Matched Tumor Tissue Research Articles

Peripheral blood-derived immune cell counts as prognostic indicators and their relationship with DNA methylation subclasses in glioblastoma patients.

Glioblastomas are known for their immunosuppressive tumor microenvironment, which may explain the failure of most clinical trials in the past decade. Recent studies have emphasized the significance of stratifying glioblastoma patients to predict better therapeutic responses and survival outcomes. This study aims to investigate the prognostic relevance of peripheral immune cell counts sampled prior to surgery, with a special focus on methylation-based subclassification. Peripheral blood was sampled in patients with newly diagnosed (n = 176) and recurrent (n = 41) glioblastoma at the time of surgery and analyzed for neutrophils, monocytes, leukocytes, platelets, neutrophil-lymphocyte ratio, lymphocyte-monocyte ratio, and platelet-lymphocyte ratio. Peripheral immune cell counts were correlated with patients' survival after combined radiochemotherapy. In addition, 850 k genome-wide DNA methylation was assessed on tissue for defining tumor subclasses and performing cell-type deconvolution. In newly diagnosed glioblastoma, patients with higher peripheral neutrophil counts had an unfavorable overall survival (OS) (p = 0.01, median overall-survival (mOS) 17.0 vs. 10.0 months). At the time of first recurrence, a significant decrease of peripheral immune cell counts was observed, and elevated monocyte (p = 0.03), neutrophil (p = 0.04), and platelet (p = 0.01) counts were associated with poorer survival outcomes. DNA methylation subclass-stratified analysis revealed a significant survival influence of neutrophils (p = 0.007) and lymphocytes (p = 0.04) in the mesenchymal (MES) subclass. Integrating deconvolution of matched tumor tissue showed that platelets and monocytes were correlated with a more differentiated, tumor-progressive cell state, and peripheral immune cell counts were most accurately reflected in tissue of the MES subclass. This study illustrates a restricted prognostic significance of peripheral immune cell counts in newly diagnosed glioblastoma and a constrained representation in matched tumor tissue, but it demonstrates a more pertinent situation at the time of recurrence and after DNA methylation-based stratification.

Prognostic value of circulating tumor DNA for progression-free survival in patients with locally advanced dMMR/MSI-H colorectal cancer managed without surgery.

256 Background: Immunotherapy has shown the ability to induce a high rate of pathologic and clinical complete response in patients with deficient mismatch repair (dMMR)/microsatellite instability-high (MSI-H) colorectal cancer (CRC). The role of circulating tumor DNA (ctDNA) as a prognostic biomarker for survival in patients who receive non-operative management (NOM) is unknown. Among patients enrolled in a phase II trial (NCT04082572) that evaluated the efficacy of pembrolizumab in patients with locally advanced dMMR/MSI-H solid tumors, we evaluated the impact of ctDNA on progression-free survival (PFS) among 12 patients with locally advanced dMMR/MSI-H CRC who received NOM. Methods: ctDNA testing was performed in the CLIA-certified laboratory at MD Anderson using a 70-gene liquid biopsy panel (LBP-70), which used digital sequencing of cell-free DNA. Formalin-fixed paraffin-embedded tumor samples and germline peripheral blood mononuclear cells were profiled using next-generation sequencing. Mutations in ctDNA were considered tumor-specific if they were confirmed with matched tumor tissue profiling. The lower limit of detection of the LBP-70 assay was a mutational variant allele frequency of <0.3%. "ctDNA clearance" and “ctDNA(-)” status were defined as the absence of any detectable tumor-specific mutations in ctDNA. Two-year progression-free survival (PFS) was estimated using Kaplan-Meier techniques and compared with log-rank tests. Results: The median follow-up between the first cycle of pembrolizumab and last radiographic assessment was approximately three years (36.7 mo; range (range 1.2 – 51.0 mo). Forty-nine LBP-70 assays were performed among the 12 patients over the course of treatment with pembrolizumab. The median number of cycles was 16 (range 1 – 16 cycles). Six patients were ctDNA(-) prior to pembrolizumab, all of whom remained ctDNA(-) after. None of these six patients experienced disease progression (PD) at their last follow-up. The other six patients were ctDNA(+) prior to pembrolizumab (median baseline VAF 0.4%, range 0.3%–4.0%). Of these six patients, three experienced ctDNA clearance while receiving pembrolizumab. None of the three patients who cleared ctDNA experienced PD as of their last follow-up. Of the three patients who did not clear ctDNA, two experienced PD in their primary tumor (at two and six months after their first cycle, respectively), while the third patient remains without PD at their last follow-up. The two-year PFS rate was 100% among the nine patients who were ctDNA(-) after pembrolizumab compared to 33% among the three patients who were ctDNA(+) after pembrolizumab (p = 0.03). Conclusions: ctDNA may be a valuable tool for assessing treatment response and improving the ability to tailor organ-sparing, curative strategies to patients with locally advanced dMMR/MSI-H CRC.

P-Glycoprotein Drives Glioblastoma Survival and Chemotherapy Resistance: Potential as a Promising Liquid Biopsy Biomarker.

