metastatic cohort, Black (72.7%; aOR 0.79, 95% CI: 0.63-0.98) or Asian or Pacific Islander (74.8%; aOR 0.59, 95% CI: 0.38-0.90) patients had lower odds of receiving hormone therapy than White patients (78.0%). Compared with White patients, Black patients had a lower likelihood of receiving chemotherapy (89.1% vs. 89.5%; aOR 0.67, 95% CI: 0.53-0.86), surgery (78.4% vs. 85.3%; aOR 0.65, 95% CI: 0.55-0.77), or trimodal therapy (81.5% vs. 87.3%; aOR 0.61, 95% CI: 0.49-0.76). American Indian, Alaska Native, or Other (65.0%; aOR 0.64, 95% CI: 0.42-0.97) and Black (63.6%; aOR 0.71, 95% CI: 0.61-0.82) patients had lower odds of receipt of radiotherapy than White patients (70.6%). In the metastatic cohort, Black patients had a lower likelihood of receiving hormone therapy (55.2% vs. 63.5%; aOR 0.61, 95% CI: 0.48-0.78), chemotherapy (78.7% vs. 78.2%; aOR 0.75, 95% CI: 0.60-0.95), surgery (28.2% vs. 35.1%; aOR 0.68, 95% CI: 0.56-0.82), or trimodal therapy (30.4% vs. 40.4%; aOR 0.63, 95% CI: 0.48-0.82) than White patients. There were no statistically significant differences in receipt of treatment between White and other racial and ethnic patients with metastatic IBC. Furthermore, we observed significantly differential rates of treatment receipts by socioeconomic factors including median household income quartile, insurance coverage, and facility type. Conclusions: In this study of a large U.S. national IBC patient cohort, racial and ethnic minority patients were less likely than White patients to have received treatment for IBC, with Black patients being the most affected. Our findings highlight racial and ethnic disparities and socioeconomic inequities in treatment receipts, suggesting the need for oncology programs to improve equitable care access and reduce these disparities in the IBC population. Citation Format: Jincong Q. Freeman, Jared H. Hara, Olasubomi J. Omoleye. Inflammatory breast cancer by metastatic status: Racial and ethnic and socioeconomic disparities in receipt of treatment [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C037.

Transcriptome-based classification to predict FOLFIRINOX response in a real-world metastatic pancreatic cancer cohort

Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at metastatic stage and typically treated with fluorouracil, leucovorin, irinotecan and oxaliplatin (FOLFIRINOX). Few patients benefit from this treatment. Molecular subtypes are prognostic in particularly resectable PDAC and might predict treatment response. This study aims to correlate molecular subtypes in metastatic PDAC with FOLFIRINOX responses using real-world data, providing assistance in counselling patients. We collected 131 RNA-sequenced metastatic biopsies and applied a network-based meta-analysis using published PDAC classifiers. Subsequent survival analysis was performed using the most suitable classifier. For validation, we developed an immunohistochemistry (IHC) classifier using GATA6 and keratin-17 (KRT17), and applied it to 86 formalin-fixed paraffin-embedded samples of advanced PDAC. Lastly, GATA6 knockdown models were generated in PDAC organoids and cell lines. We showed that the PurIST classifier was the most suitable classifier. With this classifier, classical tumors had longer PFS and OS than basal-like tumors (PFS: 216 vs. 78 days, p = 0.0002; OS: 251 vs. 195 days, p = 0.049). The validation cohort showed a similar trend. Importantly, IHC GATA6low patients had significantly shorter survival with FOLFIRINOX (323 vs. 746 days, p = 0.006), but no difference in non-treated patients (61 vs. 54 days, p = 0.925). This suggests that GATA6 H-score predicts therapy response. GATA6 knockdown models did not lead to increased FOLFIRINOX responsiveness. These data suggest a predictive role for subtyping (transcriptomic and GATA6 IHC), though no direct causal relationship was found between GATA6 expression and chemoresistance. GATA6 immunohistochemistry should be seamlessly added to current diagnostics and integrated into upcoming clinical trials.

Ewing sarcoma among children 5years of age or younger: Is it a different disease?

