Molecular Response Assessment Research Articles

Cell-Free DNA in Hematologic Malignancies.

Liquid biopsy techniques using cell-free DNA (cfDNA) play an increasingly important role in the characterization and surveillance of solid tumors. For blood cancers, molecular response assessment techniques using circulating malignant cells or bone marrow aspirates are well established in clinical care. However, cfDNA has an emerging role in hematology as well, with the opportunity for disease assessment and quantification independent of circulating disease burden or invasive biopsies. In this review, we discuss key technologies and clinical data for the utilization of cfDNA in lymphomas, myeloma, and leukemias.

Assessment of Molecular Response to Treatment of Chronic Myeloid Leukemia at Kigali University Teaching Hospital of Kigali

Abstract Introduction/Objective Chronic Myeloid Leukemia (CML) is a clonal myeloproliferative neoplasm that gives proliferation advantage to the granulocytes, it is one of the commonest chronic hematological malignancies and it is a burden to the world especially Rwanda. Since the introduction of Tyrosine Kinase Inhibitors (TKIs) especially the first line Imatinib in 2001, the outcomes of CML have been much improved and currently, in developed world, the life expectancy of patients with CML is almost the same as general population. However, it is not the case in developing world especially Rwanda due to limitation on access of all TKIs. The aim of this study is to assess molecular response on Imatinib of patients with CML. Methods/Case Report This was a one arm open label prospective cohort study that recruited 31 patients with CML and on Imatinib for at least three months and followed for 11 months. The clinical features at diagnosis and recruitment were captured from the hospitals filing systems and investigator’s own assessment at the time of recruitment respectively. Information was filled to a well-structured questionnaire. Lab results at the time of diagnosis was obtained from laboratories reporting systems. Samples for full blood count and BCR-ABL1/ABL1 were withdrawn from the patients at the time of diagnosis and they were run at University Teaching Hospital of Kigali (CHUK). Data analysis was performed using Statistical Package for the Social Sciences (SPSS 28) and South Texas Art Therapy Association (STATA 15.0). Results (if a Case Study enter NA) Better response according to European LeukemiaNet (ELN) defined as optimal response was found among only 38.7% and resistance to imatinib defined by ELN as Failure and warning was found in 45.2% and 16.1% respectively. The eleven months survival rate was 93.5% in which it is 85.7% among those in treatment failure group. Late presentation showed by presence of very high White Blood Cells above 100x109/L and massive splenomegaly at diagnosis, and poor adherence to Imatinib according to Morsiky Medication Adherence Scale (MMAS-8) are associated with poor molecular response to Imatinib. Conclusion CML is a serious disease especially to those who suffer from it; on time diagnosis, access to all available lines of TKIs and better follow up are crucial for patients with CML to access the same life expectancy as general population as it is in developed world.

A phase I trial of intratumoral STX-001: A novel self-replicating mRNA expressing IL-12 alone or with pembrolizumab in advanced solid tumors.

TPS2696 Background: STX-001 is a multi-mechanistic lipid nanoparticle encapsulated synthetic self-replicating mRNA, engineered to express the IL-12 cytokine for an extended duration when administered intratumorally. A murine surrogate of STX-001 induces deep durable responses in multiple preclinical solid tumor models. This Phase 1 open-label, multi-center first-in-human dose-escalation trial evaluates the safety, tolerability, pharmacokinetics (PK), pharmacodynamics (PD), and preliminary antitumor activity of STX-001 alone, or in combination with pembrolizumab in patients with treatment refractory advanced cancers. Methods: Approximately 30 adults ≥18 years of age with histologically confirmed advanced solid tumors that are refractory to standard treatments will be enrolled. The study will consist of two arms, an STX-001 monotherapy arm and an STX-001 + pembrolizumab combination arm, enrolling approximately 15 patients each. Key eligibility criteria include ECOG status 0 or 1, a tumor lesion amendable to injection, and confirmed prior disease progression. STX-001 will be administered every 3 weeks (q3w) for 3 doses and then every 6 weeks (q6w) for a further 3 doses. Tumor biopsies will be obtained at baseline and after the first STX-001 administration. Primary endpoints will include safety and maximum tolerated dose (MTD), with secondary endpoints encompassing pharmacokinetics and preliminary efficacy as measured by RECIST 1.1. To determine the MTD, this study will employ the Bayesian optimal interval (BOIN) design, with the 3 + 3 design run-in and a recommended phase 2 dose (RP2D) will be determined. Tumor response will be assessed using RECIST 1.1 criteria. Exploratory pharmacodynamic analyses will assess tumor-infiltrating lymphocytes and STX-001 mRNA in baseline and on-treatment biopsies, evaluate inflammatory cytokine profiles in plasma, determine immune activation in circulating immune cells, and measure circulating tumor DNA (ctDNA) for molecular response assessment. Clinical trial information: NCT06249048 .