Drug resistance is a major challenge in cancer therapy, and the expression of efflux pumps such as P-glycoprotein (P-gp, ABCB1) often correlates with poor prognosis in various tumors, including glioblastoma (GB). Considering that different roles for these proteins have been established in the biology of various tumors, this study aimed to investigate the functions of P-gp in GB-derived cells by evaluating its survival, migratory, and apoptosis-regulating capabilities, as well as its potential as a liquid biopsy biomarker. P-gp expression was diminished via siRNA to determine its exact role in GB biology. The P-gp mRNA levels were evaluated by using quantitative real-time RT-PCR. With respect to liquid biopsy, circulating cell-free RNA was extracted from plasma belonging to patients diagnosed with GB, and P-gp levels were compared with matching tumor tissues using digital PCR. The results showed that P-gp silencing significantly decreased viability, increased apoptosis, and enhanced chemotherapy sensitivity in GB cells, although it did not affect migratory patterns. Finally, P-gp expression levels in circulating cell-free RNA from patients with GB matched tumor tissue, whereas healthy volunteers seemed to bear no circulating P-gp. Taken together, the results indicate that P-gp affects GB tumor biology beyond its known role in drug resistance and could integrate a broader molecular signature for future diagnosis via liquid biopsy.

Abstract B011: Circulating tumor DNA profiling in colorectal cancer to detect guideline-based targeted mutations at a Quebec health care center

Abstract Liquid biopsy is an emerging tool in oncology, providing minimally invasive detection of tumor- specific DNA in body fluids, known as circulating tumor DNA (ctDNA). Colorectal cancer (CRC) has shown a high rate of shedding of ctDNA, making it a promising prognostic and possibly predictive biomarker in the personalized management of patients with CRC. Therefore, the half-life of ctDNA in circulation is estimated to be between 16 minutes and several hours, indicating a need for rapid processing. This study aimed to explore the concordance between the mutational profiles in tumor tissue and ctDNA from plasma obtained using EDTA tubes as well as the correlation between ctDNA and disease stage, to evaluate the potential of implementing liquid biopsy testing in CRC cases, following biobank standards. In this retrospective cohort, 58 patients with CRC stage T1 to T4 were enrolled at the Research Institute McGill University Health Centre (RI-MUHC). Tumor tissue was obtained through surgical resection or biopsies of formalin-fixed paraffin-embedded tissue, and blood samples were drawn pre-surgery using EDTA tubes. Cell-free DNA (cfDNA) was extracted from 1-2mL plasma samples using QIAamp Circulating Nucleic Acids. Next-Generation Sequencing using a 52-gene (AmpliSeq for Illumina Focus Panel) was performed to identify the tumor mutations and subsequently droplet digital PCR (ddPCR) was performed to identify the plasma mutations. Among the 58 patients, the mean age was 62 years (range 29-86), and 29 were women. Forty- one patients had left-sided tumor. At least 1 tumor-specific mutation was detected in all tissue tumor samples. Overall, the most frequently identified mutations in this cohort were: BRAF V600E (22.4%), KRAS G12D (12.1%), KRAS G12V and KRAS G13D (8.6%). Cell-free DNA was obtained from 32 patients and showed a mean concentration of 975 ng/mL (range 400- 1,995) for stage T1, 584 ng/mL (range 228-1,300) for stage T2, 1,127 ng/mL (range 249-4,160) for stage T3 and 2,083 ng/mL (range 860-3,680) for stage T4. ddPCR revealed mutation concordance between ctDNA and matched tumor tissue of 28.1%. When tumors were stratified by stage, the concordance was 0% (n=0/3) in patients with T1 tumors, 16.7% (n=1/6) in patients with T2 tumors, 25% (n=5/20) in patients with T3 tumors and 100% (3/3) in patients with T4 tumors. This study showed that ctDNA detection of mutations has excellent concordance in stage T4 tumors, highlighting the potential of ctDNA in advanced stage disease. However, in T1-3 tumor stages the concordance was low, showing the importance of preanalytical steps such as the use of cell-free DNA preservative tubes for sensitive and accurate detection of ctDNA in patients with earlier stage disease. Citation Format: Monyse de Nobrega, Kyle Dickinson, Saba Alsaddah, Alexandra Bartolomucci, Tadhg Ferrier, Anne Mahalia Olivier Mahalia Olivier, Mina Farag, Gertuda Evaristo, Sophie Camilleri-Broet, Andrea Gomez, Thupten Tsering, Lawrence Lee, Pierre Olivier Fiset, Julia V. Burnier. Circulating tumor DNA profiling in colorectal cancer to detect guideline-based targeted mutations at a Quebec health care center [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B011.

Abstract PR014: Robust disease monitoring using CSF liquid biopsies collected from children undergoing cellular therapy for malignant central nervous system tumors