Children ≤5years of age with Ewing's sarcoma (ES) possibly have a distinct disease biology, data on which are scarce. We evaluated clinical features, outcomes, and prognostic factors of ES among children with age ≤5years. Children with ES registered between 2003 and 2019 were included. Baseline clinical and treatment details were retrieved from medical records. Prognostic factors were identified using multivariable Cox regression. Clinical features and outcomes of children ≤5years were compared with those greater than 5years by chi-square and log-rank tests. Propensity score-matched (PSM) analysis was done to evaluate the impact of age on survival in the metastatic and localized subgroups. Out of the 859 patients, 86 (10%) were ≤5years of age (median age 4years, 60 males [69.8%]). The most common location was the extremities (37.2%), followed by thorax (27.9%) and head and neck (H&N) (22.1%); baseline metastases were seen in 25 patients (29.8%). The median event-free-survival (EFS) and overall survival (OS) were 25.6 and 68.7months, respectively. Metastatic disease predicted inferior OS (hazard ratio [HR]=2.54, p=.018) and EFS (HR=2.47, p=.007], symptom duration ≤3months predicted an inferior OS (HR=2.17, p=.048). Compared to age greater than 5years, younger children had more H&N and less pelvic primaries (p<.001) and lesser baseline metastases (p=.037). PSM analysis did not reveal any significant impact of age on OS in the metastatic (HR=1.59, p=.29) or localized cohort (HR=1.77, p=.09). Children with ES ≤5years of age have a distinct favorable clinical presentation. However, age is not an independent prognostic factor for survival outcomes when adjusted for confounders.

Deep Learning Artificial Intelligence Predicts Homologous Recombination Deficiency and Platinum Response From Histologic Slides.

Cancers with homologous recombination deficiency (HRD) can benefit from platinum salts and poly(ADP-ribose) polymerase inhibitors. Standard diagnostic tests for detecting HRD require molecular profiling, which is not universally available. We trained DeepHRD, a deep learning platform for predicting HRD from hematoxylin and eosin (H&E)-stained histopathological slides, using primary breast (n = 1,008) and ovarian (n = 459) cancers from The Cancer Genome Atlas (TCGA). DeepHRD was compared with four standard HRD molecular tests using breast (n = 349) and ovarian (n = 141) cancers from multiple independent data sets, including platinum-treated clinical cohorts with RECIST progression-free survival (PFS), complete response (CR), and overall survival (OS) endpoints. DeepHRD predicted HRD from held-out H&E-stained breast cancer slides in TCGA with an AUC of 0.81 (95% CI, 0.77 to 0.85). This performance was confirmed in two independent primary breast cancer cohorts (AUC, 0.76 [95% CI, 0.71 to 0.82]). In an external platinum-treated metastatic breast cancer cohort, samples predicted as HRD had higher complete CR (AUC, 0.76 [95% CI, 0.54 to 0.93]) with 3.7-fold increase in median PFS (14.4 v 3.9 months; P = .0019) and hazard ratio (HR) of 0.45 (P = .0047). There were no significant differences in nonplatinum treatment outcome by predicted HRD status in three breast cancer cohorts, including CR (AUC, 0.39) and PFS (HR, 0.98, P = .95) in taxane-treated metastatic breast cancer. Through transfer learning to high-grade serous ovarian cancer, DeepHRD-predicted HRD samples had better OS after first-line (HR, 0.46; P = .030) and neoadjuvant (HR, 0.49; P = .015) platinum therapy in two cohorts. DeepHRD can predict HRD in breast and ovarian cancers directly from routine H&E slides across multiple external cohorts, slide scanners, and tissue fixation variables. When compared with molecular testing, DeepHRD classified 1.8- to 3.1-fold more patients with HRD, which exhibited better OS in high-grade serous ovarian cancer and platinum-specific PFS in metastatic breast cancer.

Predicting immune checkpoint therapy response in three independent metastatic melanoma cohorts.

While Immune checkpoint inhibition (ICI) therapy shows significant efficacy in metastatic melanoma, only about 50% respond, lacking reliable predictive methods. We introduce a panel of six proteins aimed at predicting response to ICI therapy. Evaluating previously reported proteins in two untreated melanoma cohorts, we used a published predictive model (EaSIeR score) to identify potential proteins distinguishing responders and non-responders. Six proteins initially identified in the ICI cohort correlated with predicted response in the untreated cohort. Additionally, three proteins correlated with patient survival, both at the protein, and at the transcript levels, in an independent immunotherapy treated cohort. Our study identifies predictive biomarkers across three melanoma cohorts, suggesting their use in therapeutic decision-making.

Importance of Adequate Surgical Local Control in Fusion-Negative Para-Testicular Rhabdomyosarcoma: Data From the Cooperative Weichteilsarkom Studiengruppe Trials (CWS-96 and CWS-2002P) and the European Soft Tissue Sarcoma Registry (SoTiSaR)