Is 18F-FDG-PET/CT an Optimal Imaging Modality for Detecting Immune-Related Adverse Events after Immune-Checkpoint Inhibitor Therapy? Pros and Cons.

Immunotherapy with immune checkpoint inhibitors (ICIs) has revolutionized contemporary oncology, presenting efficacy in various solid tumors and lymphomas. However, ICIs may potentially overstimulate the immune system, leading to immune-related adverse events (irAEs). IrAEs may affect multiple organs, such as the colon, stomach, small intestine, kidneys, skin, lungs, joints, liver, lymph nodes, bone marrow, brain, heart, and endocrine glands (e.g., pancreas, thyroid, or adrenal glands), exhibiting autoimmune inflammation. 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) is commonly used in oncology for staging and assessment of therapy responses, but it may also serve as a tool for detecting irAEs. This review aims to present various patterns of metabolic activation associated with irAEs due to ICI treatment, identifiable through 18F-FDG PET/CT. It describes the advantages of early detection of irAEs, but also presents the challenges in differentiating them from tumor progression. It also delves into aspects of molecular response assessment within the context of pseudoprogression and hyperprogression, along with typical imaging findings related to these phenomena. Lastly, it summarizes the role of functional PET imaging in oncological immunotherapy, speculating on its future significance and limitations.

Circulating Tumor DNA in Diffuse Large B-Cell Lymphoma: from Bench to Bedside?

Diffuse large B-cell lymphoma (DLBCL) is a curable disease with variable outcomes due to underlying heterogeneous clinical and molecular features-features that are insufficiently characterized with our current tools. Due to these limitations, treatment largely remains a "one-size-fits-all" approach. Circulating tumor DNA (ctDNA) is a novel biomarker in cancers that is increasingly utilized for risk stratification and response assessment. ctDNA is readily detectable from the plasma of patients with DLBCL but has not yet been incorporated into clinical care to guide treatment. Here, we describe how ctDNA sequencing represents a promising technology in development to personalize the care of patients with DLBCL. We will review the different types of ctDNA assays being studied and the rapidly growing body of evidence supporting the utility of ctDNA in different treatment settings in DLBCL. Risk stratification by estimation of tumor burden and liquid genotyping, molecular response assessment during treatment, and monitoring for measurable residual disease (MRD) to identify therapy resistance and predict clinical relapse are all potential applications of ctDNA. It is time for clinical trials in DLBCL to utilize ctDNA as an integral biomarker for patient selection, response-adapted designs, and surrogate endpoints. As more ctDNA assays become commercially available for routine use, clinicians should consider liquid biopsy when treatment response is equivocal on imaging. Incorporating MRD may also guide decision-making if patients experience severe treatment toxicities. Though important barriers remain, we believe that ctDNA will soon be ready to transition from bench to bedside to individualize treatment for our patients with DLBCL.

THE SIGNIFICANCE OF MINIMAL RESIDUAL DISEASE IN ACUTE LYMPHOBLASTIC LEUKAEMIA: A SINGLE CENTRE STUDY

In Acute lymphoblastic Leukemia (ALL) assessment of molecular response to treatment, assessing minimal residual disease (MRD) is a major independent predictor of treatment outcome. Consequently, MRD is implemented in all ALL-treatment protocols to fill up or to redefine stratification of multifactorial risk with optional intensity of customized treatment. Aim: to specify the significance of MRD in the assessment of remission in children with ALL with results discordant between morphology and flow cytometry at the end of induction phase of therapy. Materials and Methods: A descriptive cross-sectional study was conducted at Jin Oncology Center from March 2019 through November 2023. Data were taken out of the records of 58 patients who had ALL less than 16 years old. All patients were less than 16 years old and treated by ukall. They were diagnosed using peripheral blood morphology, bone marrow study and/or flow cytometry when lymphoblasts in peripheral blood or bone marrow aspirate are ≥20% and was confirmed by flow cytometry. On 29th day of induction therapy, bone marrow was examined for morphology and flow cytometry. The presence or absence of MRD was determined, and CD19, CD10 and tdt were tested. By morphologic assessment they were divided patients into: Category 1, C1 (<5% blasts), Category 2, C2 (5-20% blasts), and Category 3, C3 (>20% blasts). Statistical analysis was made using SPSS version 25. P value of less than 0.05 was considered significant. Results: The study involved 58 patients who had ALL. with a median age of 6.5 years, male to females ratio of 1.76:1, mean platelet count of 96.6 x 10⁹/L ,mean hemoglobin of 8.6 g/dL, mean leucocyte count of 74.3 x 10⁹/L), 48 cases (82.7%) of B-cell lineage and 10 cases (17.3%) of T-cell lineage, 94.6% of the B-cell cases were of the common B-ALL and the rest Pro-BALL type, 54.6% of the T-cell ALL was cortical T-ALL and 44.4% Early T-cell ALL. They were tested for MRD by morphology and flow cytometry on day 29. By morphology, 46 patients had remission but by flow only 24 cases. Seventeen cases had residual blasts >5%. In 19 cases there was a discrepancy between the results of morphology and flow. Twenty-five cases (52.08% of B-cell cases) were positive for MRD by flow results. Eight of the ten cases of T-ALL (80%), were positive for MRD by flow cytometry. Among 48 cases of B-ALL, 36 were in C1 category (morphologically in remission), 11 cases were in C2 category and one case in the C3 category. Of cases in C1 category, 17 were MRD +ve and 19 were MRD –ve by flow cytometry. In the C2 category, only 2 out of the 11 cases (18.18%) had discordant results between morphology and flow results. The correlation between morphology and flow results was 100% in the C3 category. Conclusion: MRD should not be the surrogate of morphology but to be used in conjunction in order to give us a more accurate representation of status of remission.