Abstract Background: Central nervous system (CNS) tumors remain the leading cause of cancer-related mortality in children, necessitating more effective treatment options. Chimeric Antigen Receptor T-cells (CAR-T) have emerged as a promising strategy to treat CNS tumors, with B7H3 (CD276) representing an attractive target due to its high expression across a broad range of entities. B7H3-CAR-T therapy is currently being evaluated in a St. Jude Children’s Research Hospital Phase I clinical trial (NCT05835687) for the treatment of relapse/refractory pediatric CNS tumors. Monitoring disease progression after CAR-T infusion by magnetic resonance imaging (MRI) remains challenging, emphasizing the need for more sensitive biomarkers of treatment response. Detection of circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF) liquid biopsies holds tremendous potential for minimal residual disease (MRD) monitoring in the clinical setting. Here, we leverage CSF liquid biopsies for longitudinal disease profiling in pediatric CNS tumor patients receiving B7H3-CAR-T immunotherapy. Methods: CSF samples were collected from Ommaya reservoirs of 9 pediatric patients with relapse/refractory CNS tumors undergoing B7H3-CAR-T therapy. CSF was sampled at study enrollment, and weekly intervals pre- and post-infusion. Cell-free DNA (cfDNA) was extracted from 115 longitudinally collected CSF samples and subjected to enzymatic methylation sequencing (EM-seq). Implementation of a custom computational workflow enabled detection of tumor-derived copy number variations (CNVs), estimation of malignant vs. non-malignant fractions, and molecular classification of tumor entity. Results: Tumor-derived CNVs were detected in 7/9 (78%) CSF samples collected at enrollment, prior to immunotherapy. Liquid biopsy-inferred CNV profiles and entity classifications were highly concordant with matched tumor tissue profiles. Chromosomal alterations that were restricted to CSF profiles indicated clonal evolution. Increased ctDNA burden was repeatedly observed after B7H3-CAR-T infusions, suggesting subclinical antitumor activity. Transient subclonal alterations emerging in response to treatment were also identified in a subset of patients. Conclusions: EM-seq is a feasible method for serial tracking of ctDNA burden in patients receiving cellular immunotherapy. CSF liquid biopsies capture the global landscape of tumor heterogeneity and genetic alterations that arise during therapy, providing a sensitive platform for detecting clinical response and disclosing potential mechanisms of treatment resistance. Citation Format: Anna Kostecka, Kyle S Smith, Katie Han, Hong Lin, Deanna Langfitt, Tara Walhart, Stephen Gottschalk, Giedre Krenciute, Christopher DeRenzo, Kelsey Bertrand, Paul A Northcott. Robust disease monitoring using CSF liquid biopsies collected from children undergoing cellular therapy for malignant central nervous system tumors [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR014.

TMOD-15. TOWARD BRAIN CANCER ORGANOID-INFORMED PRECISION MEDICINE FOR GLIOBLASTOMA

Abstract BACKGROUND Improved preclinical models for glioblastoma are urgently needed to enhance the translation of research to clinical applications. Patient-Derived Tumor Organoids (PDTOs) offer a promising model that can be generated quickly. Here we explored their feasibility. METHODS Primary (n=16) and recurrent (n=2) PDTOs were established using the method described in Jacob et al. Cell. 2020 by dissecting tumours into small fragments, preserving their cytoarchitecture. Histological features of the parent tumour were compared to the matched PDTOs by a neuropathologist. To assess the molecular fidelity, comprehensive whole genome sequencing compared matched tumor tissue, PDTOs, and corresponding normal blood samples (n=11), along with RNA sequencing of matched tumor tissue and PDTOs (n=10). We assessed PDTO responses to regorafenib (n=18) and conventional TMZ (n=9), lomustine (n=9) and 10 Gy of ionizing radiation (IR) (n=6) using the automated imaging system IncuCyte S3® to evaluate whole spheroid brightfield and invasion areas following drug/IR treatment and assess viability. RESULTS We achieved a 100% establishment rate of primary GBMs using same-day procedures and an 80% rate if held under 3 days. Histological features were retained in the PDTO. Molecular overlap was greater than 90%, along with a high concordance in gene expression. PDTOs exhibited notable resistance to temozolomide and lomustine, however, showed a very modest response to IR and a moderate response to regorafenib. IncuCyte S3® analysis revealed discernible changes in whole spheroid brightfield and invasion area for regorafenib-treated PDTOs. Clinically relevant concentrations of regorafenib reduced GBM cell proliferation (Ki67 staining). Beyond this concentration, regorafenib exhibited efficacy in eliminating GBM cells. CONCLUSION PDTOs recapitulate the molecular and histological features of the original tumor and may enable the prediction of individual patient responses to therapies and guide more effective treatment selection. We are now applying our established methodology to assess a new set of promising drug candidates.

BIOM-61. CSF CTDNA ANALYSIS OF PATIENTS WITH DIFFUSE GLIOMAS REVEALS DIAGNOSTIC MOLECULAR ALTERATIONS

Abstract There is a critical need for better strategies to diagnose and monitor patients with diffuse gliomas. Liquid biopsies are less invasive than tissue biopsies and are amenable to serial collection at multiple timepoints. However, analysis of circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF) in patients with diffuse gliomas remains underutilized in clinical practice due to technical challenges and a scarcity of studies demonstrating clinical utility. We evaluated ctDNA in 49 CSF samples from patients with various types of diffuse gliomas with a next generation sequencing (NGS) panel interrogating 613 cancer-related genes. Cell-free DNA concentration obtained from CSF (0.4-5mL) ranged from 0.009 to 60ng/µL. Input DNA concentration ranged from 0.12-30ng. Mutations were detected in 29/49 (59.2%) samples including 22/49 (44.9%) with single nucleotide changes, 14/49 (28.6%) with copy number changes, and 1 fusion (2.0%). The majority of samples without mutations detected (n=20) had suboptimal DNA input (<30ng): 17/20 (85%). We identified diagnostic alterations in CSF including mutations in IDH1 (3/5 IDH-mutant gliomas), TERTp and EGFR amplification (7/34 glioblastomas), H3-3A (4/6 pediatric high-grade gliomas). Some of these mutations, in combination with other clinical parameters, allowed us to identify specific CNS tumor types based on the 2021 WHO classification of CNS tumors, resulting in the reclassification of 2 patients. Matched tumor tissue sequencing results were available for 23/49 (46.9%) patients and the results showed good concordance with CSF ctDNA analysis. In summary, our results suggest that the NGS analysis of CSF-ctDNA can provide clinically relevant information in patients with diffuse gliomas.