BackgroundThis study aimed to assess the impact that the quality of primary and subsequent surgeries has on the survival of patients with para-testicular rhabdomyosarcoma (PTRMS).MethodsPatients with localized (IRS I–III) and metastatic (IRS IV) PTRMS were enrolled in the two Cooperative Weichteilsarkom Studiengruppe (CWS) trials (CWS-96, CWS-2002P) and the Soft Tissue Sarcoma Registry (SoTiSaR).ResultsAmong 196 patients (median age, 8.4 years), 106 (54.1%) had primary complete resection. Image-defined lymph node (LN) disease was detected in 21 (11.5%) patients in the localized cohort and 12 (92.3%) patients in the metastatic cohort. The 5-year event-free survival (EFS) and overall survival (OS) were respectively 87.3% and 94.0% for the patients with localized PTRMS and 46.2% and 42.2% for the patients with metastatic PTRMS. Protocol violations during the primary surgery (PV-PS) were observed in 70 (42%) of the IRS I–III patients. This resulted in higher rates of R1/R2 resections (n = 53 [76%] vs n = 20 [21%]; p < 0.001) with a need for pretreatment re-excision (PRE) (n = 50 [83%] vs n = 10 [17%]; p < 0.001) compared with the patients undergoing correct primary surgery. Protocol violations during PRE occurred for 13 (20%) patients. Although PV-PS did not influence the 5-year EFS or OS in the localized PTRMS cohort, the unadjusted log-rank test showed that R status after PRE is a prognostic factor for 5-year OS (R1 vs R0 [81.8% vs 97.6%]; p = 0.02).ConclusionsThe quality of surgical local control in PTRMS is unsatisfactory. Emphasis should be placed on evaluating the resection status after PRE in further clinical trials.

Serum albumin and derived neutrophil-to-lymphocyte ratio are potential predictive biomarkers for immune checkpoint inhibitors in small cell lung cancer.

Immune checkpoint inhibitors (ICIs) have reshaped the treatment landscape of small cell lung cancer (SCLC), but only a minority of patients benefit from this therapy. Therefore, it is critical to identify potential risk factors that could predict the efficacy of ICI treatment in SCLC patients and identify patient subgroups who may benefit the most from ICI therapy. Our study included a total of 183 SCLC patients who had received at least one dose of ICI treatment. We utilized both logistic regression and Cox proportional hazard regression to evaluate whether various patient clinical factors and serum biomarkers could serve as predictors of patient response to treatment and overall survival (OS) during ICI therapy. Logistic regression showed that patients with a history of surgery (p=0.003, OR 9.06, 95% CI: (2.17, 37.9)) and no metastasis (p=0.008, OR 7.82, 95% CI: (1.73, 35.4)) exhibited a higher odds of response to ICI treatment. Cox regression analyses demonstrated that pretreatment blood albumin (p=0.003, HR 1.72, 95% CI: (1.21, 2.45)) and derived neutrophil to lymphocyte ratio (dNLR) (p=0.003, HR 1.71, 95% CI: (1.20-2.44)) were independent predictors for OS in SCLC patients. By establishing a pre-treatment prognostic scoring system based on baseline albumin and dNLR, we found that patients with high albumin and low dNLR exhibited a significantly better prognosis than those with low albumin and high dNLR in both the full (P<.0001, HR 0.33, 95% CI: 0.20-0.55) and the metastatic cohort (P<.0001, HR 0.28, 95% CI: 0.15-0.51). The better prognostic group also had younger age, higher BMI and lower systemic inflammatory biomarker values than the unfavorable group (P<.0001). Our data reveals the significant role of metastasis status and treatment history in predicting the initial response of SCLC patients to ICI treatment. However, baseline serum albumin and dNLR provide a more precise prognostic prediction for patient OS. The scoring system based on albumin and dNLR enhances the ability to stratify patient prognosis and holds the potential to guide clinical decision-making for SCLC patients undergoing ICI therapy.

A digital pathology AI model to predict immune-oncology biomarker status and pembrolizumab response in a real-world cohort of patients with colorectal and breast cancer.