Abstract 6557: Longitudinal cell-free tumor load dynamics represent an early endpoint for immunotherapy response in non-small cell lung cancer

Abstract Background: Liquid biopsies can inform treatment strategies by rapidly and accurately assessing tumor burden; with emerging data supporting the clinical utility of circulating cell-free tumor DNA (ctDNA) as an early endpoint of immunotherapy response. Methods: We performed targeted error-correction sequencing of ctDNA (n=330) and matched white blood cell (WBC) DNA (n=109) from 109 patients with advanced non-small cell lung cancer (NSCLC) who received immune checkpoint inhibitor monotherapy (n=79) or immunotherapy-containing combination regimens (n=30). Variant cellular origin was determined using a tumor-independent WBC DNA-informed approach. The maximum mutant allele fraction (maxMAF) of tumor-derived mutations was tracked longitudinally to assess changes in total cell-free tumor load (cfTL). Results: Among 3,418 variants with resolved cellular origin, 2,452 (72%) were tumor-derived, 125 (4%) were germline, while 841 (25%) were related to clonal haematopoiesis (CH). Cell-free DNA fragments harbouring tumor-derived mutations were significantly shorter than fragments containing wild-type alleles; however, fragment length alone was insufficient to distinguish CH variants from wild-type. Overall, 97 (89%) patients with >1 detectable tumor mutation were considered for cfTL tracking and molecular response assessment. Clearance of cfTL indicated molecular response (mR) whereas persistence indicated molecular progression (mPD). Time-course analyses, aiming to establish the optimal timing for molecular response assessment, revealed that early cfTL clearance within 3-9 weeks was significantly linked to improved survival outcomes. Notably, blood tumor mutation burden above or below 16 mutations/megabase showed no association with overall survival (OS; log rank p=0.98) or progression-free survival (PFS; log rank p=0.95). Of 81 patients evaluated for early on-therapy molecular responses, 28 (35%) were classified as having an mR, while 53 (65%) patients were classified in the mPD category. The median time to mR was 5 weeks in patients receiving immune checkpoint monotherapy and 6 weeks in patients receiving chemo-immunotherapy combination regimens. Patients in the mR group achieved longer OS (log rank p=0.001) and PFS (log rank p=0.0003) compared to those with mPD. Assessment of landmark PFS at 6 months demonstrated a significant association between ctDNA molecular response and durable clinical benefit (DCB) in patients receiving immune checkpoint monotherapy (p < 0.001, Fisher’s exact test), and a numerical association with DCB in patients on chemo-immunotherapy (p=0.07, Fisher’s exact test). Conclusions: Longitudinal tracking of ctDNA provides a real-time and accurate approach for monitoring immunotherapy response. These findings underscore the clinical utility of employing ctDNA molecular response to inform clinical decision-making. Citation Format: Lavanya Sivapalan, Bahar Alipanahi, Archana Balan, Jamie E. Medina, Noushin Niknafs, Erica Peters, Jaime Wehr, Alissa Konicki, Mimi Najjar, Bryan Chesnick, Gavin Pereira, Sarah Rongione, Nisha Rao, Michael Rongione, Brittany Shavatt, Lorenzo Rinaldi, Benjamin Levy, Victor E. Velculescu, Patrick M. Forde, Valsamo Anagnostou. Longitudinal cell-free tumor load dynamics represent an early endpoint for immunotherapy response in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6557.