Cancer-associated fibroblasts affect breast cancer cell sensitivity to chemotherapeutic agents by regulating NRBP2.

To uncover the role of nuclear receptor-binding protein 2 (NRBP2) in cancer-associated fibroblasts (CAFs), and CAFmediated TAM sensitivity in breast cancer (BC). 10 pairs of matched tumor tissues and adjacent normal tissues were collected and CAFs and normal fibroblasts (NFs) were isolated. CCK-8 as well as colony formation assays showed the effects on cell growth. qPCR and Immunoblot showed the expression of NRBP2 in CAFs. FCM as well as Immunoblot assays exhibited the effects on cell apoptosis. Immunoblot further confirmed the mechanism. CAFs contributed to BC cell growth. In addition, the expression of NRBP2 is downregulated in CAFs. NRBP2 suppressed CAF-induced resistance in BC cells. Further, NRBP2 expression in CAF group increased TAM induced apoptosis. Mechanically, NRBP2 in CAFs inhibited Akt pathway, therefore suppressed resistance in BC cells. CAFs affected BC cell sensitivity to TAM by regulating NRBP2.

Comparing baseline VAF in circulating tumor DNA and tumor tissues predicting prognosis of patients with colorectal cancer liver metastases after curative resection

IntroductionThe prognostic value of baseline variant allele frequency (VAF) in circulating tumor DNA (ctDNA) of colorectal cancer liver metastases (CRLM) patients after curative resection was rarely investigated. MethodsA single-center prospective study was performed to investigate the prognostic impact of baseline VAF in ctDNA and matched tumor tissues of CRLM patients after curative resection between May 2019 and May 2021 by the Illumina NovoSeq 6000 platform. The relationship of the tumor burden score (TBS) and the VAF in ctDNA and matched tumor tissues was evaluated by the Pearson correlation method. The survival curves of recurrence-free survival (RFS) and overall survival (OS) were plotted. Factors associated with RFS were calculated using Cox regression analysis, and an integrated prognostic model using significant baseline variables was proposed. ResultsThere were 121 patients with baseline ctDNA and matched tumor tissues enrolled in the study. A total of 417 mutations spanning 20 genes were identified in baseline tumor tissues of 119/121 (98.3 %) cases. The overall mutations in tumor tissues were completely covered by ctDNA in 52 of 121(43.0 %) patients. Baseline VAF in ctDNA but not in tumor tissues was significantly correlated to TBS of CRLM (R = 0.36, p < 0.001). Significantly longer RFS but not OS was observed in patients with lower VAF in ctDNA compared to those with higher one (p < 0.001 and p = 0.33 respectively). Multivariate Cox regression analysis showed higher VAF in baseline ctDNA was an independent risk factor for RFS. An integrated prognostic model including baseline metastasis location and VAF in ctDNA outperformed the traditional CRS model in predicting RFS. ConclusionBaseline VAF in ctDNA but not in tumor tissues influenced RFS of CRLM patients after curative resection.

Perioperative systemic IL-6 and immune-adipose- metabolism transcription in tumour and tumour adjacent breast cancer.

Surgical resection is the primary treatment approach for patients with breast cancer. Despite optimal multimodal treatment, metastatic recurrence remains a risk. Surgery-mediated systemic inflammation and local tissue inflammation generate an immunosuppressive and wound-healing environment that may accelerate cancer recurrence and metastasis post-operatively. Investigating the impact of surgery on local and systemic inflammation may provide knowledge for improvement of patient prognosis and treatment opportunities. Systemic cytokines were quantified in the blood plasma of patients with breast cancer pre-operatively, early post-operatively, and late post-operatively. Early post-operative levels of IL-6 were significantly elevated in patients who underwent mastectomy compared with wide local excision. Post-operative IL-6 levels correlate with clinicopathological features (age and BMI). The transcriptomes of local matched tumour and normal tumour adjacent (normal) breast tissue, from patients with breast cancer, were analysed by RNA-Seq. Elevated gene expressions of IL6, ADIPOQ, FABP4, LPL, PPARG, and CD36 in normal tissue were associated with worse overall survival of patients with ER-positive breast cancer. In tissue with higher expression of IL6 and ADIPOQ, a higher abundance of M2-like macrophage gene expression was identified. This study revealed perioperative systemic dynamics of inflammatory mediators and identified local immune-adipose-metabolism gene expression in tumour-adjacent tissue associated with pro-tumour function.

Germline variants in patients diagnosed with pediatric soft tissue sarcoma.

While soft tissue sarcomas affect younger patients, few studies have assessed the distribution of underlying pathogenic germline variants. We retrospectively identified all pediatric and young adult patients (0-22 years) at Haukeland University Hospital, Norway (1981-2019), through clinical and pathological records. We identified n = 46 eligible patients. From these 46 patients, adequate material representing normal tissue was available for n = 41 cases (n = 24 diagnosed with rhabdomyosarcoma, 9 with synovial sarcomas, 2 with Ewing sarcomas, and 6 without further classification), with matching tumor tissue for n = 40. Normal tissue samples were analyzed for germline pathogenic variants (PVs) by targeted sequencing of 360 cancer genes. Out of the 41 analyzed cases, we found PVs or likely PVs in 7 (17%). These variants were found in TP53, MUTYH, FANCC, DICER1, FANCA, MYO3A, and MYO5B. Supporting the causality of these PVs, four cases revealed loss of heterozygosity (LOH) of the wild-type allele in the tumor tissue, one patient with a PV in DICER1 had a second somatic variant in DICER1, and a patient with a PV in TP53 had the altered allele amplified in the tumor. For three out of five with available family history, a history of other cancers in relatives was recorded. Among genes with variants of uncertain significance, CHD1L was of particular interest, revealing a stop-gain and a missense variant. A high fraction of young patients with soft tissue sarcoma harbor PVs. Among the genes affected, we substantiate a potential role of MYO5B and propose a potential role for MYO3A.