e13617 Background: Deep learning (DL) algorithms have garnered significant attention for prediction of biomarker status in digitized tissue slides. Here, we trained and validated a digital pathology algorithm to predict microsatellite instability (MSI)/mismatch repair deficiency (MMRd) in colorectal cancer (CRC) and PD-L1 status in breast cancer (BC) using a large real-world patient cohort. Methods: H&amp;E and immunohistochemistry (IHC) slides of CRC and BC from Caris Life Sciences (Phoenix, AZ) with known biomarker status were digitally scanned (CRC: N=27,494, 6.6% MSI-high by next-generation sequencing [NGS]; N=25,788, 6.4% MMRd by IHC; BC: N=16,069, 15.8% PD-L1+ by IHC). A transformer-based DL model (Wagner, Sophia J., et al., 2023) was trained to predict biomarker status, with 5-fold cross-validation. Accuracy, F1 score, area under the curve (AUC), and other metrics were calculated comparing the model to NGS/IHC “truth”. Risk stratification was performed on holdout datasets of pembrolizumab-treated CRC (N=422-454) and triple negative breast cancer (TNBC; N=513) pts. Post-treatment overall survival (OS) was calculated from start of pembrolizumab to last contact, per insurance claims data. Hazard ratios (HR) and 95% confidence intervals (CI) were calculated by Cox-Proportional hazards and compared between model and “truth”. Results: When applied to holdout datasets for biomarker prediction, the validated model achieved AUC of 0.78-0.95. In CRC and BC, performance was better among primary specimens than metastatic. For MSI-H/MMRd risk stratification in pembrolizumab-treated CRC, HR for OS were comparable between model and “truth” for primary and metastatic cohorts. When applied to the TNBC holdout dataset, the model performed better than “truth” for PD-L1 risk stratification in pembrolizumab-treated pts. Conclusions: A digital pathology DL model predicts biomarker status with high accuracy and is non-inferior to NGS/IHC for risk stratification of pembrolizumab-treated CRC and TNBC pts. These results support further investigation of AI algorithms developed from large datasets as possible rapid screening tools for biomarker detection in molecular testing programs. [Table: see text]

Prognostic and predictive value of ultrasensitive ctDNA monitoring in a metastatic pan-cancer cohort treated with immune checkpoint inhibitors in the context of phase 1 clinical trials.

2510 Background: Determining which patients will achieve clinical benefit from immune checkpoint inhibition (ICI) therapy remains an open question. Liquid biopsy tests to assess baseline and early dynamics of circulating tumor DNA (ctDNA) may allow clinicians to track response more granularly and predict ICI response or resistance prior to imaging. However, lack of sensitivity may hinder accurate detection of low ctDNA levels in tumors with low shedding rates or during substantial drops and clearance in response. Methods: This study represents a cohort of 175 patients with refractory metastatic tumors from 18 different cancer types, who received 1-3 successive lines of ICI treatment in the context of phase-1 clinical trials. Thus far, 609 plasma samples from 90 stage-IV cancer patients receiving immune checkpoint inhibitor (ICI) treatment have been processed. ctDNA was profiled using the NeXT Personal assay, a liquid biopsy platform that leverages whole-genome sequencing of tumor and normal samples to create custom, patient-specific panels that include up to 1,800 somatic variants. This enables the detection of molecular residual disease (MRD) down to a detection threshold of 1 part per million (PPM) of ctDNA. Results: NeXT Personal assay detected positive levels of ctDNA in 99% (81/82) of plasma baseline samples, with a wide dynamic range, extending from 4.2 PPM (~0.00042% TF) to ~640,000 PPM (~64% TF) (median limit of detection = 2 PPM, 0.0002% TF). Lower ctDNA values at baseline were correlated with increased duration of PFS (log-rank p=0.017, HR=0.57, 95% CI 0.36-0.91) and extended OS (log-rank p=0.002, HR=0.46, 95% CI 0.28-0.75). Early reduction in ctDNA level from baseline to treatment cycle 3 was associated with significant increases in PFS (log-rank p=0.001, HR=0.36, 95% CI 0.19-0.67) and OS (log-rank p=0.015, HR=0.44, 95% CI 0.22-0.87), representing a &gt;3-fold increase in both median PFS and OS. ctDNA clearance resulted in significant improvement in both PFS and OS (PFS: log-rank p=0.002, HR=0.24, 95% CI 0.09-0.62; OS: log-rank p=0.01, HR=0.29, 95% CI 0.1-0.8). All plasma timepoints from periods of durable complete response (CR) assessed via RECIST 1.1 were ctDNA-negative, with a molecular clearance lead time of 277 days over radiographically confirmed CR. Conclusions: We demonstrate that early ctDNA dynamics are predictive of long-term ICI response in the advanced, pan-cancer ECT setting. Even in this refractory advanced cancer cohort, an ultra-sensitive assay was required for accurate MRD status determination, with low ctDNA detections down to 4.2 PPM that might otherwise have been missed. Taken together, these findings suggest a high sensitivity ctDNA assay is crucial for accurate monitoring of ICI response, providing information for more accurate patient management.