Abstract 971: Validation of a tumor-naïve circulating tumor DNA (ctDNA) response monitoring panel in advanced non-small cell lung cancer (aNSCLC)

Abstract Introduction: Monitoring of ctDNA can be a minimally invasive complement to tumor imaging for assessing treatment effect. Technical limitations require methods to distinguish tumor signal from clonal hematopoiesis (CH), often including non-tumor sequencing. We developed a tumor-naïve panel (FoundationOne® Monitor) to quantify ctDNA tumor fraction (TF). TF analytical validation used peripheral blood mononuclear cell (PBMC) sequencing. We then leveraged plasma collected serially from patients with aNSCLC in the real-world (rw) Prospective Clinico-Genomic (PCG; NCT04180176) study to investigate the utility of TF for monitoring therapy (tx) response. Methods: TF was quantified using a combination of aneuploidy and variant allele frequencies of genomic alterations (GAs), while excluding CH mutations and aneuploidy using fragmentomic signal from cfDNA. In the PCG study, data from consenting patients were collected from electronic health records from 23 participating Flatiron Health Research Network sites. We analyzed plasma collected 6-15 weeks after start of tx in exploratory and validation cohorts per prespecified criteria. We defined molecular response (MR) as undetectable TF on tx regardless of baseline TF. Hazard ratios (HR) and 95% confidence Interval (CI) were calculated with univariate Cox proportional hazard regression. Results: For TF validation, 1135 samples separate from the PCG study with paired PBMC results were included. Overall, 24/4274 (0.56%) CH derived non-aneuploidy GAs detected in 1134 samples were falsely classified as somatic. Of these, 4 were detected among 317 samples with no tumor signal, resulting in a false positive TF value (specificity = 98.7%). CH derived aneuploidy was observed in 27 PBMCs and was appropriately filtered during TF estimation in all cases. Assessing the impact of CH aneuploidy filtering on sensitivity, we only identified 1/320 (0.31%) samples where non-CH derived aneuploidy was omitted. To assess clinical validity, 222 patients were analyzed from the PCG study. MR was assessed after a median of 10.8 weeks of tx (IQR 8.9-12.0). In a subset of 152 patients treated with physicians’ choice, MR was associated with favorable rw progression free survival (rwPFS: 9.4 v 2.8 months [mo]; HR = 0.30; 95% CI: [0.21-0.44]) and rw overall survival (rwOS: 22.0 v 7.5 mo; HR = 0.33 [0.22-0.49]). We validated this finding on 70 patients receiving immunotherapy (50 with chemo). Again, MR was associated with favorable rwPFS (9.0 v 2.8 mo; HR = 0.28 [0.16-0.51]) and rwOS (20.2 v 9.4 mo; HR = 0.42 [0.23-0.78]). Conclusions: We describe a highly specific tumor naïve algorithmic filtration of non-tumor signal to enable high confidence ctDNA quantification and MR assessment. On tx MR is associated with favorable outcomes. These findings may enable personalized tx approaches tailored to a patient’s risk of progression and downstream cancer morbidity. Citation Format: Anne C. Chiang, Russell W. Madison, Yanmei Huang, Alexander Fine, Dexter X. Jin, Geoffrey R. Oxnard, Jason Hughes, Zoe June Assaf, Yi Cao, Vladan Antic, Ole Gjoerup, Amanda Young, David Fabrizio, Shaily Lakhanpal, Richard Zuniga, Katja Schulze, Lincoln W. Pasquina. Validation of a tumor-naïve circulating tumor DNA (ctDNA) response monitoring panel in advanced non-small cell lung cancer (aNSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 971.

Early and Sustained Circulating Tumor DNA Response Dynamics after Loncastuximab Tesirine for Relapsed/Refractory Diffuse Large B-Cell Lymphoma