Targeting AKR1B10 by Drug Repurposing with Epalrestat Overcomes Chemoresistance in Non-Small Cell Lung Cancer Patient-Derived Tumor Organoids.

Systemic treatments given to patients with non-small cell lung cancer (NSCLC) are often ineffective due to drug resistance. In the present study, we investigated patient-derived tumor organoids (PDTO) and matched tumor tissues from surgically treated patients with NSCLC to identify drug repurposing targets to overcome resistance toward standard-of-care platinum-based doublet chemotherapy. PDTOs were established from 10 prospectively enrolled patients with non-metastatic NSCLC from resected tumors. PDTOs were compared with matched tumor tissues by histopathology/immunohistochemistry, whole exome sequencing, and transcriptome sequencing. PDTO growths and drug responses were determined by measuring 3D tumoroid volumes, cell viability, and proliferation/apoptosis. Differential gene expression analysis identified drug-repurposing targets. Validations were performed with internal/external data sets of patients with NSCLC. NSCLC cell lines were used for aldo-keto reductase 1B10 (AKR1B10) knockdown studies and xenograft models to determine the intratumoral bioavailability of epalrestat. PDTOs retained histomorphology and pathological biomarker expression, mutational/transcriptomic signatures, and cellular heterogeneity of the matched tumor tissues. Five (50%) PDTOs were chemoresistant toward carboplatin/paclitaxel. Chemoresistant PDTOs and matched tumor tissues demonstrated overexpression of AKR1B10. Epalrestat, an orally available AKR1B10 inhibitor in clinical use for diabetic polyneuropathy, was repurposed to overcome chemoresistance of PDTOs. In vivo efficacy of epalrestat to overcome drug resistance corresponded to intratumoral epalrestat levels. PDTOs are efficient preclinical models recapitulating the tumor characteristics and are suitable for drug testing. AKR1B10 can be targeted by repurposing epalrestat to overcome chemoresistance in NSCLC. Epalrestat has the potential to advance to clinical trials in patients with drug-resistant NSCLC due to favorable toxicity, pharmacological profile, and bioavailability.

Highly consistency of PIK3CA mutation spectrum between circulating tumor DNA and paired tissue in lung cancer patients

BackgroundPhosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutations are associated with drug resistance and prognosis in lung cancer; however, the consistency and clinical value of PIK3CA mutations between tissue and liquid samples are unknown. MethodsCirculating tumor DNA (ctDNA) and matched tumor tissue samples from 405 advanced lung cancer patients were collected at Jilin Cancer Hospital between 2018 and 2022, and the PIK3CA mutation status was sequenced using next-generation sequencing based on a 520 gene panel. The viability of different mutant lung cancer cells was detected using MTT assay. ResultsPIK3CA mutations were detected in 46 (5.68 %) of 810 lung cancer samples, with 21 (5.19 %) of 405 plasma samples and 25 (6.17 %) of 405 matched tissues. p.Glu542Lys, p.Glu545Lys, and p.His1047Arg were the most common mutation types of PIK3CA in both the ctDNA and tissue samples. The concordance of PIK3CA mutations was 97.53 % between ctDNA and matched tissues (kappa: 0.770, P = 0.000), with sensitivity/true positive rate of 72.0 %, specificity/true negative rate of 99.2 %, and negative predictive value and positive predictive value of 0.982 and 0.857, respectively (AUC = 0.856, P = 0.000). Furthermore, the concordance of PIK3CA mutations was 98.26 % in lung adenocarcinoma and 96.43 % in lung squamous cell carcinoma. TP53 and EGFR were the most common concomitant mutations in ctDNA and tissues. Patients with PIK3CA mutations showed a high tumor mutational burden (TMB) (P < 0.001) and a significant correlation between bTMB and tTMB (r = 0.5986, P = 0.0041). For the tPIK3CAmut/ctDNA PIK3CAmut cohort, PI3K pathways alteration was associated with male sex (P = 0.022), old age (P = 0.007), and smoking (P = 0.001); tPIK3CAmut/ctDNA PIK3CAwt patients harbored clinicopathological factors of adenocarcinoma stage IV, with low PS score (≤1) and TMB. ConclusionThis study showed that ctDNA is highly concordant and sensitive for identifying PIK3CA mutations, suggesting that PIK3CA mutation detection in liquid samples may be an alternative clinical practice for tissues.