Impact of circulating tumor DNA genomic mutations and circulating tumor cells biomarker duo on clinical concordance in localized, progressive, and metastatic disease.

e14546 Background: Genomic mutations have been identified from circulating tumor DNA (ctDNA) that correlates positively with clinical disease status. EGFR and intracellular cell progression/proliferation pathway-BRCA1/2 and TP53 genes drive high ctDNA load in progressive cancer patients. Circulating tumor cells (CTC) indicate Cellular Residual Disease (CRD). ctDNA and CTC as dual biomarkers offer prediction of tumor progression and metastasis implicative for early detection and treatment modifications. Methods: Retrospectively in 96 cancer patients (lung, colon-rectal, breast, stomach, etc.) who recently underwent treatment were investigated for presence of CTCs and genomic mutations from ctDNA using OncoMonitor Test. Libraries were prepared using a hybridization-capture method covering 1000 targets with mean sequencing depth 5000X on Illumina Nextseq 2000. Test detected genomic alterations from single nucleotide variation (SNVs), small insertions and deletions (INDELs), copy number variations (CNVs), and translocations (fusions) using a 96 gene panel. CTCs were isolated using the OncoDiscover platform, with CK18+, PD-L1+, CD45- in1.5 ml of blood. Results: In 96 pan-cancer patients, 15.6% patients (n=15) were identified with localized progressive disease with no metastasis from radiological findings, of which 60% (n=9) patients showed at least 1 genomic finding from ctDNA.12.5% (n=12) patients were identified as metastatic from their radiological findings of which 58.3% (n=7) showed presence of at least 1 CTC. 33.3% (n=4) patients showed 2 CTCs and 5 patients had no CTCs. In addition, these metastatic patients showed the presence of ctDNA load in 66.6% (n=8) patients with at least 1 genomic finding. In metastatic disease cohort, CTC enumeration showed concordance of 58.3% (n=7) with metastatic radiological findings and genomic findings from ctDNA showed concordance in 66.6% (n=8) patients with metastatic radiological findings. 23.9% (n=23) patients from the cohort were radiological identified with stable/treatment responsive disease of which 73.9% (n=17) patients were not detected with genomic mutations from ctDNA and 26.0% (n=6) patients were CTC -ve, concordant with radiological findings. 26.0% (n=6) patients had at least 1 genomic finding contributing to discordance with the radiological findings. Genomic findings from duo offered concordance with radiological findings in 26.6% (n=4) patients with progressive disease, 41.6% (n=5) in metastatic disease, and 17.3% (n=4) in patients with stable/treatment responsive disease. Conclusions: Patients with progressive and metastatic disease from radiological findings showed concordance with the dual ctDNA and CTC biomarkers. Concordance of ctDNA in progressive disease and CTC in metastatic disease is indicative of individual significance.

Characterization of mutational signatures demonstrating adaptive mutability post anti-EGFR therapy in a real-world metastatic colorectal cancer cohort.

3545 Background: Clinical benefit from anti-EGFR therapy (EGFRi) for RAS/RAF WT metastatic colorectal cancer (mCRC) is limited by secondary mutations in mitogen-activated protein kinases. The source of these new clones has been debated. In contrast to the outgrowth of pre-existing rare subclones, a new model, termed adaptive mutability, proposes the transient loss of DNA repair genes and concurrent induction of error-prone polymerase repair mechanisms (Russo et al Science, ’19). However, clinical evidence for this effect in a large patient cohort is lacking. Using longitudinal circulating tumor DNA (ctDNA) in a real-world cohort, we sought to explore mutational signatures and assess the presence of adaptive mutability in mCRC patients after EGFRi treatment. Methods: 288 patients from Guardant Health’s GuardantINFORM database with mCRC who received EGFRi and underwent longitudinal ctDNA NGS testing by Guardant360 (Redwood City, CA) between December 2014 and March 2023 were included. We extracted de novo single-nucleotide variant mutational signatures from the somatic ctDNA mutations per-cohort level, comparing pre- to post-treatment mutational profiles. Extracted mutational signatures were compared against COSMIC catalogue. Results: Of the 288 patients identified, 99.7% (287/288) were MSS/MSI-L prior to treatment. Pre-treatment, patients had a mean and median of 3 reportable variants per sample, with 30.2% (87/288) samples with &gt;5 variants. Post-treatment, patients had a mean of 5 and a median of 4 reportable variants, with 64.6% (186/288) of patients with &gt;5 variants. Overall mean shift in reportable variants between pre- and post-EGFRi was 5 variants, with a median of 4 changes. In comparing pre- and post-EGFRi cohorts for new mutations, three mutational signatures emerged: SBS17b, SBS15, and SBS3. SBS15 is associated with mismatch repair (MMR) deficiency and classically seen in MSI-H tumors, though notably this cohort was overwhelmingly MSS. SBS15 has been associated with polymerase epsilon exonuclease (POLE) defects and likely reflects repair by alternate error-prone polymerases such as Polι, Polλ, and Polκ. SBS3 has been associated with homologous recombination (HR) deficiency. SBS17b has been associated with exposure to 5-FU based chemotherapy in CRC patients, which was co-administered in many of the EGFRi treated patients. Conclusions: New mutations arising with EGFR inhibition demonstrate strong evidence for adaptive mutability, showcasing loss of mismatch repair and HR fidelity, and reliance on error-prone polymerases. This is the first large cohort to indirectly demonstrate evidence for this genomic mechanism underlying secondary acquired resistance. Further validation of the adaptive mutability signatures may support therapeutic strategies leveraging this vulnerability to extend benefit from targeted therapies.