Introduction: Circulating tumor DNA (ctDNA) has emerged as a tool to characterize tumors and track minimal residual disease (MRD) in many malignancies, including diffuse large B-cell lymphoma (DLBCL). ctDNA levels have been shown as prognostic after first-line treatment and CD19-targeted chimeric antigen receptor (CAR19) T cell therapy in DLBCL. Loncastuximab tesirine (loncastuximab tesirine-lpyl [Lonca]), an antibody-drug conjugate comprising an antibody targeting CD19 and a pyrrolobenzodiazepine dimer cytotoxin, is approved for relapsed/refractory (R/R) DLBCL. The ultrasensitive ctDNA-MRD detection method, phased variant enrichment and detection sequencing (PhasED-Seq) was applied to evaluate molecular response and mutational genotypes in patients (pts) undergoing Lonca treatment. Methods: LOTIS-2 study (NCT03589469) evaluated the efficacy of Lonca in R/R DLBCL after ≥ 2 lines of prior systemic therapy. Samples from 33 LOTIS-2 pts were profiled by PhasED-Seq (Foresight Diagnostics), representing a range of best responses to therapy, including 8 complete response (CR), 14 partial response (PR), and 11 progressive disease (PD). Pts received a median of 4 treatment cycles with Lonca (range 2-22). Baseline plasma and peripheral blood mononuclear cells were used to identify tumor-specific phased variants (PVs), which were used to monitor ctDNA-MRD after 1 cycle of treatment (cycle 2, day 1 [C2D1]) and at the end of treatment (EOT). Samples were reported quantitatively with levels of ctDNA-MRD and qualitatively as ctDNA-MRD positive or negative. Absolute ctDNA levels and log-fold change (LFC) in ctDNA were compared with outcomes including best overall response, progression-free survival (PFS), and overall survival (OS), as determined by the independent review committee. The ctDNA mutational profile of each pt was evaluated at baseline and EOT to assess emerging clonal alterations with emphasis on CD19. Results: PVs were successfully genotyped from pretreatment plasma in 31/33 pts (94%) with sufficient material for analysis. The median pretreatment ctDNA level was 141 haploid genome equivalents /mL (hGE/mL) (range 0.4-3608), similar to previous DLBCL studies in first-line and relapsed settings. Interestingly, pretreatment ctDNA levels were not predictive of outcomes to treatment (hazard ratio [HR] 0.99, P=0.96). The prognostic value of ctDNA levels was assessed at C2D1. Absolute ctDNA levels and the change from baseline levels were significantly prognostic for the response to treatment. Pts achieving either a CR or a PR had significantly greater reduction in their ctDNA levels than those failing to respond (CR vs PD, median LFC -1.5 vs 0.1, P=0.001; PR vs PD, median LFC -1.1 vs 0.1, P=0.006) (Fig 1A). Interestingly, pts achieving a CR or a PR did not have significantly different changes in ctDNA at C2D1 ( P=0.15). When dividing pts at the median into those with high vs low ctDNA levels at C2D1, lower levels of ctDNA were significantly associated with superior PFS and OS (PFS: HR 4.4, P=0.009; OS: HR 3.2, P=0.01) (Fig 1B). At the EOT, 5 of 6 CR pts had cleared their ctDNA-MRD to undetectable levels vs 1 of 6 at C2D1. The CR pt who did not show deepening of molecular response was the only CR pt who ended Lonca treatment for radiographic disease progression; all other CR pts ended treatment for other reasons (e.g., toxicity, transplant, or persistent complete remission). To assess for emergent clonal mutations, the mutational profiles of pts were evaluated before Lonca treatment and at EOT. Prior studies in DLBCL after CAR19 T-cell therapy have revealed recurrent, although infrequent, mutations in CD19 as a mechanism of resistance. In this cohort, no emergent alterations in CD19 at the EOT (0/31 pts) were observed. One pt was identified with a baseline mutation in CD19 (R363C); this pt achieved a PR followed by PD after 3 cycles of treatment with persistence of the mutation in CD19. Conclusions: ctDNA molecular response assessment using PhasED-Seq is prognostic for outcomes in pts receiving Lonca monotherapy. ctDNA levels as early as C2D1 can predict outcomes and are indicative of a fast response to Lonca. Furthermore, molecular responses can deepen with additional cycles. CD19 alterations do not appear to be a common emergent mechanism of resistance to Lonca. In this exploratory study, ctDNA-MRD predicts Lonca efficacy and outcomes and should be further considered as a universal biomarker in DLBCL.

Asciminib (ASC) Once-Daily (QD) Dosing Demonstrates Comparable Tolerability and Efficacy to Twice-Daily (BID) Dosing: Results from the ASC in Monotherapy 4 CML (AIM4CML) Study in Patients (Pts) with Chronic Myeloid Leukemia in Chronic Phase (CML-CP)