BIOM-02. DISSECTING CDK4/6 INHIBITOR RESISTANCE MECHANISMS IN RECURRENT PEDIATRIC BRAIN TUMORS WITH LONGITUDINAL CSF LIQUID BIOPSIES FROM THE SJDAWN CLINICAL TRIAL

Abstract BACKGROUND SJDAWN (NCT03434262) is a St. Jude Children’s Research Hospital phase 1 trial that assessed the safety and benefit of CDK4/6 inhibitor-based therapy in patients with relapsed CNS tumors. To capture tumor evolution dynamics and arising resistance mechanisms in response to treatment, 143 longitudinal CSF samples were collected from 34/68 (50%) patients for cell-free DNA (cfDNA) analysis. METHODS cfDNA was extracted from CSF liquid biopsies and analyzed using a novel methylation-based platform that integrates copy number, tumor classification, and deconvolution of methylation signatures into normal vs. disease fractions. Samples with measurable residual disease (MRD) were further characterized by deep whole-genome sequencing to discover mutation-driven resistance mechanisms. When available, pre- and post-SJDAWN tumor tissues were processed for single-nucleus multi-omics to track tumor evolution at single-cell resolution. RESULTS In the context of CDK4/6 inhibitor-based therapy, longitudinal cfDNA assessment revealed treatment-induced selection for subclones with focal amplification of positive cell cycle regulators CDK6, CCND2, and MYCN. Emergence of these resistance mechanisms notably preceded disease progression on MRI and CSF cytology by up to 6 months. Of the 68 patients enrolled on SJDAWN, 4 patients (3 Group 3/4, subtype III medulloblastomas and 1 anaplastic ependymoma) achieved &amp;gt;2-year progression-free survival. Interestingly, serial cfDNA profiling of 1 long-term survivor (Group 3/4, subtype III medulloblastoma) exhibited undetectable MRD status for &amp;gt;1.5 years prior to reemergence, suggesting tumor senescence by CDK4/6 inhibition may impede circulating tumor DNA (ctDNA) release kinetics. CSF liquid biopsies were further evaluated in comparison to matched tumor tissues, and changes in CSF-specific subclones were observed in response to treatment. CONCLUSIONS In addition to early MRD detection, liquid biopsies capture tumor evolution dynamics and can inform developing resistance mechanisms. Focal amplification of CDK6, CCND2, and MYCN facilitates CDK4/6 inhibitor resistance. In responders, treatment-induced senescence may inhibit ctDNA release kinetics.

Improved detection of homologous recombination deficiency using WES sequencing: Insights into a Chinese pan-cancer cohort.

e17503 Background: Homologous recombination (HR) deficiency has emerged as a novel biomarker for the clinical use of PARP inhibitors in advanced ovarian cancer, and may also be of value in guiding the clinical use of PARP inhibitors and platinum-based drugs in breast cancer, prostate cancer, and other tumors. This significant finding assists in precision medication and prognosis judgments for patients. Methods: This research incorporated a Chinese pan-cancer cohort comprising 1033 patients diagnosed across thirteen cancer types. All matched tumor tissues and peripheral blood samples were processed for the whole exome sequencing. The HRD scoring was conducted with ScarHRD R package with defined parameters for the heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LST) status. HR deficiency were defined as an HRD-score ≥50 or BRCA1/2 deficient, while HR proficiency were defined as an HRD-score &lt;50 and BRCA1/2 intact. Results: Ovarian cancer demonstrates the highest HRD prevalence at 51.85%, surpassing the BRCA1/2 mutation rate of 20.37%. Breast cancer follows with an HRD rate of 45.45%, yet no BRCA1/2 mutations are detected. Other cancers like pancreatic, gastric, and sarcomas also present notable HRD rates (29.41%, 36.84%, and 29.79%, respectively) without corresponding BRCA1/2 mutations. In contrast, cancers such as urological, lung, intestinal, and neurological tumors exhibit a mismatch between HRD rates and BRCA1/2 mutation presence, few patients with notable BRCA1/2 mutations did not have consisted HR-deficient rate, and vice versa. Conclusions: Analysis HRD-score can help to screen a larger population of PARP inhibitor beneficiaries and provide hope to more patients. In the future we will do more dimensional data analysis statistics on this cohort. [Table: see text]

Circulating tumor DNA as a predictive biomarker for pathologic response after treatment with neoadjuvant immunotherapy for localized dMMR/MSI-H colorectal cancer.

3612 Background: Neoadjuvant immunotherapy (IO) has shown promise as a potential non-surgical, curative therapy in pts with localized dMMR/MSI-H CRC. However, response assessment to IO is challenging due to difficulty measuring luminal tumors, the invasive nature of endoscopy, and known discordance between these assessment modalities. ctDNA may serve as an important, novel marker of response in this population. We evaluated pre-treatment ctDNA and ctDNA clearance and their association with pathologic complete response (pCR) in pts with localized dMMR/MSI-H CRC treated with IO. Methods: We performed a 70-gene, tumor-agnostic, NGS-based ctDNA assay (LB-70) to detect somatic mutations in a CLIA setting on 49 plasma samples collected serially from 13 pts with localized dMMR/MSI-H CRC treated with neoadjuvant pembrolizumab (mean and median cycles per pt was 8; range 1 - 16) prior to definitive surgery as part of a prospective phase 2 trial (NCT04082572). NGS was also performed on each pt’s tumor tissue to confirm mutations identified in ctDNA were tumor-specific. We defined “ctDNA clearance” as a reduction in mutational variant allele frequency (VAF) to a threshold below LB-70’s limit of detection (&lt;0.3% VAF) after neoadjuvant IO in mutations that were present in both plasma and tumor tissue. We conducted a descriptive analysis to evaluate the association between the presence of pre-treatment (“baseline”) ctDNA, ctDNA clearance, and pCR. Results: On a median number of 3 samples per pt, mutations in baseline ctDNA were detected in 7/13 pts and were confirmed orthogonally in all pts with matched tumor tissue. The mean and median VAF was 8.5% and 0.7% (range 0.3% - 26.9%). Among 10/13 pts with a pCR, none recurred clinically after median follow-up 29.7 mo. Three pts did not experience a pCR, 1 of whom had disease recurrence after surgery. pCR was observed in 6/6 pts without detectable ctDNA at baseline, while only 4/7 pts with detectable ctDNA at baseline had a pCR (100% vs 57%). Of the 7 pts with detectable ctDNA at baseline, 5 cleared their ctDNA in the neoadjuvant period, among whom, 4 had a pCR (80% likelihood of pCR with ctDNA clearance). Notably, the 1 pt who did not have a pCR despite clearing ctDNA had a near-pCR (carcinoma identified in 1/91 lymph nodes, none in cecum or colon). The mean and median number of cycles to ctDNA clearance was 2.8 and 2 (range 1 - 8). For the 2 pts who did not clear their ctDNA, neither (0%) had a pCR. Conclusions: Clearance of ctDNA following neoadjuvant IO appears to predict pCR in this pilot analysis of pts with localized dMMR/MSI-H CRC, even after a median of 2 cycles. The absence of detectable ctDNA at baseline, perhaps a surrogate for lower tumor burden at initial diagnosis, may also predict a higher likelihood for pCR. Our work suggests utility of ctDNA as a biomarker for improving risk-stratification and response assessment sensitivity.