Abstract PO5-14-10: Dynamics and prognostic value of subtype specific TROP2 expression in matched pair samples of primary (PBC) and metastatic breast cancer (MBC) tissues

Abstract Background: The genotype and phenotype of breast cancer may change during disease progression. This is of particular interest in the advent of targeted treatment adressing extracellular targets such as TROP2, which serves as chemotherapy carrier rather than being required for tumor cell survival. In addition, technical issues may affect biomarker assessment when comparing primary breast cancer (PBC) tissues with biopsies of metastatic breast cancer (MBC) tissues at distant sites. Here we analyzed TROP2 expression on mRNA level by RT-qPCR in primary tumor and metastatic tissues on basis of molecular subtyping to determine subtype specificity and target gene stability/dynamics. Methods: The tumor bank of a single institution was screened for paraffin-embedded pairs of PBC and MBC tissue samples and a total of 34 matched PBC and MBC pairs were retrieved. RNA was extracted using a bead-based extraction method (RNXtract® IVD kits, Cerca Biotech). Multiplex RT-qPCR was performed using TaqMan® based primer probe sets for ESR1/PGR/ERBB2 and MKI67 (MammaTyper® IVD kits, Cerca Biotech) as well as TROP2 (TargetTyper RUO kits, STRATIFYER Molecular Pathology GmbH). Correlation analysis, Scatter Plots, Partitioning tests and Kaplan Meier analysis were performed using the SAS JMP® 9.0.0 software. Results: Samples from 34 patients with MBC and PBC were available. Positivity of PBC RT-qPCR for ESR1, PGR and HER2 was 78%, 70% and 3%. The overall agreement between matched primary and metastatic lesions 90%, 70% and 100% for RT-qPCR of ESR1, PGR and HER2. Median expression of TROP2 was 2 fold lower in metastatic tissues compared to matched primary tumor tissues, while the lower quartile of mRNA expression dropped 4 fold. In primary tumor tissues TROP2 expression was significantly associated with PGR and HER2 expression (Spearman r=0.5284 p=0.0013 and r=0.3950 p=0.0208; respectively), while no significant association was found for ESR1 and MKI67. In contrast, no significant association with neither PGR nor HER2 was found (Spearman r=0.0461 p=0.8041 and r=0.0461 p=0.7955; respectively), while TROP2 trended to be associated with MKI67 in metastatic lesions (Spearman r=0.3247 p=0.0610). In line with the strong positive association of TROP2 with PGR in primary tumor tissues, elevated TROP2 levels were associated with substantially longer median distant metastasis free survival of 72 months, while TROP2 negative tumors exhibited a median DDFS of only 24 months (p=0,0091). In contrast, no prognostic value for TROP2 mRNA level could be determined from metastatic lesions and determining the time from initial metastasis until death. Conclusion: In this selected matched pair, metastatic cohort, TROP2 mRNA in primary tumors is strongly associated with luminal type of breast cancer expressing higher levels of PGR mRNA, while no such correlation was found in matched metastatic tissues. Moreover, TROP2 is significantly downregulated in metastatic lesions. As TROP2 is expressed in luminal tumors, it may serve as a valuable target for luminal tumors of higher progression risk. However, TROP2 expression is unstable and requires careful decision making on actual biopsies rather than archival tissue samples. Citation Format: Thomas Deutsch, Ralph Wirtz, Stefan Stefanovic, Andreas Hartkopf, Hans-Peter Sinn, Andreas Schneeweiss, Markus Wallwiener. Dynamics and prognostic value of subtype specific TROP2 expression in matched pair samples of primary (PBC) and metastatic breast cancer (MBC) tissues [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-14-10.

Abstract PO5-25-04: Predictive value of neutrophil-to-lymphocyte and platelet-to-lymphocyte ratios in patients with triple negative breast cancer treated with pembrolizumab