CONCLUSIONS ASC is the only approved BCR::ABL1 inhibitor that Specifically Targets the ABL1 Myristoyl Pocket, distinguishing it from other approved treatments that target the ATP binding site. In the phase III ASCEMBL trial (NCT03106779) ASC 40 mg BID was well tolerated and demonstrated superior efficacy vs bosutinib 500 mg QD in pts previously treated with ≥2 TKIs, with major molecular response (MMR; BCR::ABL1IS ≤0.1%) rates of 25.5% vs 13.2% at wk 24 and 37.6% vs 15.8% at wk 96. We present an interim analysis of the primary endpoint of the AIM4CML trial (NCT04666259), which was initiated to assess the safety, efficacy, and QD dosing of ASC in a similar population of pts with CML-CP. This is a multicenter, phase IIIb, open-label study of ASC in pts with CML-CP without the T315I mutation after ≥2 prior TKIs and pts with the T315I mutation after ≥1 prior TKI. Adults aged ≥18 years with CML-CP who had treatment failure with or intolerance of the most recent TKI were eligible. Pts without the T315I mutation were randomized to receive ASC 40 mg BID (cohort A) or 80 mg QD (cohort B). Results for pts with the T315I mutation who received ASC 200 mg BID (cohort C) will not be presented for this analysis. The primary endpoints include adverse events (AEs) and serious AEs by wk 24 in cohorts A and B, with additional safety and efficacy secondary endpoints. This study was not powered to detect statistical differences between cohorts. End of study is when the last pt completes 72 wks of treatment or discontinues prematurely. The numbers of enrolled pts in cohorts A, B, and C were 26, 27, and 3, respectively. This interim analysis included 42 pts randomized to cohort A (n=22) or cohort B (n=20), who reached 24 wks after cycle 1 day 1 of treatment by February 17, 2023. Most baseline characteristics in cohorts A and B were comparable, but median time since initial diagnosis and median baseline BCR::ABL1IS levels were longer and higher, respectively in cohort B (Table). Median duration of exposure was 23.1 (range, 2.7-72.3) wks in cohort A and 24.1 (range, 1.3-71.0) wks in cohort B. Prior to wk 24, treatment was discontinued in 7 and 4 pts in cohorts A and B, respectively. Reasons for discontinuation included physician decision (cohort A, n=4; cohort B, n=2), AEs (cohort A, n=2; cohort B, n=1), or pt decision (cohort A, n=1; cohort B, n=1). At the time of this interim analysis, discontinuation due to treatment failure was reported only in cohort B in 2 pts that discontinued due to physician decision. Cohorts A and B had comparable all-grade, grade 3, and grade 4 AEs. Treatment-emergent all-grade AEs occurring in ≥20% in cohorts A and B were fatigue (32% and 25%), headache (27% and 20%), abdominal pain (27% and 15%), rash (23% and 5%), dyspnea (23% and 10%), nausea (14% and 30%), hypertension (14% and 20%), cough (18% and 20%), and arthralgia (9% and 20%). While many pts had AEs requiring additional therapy, few had serious AEs, and similar numbers of pts in cohorts A and B had AEs leading to dose adjustments/interruptions and treatment discontinuation (Figure). One pt in cohort B had a fatal AE due to sepsis that was not attributed to study treatment. This trial is ongoing; data for the wk 24 primary endpoint for all enrolled pts will be available at the time of presentation. Pts with ≥1 molecular response assessment by wks 4, 12, and 24 were 18, 19, and 20 in cohort A, respectively, and 17, 17, and 18 in cohort B, respectively. The proportions of pts who maintained or achieved BCR::ABL1IS ≤1% by wks 4, 12, and 24 were higher in cohort B with 52.9%, 76.5%, and 88.9%, respectively than in cohort A with 50.0%, 63.2%, and 65.0%, respectively, likely due to higher baseline BCR::ABL1IS levels in cohort B (Table). MMR rates by wks 4, 12, and 24 were 33.3%, 42.1%, and 45.0% in cohort A and 23.5%, 47.1%, and 61.1% in cohort B, respectively. Deep molecular response (MR 4; BCR::ABL1IS ≤0.01%) rates by wks 4, 12, and 24 were 27.8%, 31.6%, and 30.0% in cohort A and 5.9%, 11.8%, and 27.8% in cohort B, respectively. This interim analysis of the AIM4CML trial further demonstrates the tolerability and efficacy of ASC and is among the first clinical reports on QD dosing of ASC in pts with CML-CP. Safety was comparable between the 80-mg QD and 40-mg BID doses, with both demonstrating safety profiles consistent with prior reports. Pts receiving ASC at both doses achieved and maintained molecular responses, which deepened over time. These results support the flexibility of QD dosing with ASC.

POSTER: ALL-022 Assessment of Molecular Response to Tyrosine Kinase Inhibitors in Tunisian Patients With Ph+ Acute Lymphoblastic Leukemia

POSTER: ALL-022 Assessment of Molecular Response to Tyrosine Kinase Inhibitors in Tunisian Patients With Ph+ Acute Lymphoblastic Leukemia

ALL-022 Assessment of Molecular Response to Tyrosine Kinase Inhibitors in Tunisian Patients With Ph+ Acute Lymphoblastic Leukemia

ALL-022 Assessment of Molecular Response to Tyrosine Kinase Inhibitors in Tunisian Patients With Ph+ Acute Lymphoblastic Leukemia

Failure rates of mutation-based ctDNA assays in lung cancer treatment monitoring.