Molecular residual disease (MRD) interception in locoregionally advanced head and neck squamous cell carcinoma (LA-HNSCC): MERIDIAN study.

TPS6122 Background: The detection of circulating tumor DNA (ctDNA) after definitive treatment or MRD is associated with recurrence across different tumor types. We previously showed that ctDNA detection using a bespoke tumor-informed assay (RaDaR), in LA-HNSCC patients (pts) after surgery, definitive radiation (RT) or chemoRT (CRT), is associated with recurrence within a year (Sanz-Garcia et al, ASCO 2023). To date, the impact of intercepting MRD prior to progression in HNSCC has not been explored. Anti-PD-1 blockade has shown benefit in recurrent/metastatic HNSCC but the efficacy in LA-HNSCC is still uncertain. TIGIT is overexpressed in HNSCC and could be a potential target to improve immunotherapy (IO) outcomes. Rilvegostomig (AZD2936) is a monovalent bispecific TIGIT/PD-1 antibody that has shown acceptable safety in phase I studies, currently in phase III studies. We hypothesize that IO (AZD2936) could induce ctDNA clearance post-definitive treatment and avoid, or delay recurrence. Methods: This study will recruit 200 pts with high-risk LA-HNSCC treated with curative intent: surgery ± adjuvant therapy, definitive RT or CRT; stage III Human Papilloma virus (HPV) positive or III-IVB HPV negative. Archival tissue must be available for whole exome sequencing (WES). Pts will be enrolled in part A (definitive therapy) and part B (follow up – FU - post-definitive therapy). Plasma samples will be collected in part A (pre-treatment and post-surgery prior to adjuvant therapy) and part B (at 4-6 weeks: FU1 and 8-12 weeks: FU2). These FU samples will be analyzed in real time for ctDNA using RaDaR, an assay that targets patient specific somatic variants identified by WES of matched tumor tissue. MRD+ pts (defined as having ctDNA detected at FU2) will be enrolled to part C (interception) and randomized 3:1 to receive AZD2936 750mg IV q3w for 6 cycles or observation. 30% of pts (N=60) will be enrolled in part C. Tumor must be positive for PD-L1 (CPS≥1) and there should not be residual primary tumor or distant metastases at FU2; residual lymph nodes are allowed if neck dissection is performed. Part D will consist of long term FU of MRD+ pts; RaDaR will be performed at week 2 (W2) and week 10 (W10), and radiological assessments will be performed at W2. MRD- pts will be enrolled in part E (long term FU). The primary endpoint of MERIDIAN is ctDNA clearance in MRD+ pts, defined as no detection of ctDNA at Part D W2 and W10. We will have 87% power to identify a significant improvement in ctDNA clearance rate from 10% (observation) to 40% (AZD2936) given a significance level of 0.1. Secondary objectives include survival and safety. Exploratory analyses include: ctDNA detection using other assays (HPV DNA, methylated ctDNA), ctDNA detection in part E and beyond W10 in part D, quality of life assessments (FACT-ICM, EORTC-HN43), health economics and radiomics. As of February 2024, 19 patients are recruited. Clinical trial information: 05414032.

Pelareorep driven blood TIL expansion in patients with pancreatic, breast and colon cancer.