Abstract Background: Immune checkpoint inhibitors (ICIs) offer new treatment possibilities for women with triple-negative breast cancer (TNBC) – one of the most challenging breast cancer subtypes. The PD-1 inhibitor pembrolizumab (pembro; Keytruda®) is approved in metastatic TNBC (mTNBC) patients with PD-L1(+) tumors, and for neoadjuvant treatment (NAT) in stage II/III TNBC [1, 2]. Residual cancer burden (RCB) after NAT is highly prognostic, with pathologic complete response (pCR, RCB 0) anticipating long-term survival [3]. In mTNBC, pembro plus chemotherapy in the 1st-line improves progression free survival (PFS), but durable responses are rare. Optimizing ICI use in TNBC thus remains an unmet need, and defining easily assessable markers of response is crucial. Neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are peripheral blood surrogates of tumor inflammation and have prognostic and predictive value in TNBC [4-8]. Elevated NLR (≥ 5) and PLR (≥ 200) correlate with worse outcomes upon ICIs in melanoma and non-small-cell lung cancer [9, 11-14]; however, this has not been studied in breast cancer [9, 10]. We evaluated the relationship of baseline NLR and PLR with pembro responses in TNBC patients. Methods: We retrospectively reviewed data from TNBC patients who completed pembro between 10/2/20 - 6/1/23 at Weill Cornell. Patients on NAT who did not complete treatment were excluded. RCB score (pCR/0, 1, 2, 3) was calculated from surgical resection pathology reports using the MD Anderson RCB Calculator [15, 16]. Baseline laboratory data were obtained from clinical records. Associations between NLR and PLR with RCB levels were examined using the non-parametric Kruskal-Wallis test (if &amp;gt;2 levels), the Wilcoxon rank sum test (if 2 levels), or the Spearman’s rank correlation. NLR and PLR were also correlated with PFS (measured from pembro start date to date of progression) in metastatic patients. PFS data for metastatic patients without interval imaging since pembro initiation were censored at the date of data analysis, and PFS was not calculated for patients who received only 1 cycle of pembro. Results: We identified 63 eligible patients: 24 were excluded due to lack of TNBC diagnosis (n=20), or because they only received adjuvant pembro (n=4). Of the 39 remaining patients, 5 did not complete NAT and 2 had missing data, leaving 32 evaluable patients (17 in the NAT cohort and 15 in the mTNBC cohort). Overall, the median age was 51 years, and 16% were Hispanic, 11% Asian, 57% non-Hispanic, 24% Black, and 65% Non-Black. Neoadjuvant cohort: The pCR rate was 30%. Patients with both NLR ≥ 5 and PLR ≥ 200, had a pCR rate of 0%; in patients with NLR &amp;lt; 5 or PLR &amp;lt; 200, pCR rate was 43%. Median NLR in pCR vs. non-pCR groups was 1.91 [IQR: 1.72- 2.73] vs. 2.44 [IQR: 1.97- 5.24] (p=0.3), with trends towards significance when NLR was compared between RCB levels &amp;gt;1 (2.67; IQR: 2.05, 6.49) vs. RCB levels ≤1 (1.91; IQR: 1.63, 2.58) (p=0.14). Mean PLR was higher in patients with RCB 2-3 (409) compared to those with pCR or RCB 1 (167) (p=0.146). Metastatic cohort: The overall mean PFS was 7.8 months. Visceral metastases were seen in 80% of patients (17% liver, 33% brain). In patients with brain mets, baseline NLR and PLR were higher than in the overall cohort (NLR, 4.86 vs. 2.78; PLR, 429 vs. 186). Conclusions: Our study is the first to evaluate NLR and PLR as response biomarkers in TNBC patients receiving pembro and is the first report of our real-world data of TNBC patients on pembro. In our neoadjuvant cohort, higher baseline NLR and PLR correlated with higher RCB levels, with a trend towards statistical significance. Further investigation and correlation of NLR and PLR with tumor microenvironment features will help to clarify these relationships. Citation Format: Ashley Schreier, Roberta Zappasodi, Inna Serganova, Laura Munoz Arcos, Xi Kathy Zhou, Massimo Cristofanilli, Eleni Andreopolu. Predictive value of neutrophil-to-lymphocyte and platelet-to-lymphocyte ratios in patients with triple negative breast cancer treated with pembrolizumab [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-25-04.

ProstaMine: a bioinformatics tool for identifying subtype-specific co-alterations associated with aggressiveness in prostate cancer.