e18752 Background: Despite the wide adoption of noninvasive liquid biopsy approaches for cancer genotyping, little is known about the longitudinal performance of these assays for monitoring therapeutic responses in patients with advanced disease. Here, we report results of a pooled analysis that collects existing evidence regarding the failure rates of circulating tumor DNA (ctDNA) assays designed for therapeutic monitoring in patients with advanced or metastatic lung cancer. Methods: We searched PubMed for original studies published between February 2012 and January 2022, following these inclusion criteria: (1) Adults older than 18 years old with advanced or metastatic lung cancer treated with chemotherapy, targeted therapy, or immunotherapy; (2) Tumor-informed or plasma-only circulating tumor DNA assays based on droplet digital PCR (ddPCR) or targeted deep sequencing technologies for the detection of tumor-specific allele fractions; (3) Measurement of circulating tumor DNA levels at sequential timepoints. We defined failures as a lack of detectable mutant allele fraction (MAF) in patients with metastatic lung cancer in samples collected before treatment initiation. Two reviewers independently screened studies, extracted data, assessed the risk of bias, and evaluated the quality of evidence. Divergences were resolved by a third independent reviewer reaching a consensus. Study quality assessment covered: (1) representativeness of patient population, (2) risk of funding bias, (3) description of ctDNA analysis and outcomes, and (4) statistical quality and interpretation. Results: From 142 studies retrieved by an automated PubMed query, we extracted data from 42 studies which fulfilled the eligibility criteria - 11 registered trials, 31 prospective/retrospective cohorts. MAF levels in the circulation were measured using PCR-based assays (23/42, 55%); the remainder used NGS-based approaches (19/42, 45%). The median number of targeted genes was 1 (range 1-6) vs 73 (range 36-214), respectively. The median number of samples analyzed per study was 79 (range 3-334). On average, 31% of samples collected before treatment did not have a detectable MAF in any of the target genes analyzed, despite the high disease burden typically experienced in patients with metastatic lung cancer. Only 57% of PCR-based and 78% NGS-based studies succeeded in providing molecular response assessment metrics. We identified 10/42 studies with critical quality assessment concerns and 18 studies had funding provided by a company with investments in the commercial cfDNA assay. Conclusions: Available liquid biopsy assays that report tumor-specific mutations have a high rate of failure for measuring disease burden and response outcomes during therapy. Approaches that could be reliably used for monitoring patients with advanced cancers undergoing treatment are needed to improve patient care.

Retrospective clinical analysis of circulating tumor DNA (ctDNA)–based molecular response (MR) and baseline blood-based tumor mutational burden (bTMB) for monitoring response in phase 3 trial of bintrafusp alfa vs. pembrolizumab treatment of non-small cell lung cancer (NSCLC).

9098 Background: The clinical utility of ctDNA-based approaches, such as bTMB and MR, to monitor and predict response during chemo-immunotherapy was evaluated using longitudinal cohort samples from a Phase 3 study of bintrafusp alfa versus pembrolizumab as a first-line treatment in patients with PD-L1 expressing advanced NSCLC. Methods: ctDNA was collected at baseline and day 42 after treatment with bintrafusp alfa (Q2W, 1200mg) or pembrolizumab (Q3W, 200mg). The GuardantOMNI liquid biopsy (LBx) assay was used to detect somatic alterations in 497 genes and generate bTMB from baseline, and MR scores from baseline and day 42 (n = 424 samples). bTMB and somatic alterations influencing response were explored. MR scores were calculated using the validated Guardant Response algorithm. Associations between ctDNA metrics and PFS were assessed. Results: 418/424 samples passed sequencing QC; of these, somatic mutations were detected in 236/237 baseline samples and 177/181 day 42 samples. Of 212 NSCLC patients with eligible bTMB results at baseline, 104 (49.1%) patients received bintrafusp alpha and 108 (50.9%) received pembrolizumab. bTMB high (bTMB-H) is defined as >20mut/MB. In the bintrafusp alpha arm, PFS was significantly longer in patients with bTMB-H (median 8.3 months vs 2.7 months, p = 0.00086). In the pembrolizumab arm, PFS was also longer in patients with bTMB-H (median 5.65 months vs 5.5 months, p = 0.0898). Of 132 NSCLC patients with eligible MR results, 67 (50.8%) patients received bintrafusp alpha and 65 (49.2%) patients received pembrolizumab. In the bintrafusp alpha arm, molecular responders had significantly longer PFS (median 7.9 months vs 4.2 months, p = 0.00042). In the pembrolizumab arm, molecular responders also had significantly longer PFS (median 8.95 months vs 4.1 months, p = 0.00054). Conclusions: ctDNA analysis from plasma samples supported MR assessment in patients treated with ICI, indicating its utility as an adjunct to RECIST in monitoring of tumor response. Blood-based TMB-high was associated with immunotherapy treatment benefit. Analysis of b-TMB and MR allowed identification of patients with improved PFS in both treatment arms. Investigation of treatment specific TMB cut off selection and potential clinical utility of defined somatic mutations is ongoing. Clinical trial information: NCT03631706 .