e14625 Background: Tumor infiltrating lymphocytes (TILs) represent a major immunological tumor control mechanism that is associated with better prognosis in cancer. One emerging cancer treatment approach to leverage the therapeutic potential of TILs is the expansion and adoptive cell transfer of autologous TILs, commonly referred to as autologous adoptive therapy (ACT). ACT clinical studies have shown encouraging results. While the majority of these trials have targeted melanoma, impressive clinical benefit has also been observed in cervical cancer, with preliminary efficacy in colorectal cancer (CRC), cholangiocarcinoma, non-small cell lung cancer, and breast cancer. Pelareorep (pela) is a live, replication competent reovirus (T3D) that selectively replicates in cancer cells and represents a new class of immunotherapy currently being explored in multiple clinical settings. To examine the effect of pela therapy on TIL expansion we applied T cell receptor sequencing of matched tumor tissue and whole blood pre- and post-treatment in a subset of breast, pancreatic, and (CRC) subjects receiving chemotherapy and atezolizumab, an anti-PD-L1 therapy, and intravenous treatment with pela. Methods: Identification of TIL clones was performed by immunosequencing of the CDR3 regions of human T-cell receptor-β (TCRβ) chains (ImmunoSEQ Assay, Adaptive Biotechnologies). DNA was isolated from tissue and blood at baseline and from blood collected post-treatment. TCRβ CDR3 regions were amplified by a multiplex, bias-controlled PCR with primers targeting the V and J genes of T cells as well as primers targeting housekeeping genes to quantitate the total nucleated cells in each sample. PCR products were sequenced on an Illumina NextSeq. Results: Pela treatment was observed to increase the expansion of pre-existing and new TIL clones in the blood in from all tumor samples after one cycle of treatment. We also observed that pre-existing TIL clonal expansion in the blood seemed to correlate with reductions in tumor volume in pancreatic cancer and to a lesser extent in CRC patients who received multiple cycles of therapy. Interestingly, unlike atezolizumab, pela’s clinical activity was lost when combined with avelumab, a PD-LI inhibitor capable of binding Fc receptors and inducing ADCC. The addition of avelumab eliminated pre-existing TIL expansion in the blood highlighting the importance of TIL expansion following pela therapy. Conclusions: These findings, while preliminary, suggest that the clinical benefits observed following pela immunotherapy may be mechanistically analogous to ACT. Accordingly, pela therapy may offer a means to directly expand TILs without the need for tumor resection, ex vivo TIL expansion, T cell ablation and IL-2 therapy. Clinical trial information: Eudra-CT: 2020-003996-16 .

Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors.

Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) as sources for "liquid biopsy" in pediatric brain tumors. CSF samples were collected by lumbar puncture, ventriculostomy, or surgery from pediatric patients with CNS tumors. Following extraction, CSF-derived cfDNA was sequenced using UW-OncoPlex™, a clinically validated next-generation sequencing platform. CSF-derived cfDNA results and paired plasma and tumor samples concordance was also evaluated. Seventeen CSF samples were obtained from 15 pediatric patients with primary CNS tumors. Tumor types included medulloblastoma (n = 7), atypical teratoid/rhabdoid tumor (n = 2), diffuse midline glioma with H3 K27 alteration (n = 4), pilocytic astrocytoma (n = 1), and pleomorphic xanthoastrocytoma (n = 1). CSF-derived cfDNA was detected in 9/17 (53%) of samples, and sufficient for sequencing in 8/10 (80%) of extracted samples. All somatic mutations and copy-number variants were also detected in matched tumor tissue, and tumor-derived cfDNA was absent in plasma samples and controls. Tumor-derived cfDNA alterations were detected in the absence of cytological evidence of malignant cells in as little as 200µl of CSF. Several clinically relevant alterations, including a KIAA1549::BRAF fusion were detected. Clinically relevant genomic alterations are detectable using CSF-derived cfDNA across a range of pediatric brain tumors. Next-generation sequencing platforms are capable of producing a high yield of DNA alterations with 100% concordance rate with tissue analysis.

Abstract PO1-02-01: T Cell Receptor Sequencing to Monitor Pelareorep-Induced Expansion of Tumor Infiltrating Lymphocytes

Abstract Background: Tumor infiltrating lymphocytes (TILs) represent a major immunological tumor control mechanism that is associated with better prognosis in breast cancer. We have previously reported the effect of pelareorep (pela), an intravenously delivered, non-engineered oncolytic reovirus, on a composite measurement of TILs and tumor cellularity (CelTIL) from the AWARE-1 window-of-opportunity study in patients with early breast cancer (eBC). These results showed treatment increased in CelTIL scores especially in the atezolizumab group. To confirm and extend these findings we applied T cell receptor sequencing of matched tumor tissue and whole blood pre and post-treatment from the AWARE-1 study to further explore the effects of pela therapy on TILs. Methods: Newly diagnosed HR+/HER2- eBC patients were enrolled into two cohorts: Cohort 1: pela + letrozole (n=10); and Cohort 2: pela + letrozole + atezolizumab (n=10). Pela was administered on days 1, 2 and 8, 9, and atezolizumab was given on day 3. Tumor biopsies (FFPE samples) collected pre-treatment (~D-23) and on day ~21 when tumors were surgically removed. T cell fraction analysis and T cell receptor sequencing were performed by Adaptive Biotechnology (Seattle, Washington) Immunoseq protocol. Results: As was shown for the CelTIL scores, an increase in the tumor T cell fraction, a direct measurement of TILs, was observed at 1-month post-treatment in both cohorts with a mean percent increase of 21% for Cohort 1 and 67% for Cohort 2. Through TCR-sequencing of tumor tissue, we identified TIL clones and tracked their differential abundance in tumor tissue and blood post-treatment. The results of this analysis at Day 21 showed a mean post-treatment expansion of 10 tumor specific clones in the blood for Cohort 1, and a mean post-treatment increase of 40 tumor specific clones for Cohort 2. Conclusions: These results confirm the previously reported CelTIL results from AWARE-1 on pela-induced increases in TILs and demonstrate the expansion of these clones in both tumor and blood as a consequence of pela therapy for HR+/HER2- breast cancer. Citation Format: Richard Trauger, Houra Loghmani, Matt Coffey, Fernando Salvador, Joaquín Gavilá, Luis Manso, Tomás Pascual, Aleix Prat, Thomas Heineman. T Cell Receptor Sequencing to Monitor Pelareorep-Induced Expansion of Tumor Infiltrating Lymphocytes [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 PO1-02-01.