Prostate cancer is a leading cause of cancer-related deaths among men, marked by heterogeneous clinical and molecular characteristics. The complexity of the molecular landscape necessitates tools for identifying multi-gene co-alteration patterns that are associated with aggressive disease. The identification of such gene sets will allow for deeper characterization of the processes underlying prostate cancer progression and potentially lead to novel strategies for treatment. We developed ProstaMine to systematically identify co-alterations associated with aggressiveness in prostate cancer molecular subtypes defined by high-fidelity alterations in primary prostate cancer. ProstaMine integrates genomic, transcriptomic, and clinical data from five primary and one metastatic prostate cancer cohorts to prioritize co-alterations enriched in metastatic disease and associated with disease progression. Integrated analysis of primary tumors defined a set of 17 prostate cancer alterations associated with aggressive characteristics. We applied ProstaMine to NKX3-1-loss and RB1-loss tumors and identified subtype-specific co-alterations associated with metastasis and biochemical relapse in these molecular subtypes. In NKX3-1-loss prostate cancer, ProstaMine identified novel subtype-specific co-alterations known to regulate prostate cancer signaling pathways including MAPK, NF-kB, p53, PI3K, and Sonic hedgehog. In RB1-loss prostate cancer, ProstaMine identified novel subtype-specific co-alterations involved in p53, STAT6, and MHC class I antigen presentation. Co-alterations impacting autophagy were noted in both molecular subtypes. ProstaMine is a method to systematically identify novel subtype-specific co-alterations associated with aggressive characteristics in prostate cancer. The results from ProstaMine provide insights into potential subtype-specific mechanisms of prostate cancer progression which can be formed into testable experimental hypotheses. ProstaMine is publicly available at: https://bioinformatics.cuanschutz.edu/prostamine.

Nivolumab with or without ipilimumab in patients with recurrent or metastatic cervical cancer (CheckMate 358): a phase 1–2, open-label, multicohort trial

In preliminary findings from the recurrent or metastatic cervical cancer cohort of CheckMate 358, nivolumab showed durable anti-tumour responses, and the combination of nivolumab plus ipilimumab showed promising clinical activity. Here, we report long-term outcomes from this cohort. CheckMate 358 was a phase 1-2, open-label, multicohort trial. The metastatic cervical cancer cohort enrolled patients from 30 hospitals and cancer centres across ten countries. Female patients aged 18 years or older with a histologically confirmed diagnosis of squamous cell carcinoma of the cervix with recurrent or metastatic disease, an Eastern Cooperative Oncology Group performance status of 0 or 1, and up to two previous systemic therapies were enrolled into the nivolumab 240 mg every 2 weeks group, the randomised groups (nivolumab 3 mg/kg every 2 weeks plus ipilimumab 1 mg/kg every 6 weeks [NIVO3 plus IPI1] or nivolumab 1 mg/kg every 3 weeks plus ipilimumab 3 mg/kg every 3 weeks for four cycles then nivolumab 240 mg every 2 weeks [NIVO1 plus IPI3]), or the NIVO1 plus IPI3 expansion group. All doses were given intravenously. Patients were randomly assigned (1:1) to NIVO3 plus IPI1 or NIVO1 plus IPI3 via an interactive voice response system. Treatment continued until disease progression, unacceptable toxicity, or consent withdrawal, or for up to 24 months. The primary endpoint was investigator-assessed objective response rate. Anti-tumour activity and safety were analysed in all treated patients. This study is registered with ClinicalTrials.gov (NCT02488759) and is now completed. Between October, 2015, and March, 2020, 193 patients were recruited in the recurrent or metastatic cervical cancer cohort of CheckMate 358, of whom 176 were treated. 19 patients received nivolumab monotherapy, 45 received NIVO3 plus IPI1, and 112 received NIVO1 plus IPI3 (45 in the randomised group and 67 in the expansion group). Median follow-up times were 19·9 months (IQR 8·2-44·8) with nivolumab, 12·6 months (7·8-37·1) with NIVO3 plus IPI1, and 16·7 months (7·2-27·5) with pooled NIVO1 plus IPI3. Objective response rates were 26% (95% CI 9-51; five of 19 patients) with nivolumab, 31% (18-47; 14 of 45 patients) with NIVO3 plus IPI1, 40% (26-56; 18 of 45 patients) with randomised NIVO1 plus IPI3, and 38% (29-48; 43 of 112 patients) with pooled NIVO1 plus IPI3. The most common grade 3-4 treatment-related adverse events were diarrhoea, hepatic cytolysis, hyponatraemia, pneumonitis, and syncope (one [5%] patient each; nivolumab group), diarrhoea, increased gamma-glutamyl transferase, increased lipase, and vomiting (two [4%] patients each; NIVO3 plus IPI1 group), and increased lipase (nine [8%] patients) and anaemia (seven [6%] patients; pooled NIVO1 plus IPI3 group). Serious treatment-related adverse events were reported in three (16%) patients in the nivolumab group, 12 (27%) patients in the NIVO3 plus IPI1 group, and 47 (42%) patients in the pooled NIVO1 plus IPI3 group. There was one treatment-related death due to immune-mediated colitis in the NIVO1 plus IPI3 group. Nivolumab monotherapy and nivolumab plus ipilimumab combination therapy showed promise in the CheckMate 358 study as potential treatment options for recurrent or metastatic cervical cancer. Future randomised controlled trials of nivolumab plus ipilimumab or other dual immunotherapy regimens are warranted to confirm treatment benefit in this patient population. Bristol Myers Squibb and Ono Pharmaceutical.