Abstract 5597: Enhanced detection and classification of cell-free DNA alterations through matched normal analyses with PGDx elioTM plasma complete

Abstract Liquid biopsies represent a transformation in the management of cancer as they have the potential to detect, characterize, and monitor cancers earlier than can be achieved with conventional diagnostic modalities. However, cell-free DNA (cfDNA)-based alterations can be derived from the tumor, germline, or may be associated with clonal hematopoiesis (CH), which can confound non-invasive tumor profiling, molecular response assessment, and clonal evolution analyses through inaccurate variant classification. To facilitate global access to a decentralized liquid biopsy solution to address this, we developed and validated the 521 gene PGDx elio plasma complete test for paired analysis of cfDNA and matched leukocyte DNA. PGDx elio plasma complete enables detection of single nucleotide variants, insertions and deletions, copy number amplifications, translocations, microsatellite instability, blood tumor mutation burden, and loss of heterozygosity. We first optimized the assay workflow to incorporate genomic DNA derived from leukocytes to facilitate direct detection and characterization of germline alterations as well as those that may be associated with CH, resulting in de-duplicated, error-corrected sequencing coverage of approximately 1,750-fold. A fully automated bioinformatics algorithm was then developed and validated to perform integrated analyses of cfDNA-derived alterations to assign the appropriate biological source of these variants. To assess the impact of these paired sample analyses, we analyzed the blood samples obtained from 24 patients representing seven different solid tumor types (breast, colorectal, gastric, gastro-esophageal junction, lung, and melanoma). Across this cohort, of the alterations detected in cfDNA (n=322), 87.3% were correctly classified as somatic, germline or CH without the patient-matched normal blood sample. Specifically, of the variants that were determined to be associated with CH (n=26), only 35% were appropriately assigned without the paired comparison. Additional sources of discordance for somatic and germline alterations were primarily attributed to patients with high levels of ctDNA where differentiation of these variant sources can be challenging through solely computational-based techniques. Taken together, these data demonstrate that through the integrated analysis of cell-free DNA and matched leukocyte DNA, classification of the source of cfDNA-derived alterations can be achieved, which may improve the accuracy of non-invasive tumor profiling, molecular response assessment, and clonal evolution analyses. Citation Format: Tonya N. Watkins, Paul McGregor, David Riley, Tolga Ayazseven, Kristy Waskiewicz, Kelly M. Gerding, Ellen L. Verner, Amy Greer, Aanavi Karandikar, Rami Zahr, Kenneth C. Valkenburg, Jamie Platt, Samuel V. Angiuoli, Mark Sausen. Enhanced detection and classification of cell-free DNA alterations through matched normal analyses with PGDx elioTM plasma complete. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5597.

Abstract 2299: Misclassification of clonal hematopoietic mutations as tumor-derived confound accurate ctDNA-response assessment in patients with metastatic non-small-cell lung cancer: analyses from the phase 3 MYSTIC trial

Abstract Introduction: Circulating tumor DNA (ctDNA) can act as a molecular response (MR) biomarker. Non-tumor informed, plasma-only ctDNA assays are an accessible and rapid mechanism to assess ctDNA levels in patients undergoing treatment for lung cancer but may be impacted by clonal hematopoietic (CH) mutations misclassified as tumor derived. Here, we assess the impact of CH on MR measurement in patients receiving durvalumab, with or without tremelimumab, versus chemotherapy in the Phase III MYSTIC trial. Methods: Using a non-tumor informed, mutation based, ctDNA assay that assesses 500-genes (Guardant Health [GH] Omni, subset to the GH360 genomic coordinates [74-genes] for additional analyses) we calculated plasma-only molecular response (MR) based on change in ctDNA levels between baseline and a 4 or 6-week on-treatment timepoint in 713 patients. FoundationOne CDx tissue data subset to GH Omni genomic coordinates enabled “in-silico” tumor-informed MR analysis where only mutations detectable in tumor tissue were followed as response indicators, in 273 of 713 patients. Targeted duplex-sequencing of peripheral blood mononuclear cell (PBMC) DNA was performed to assess the presence of CH mutations misclassified as tumor derived through plasma-only analyses. Results: Plasma-only MR assessment associated with survival outcomes in immunotherapy treatment arms but not the chemotherapy arm; tumor shrinkage on imaging at 6-week radiological evaluation also predicted survival outcomes only in the immunotherapy arms, suggesting that early tumor response is a stronger predictor of outcome for patients treated with immunotherapy. In-silico tumor-informed MR analyses led to an improved association between MR and outcome across all treatment arms and an increased rate in observed ctDNA clearance. Early tumor-informed ctDNA clearance strongly indicated survival benefit in patients receiving durvalumab and tremelimumab. Targeted analyses of mutations categorized as tumor derived in plasma-only analyses, but absent from tumor tissue sequencing analyses in the same patient, revealed that 87/154 (57%) were PBMC-derived highlighting CH as capable of confounding plasma-only analyses. Conclusion: These exploratory analyses from a phase III randomized study support early-ctDNA kinetics as predictive of long-term benefit in metastatic NSCLC patients and support technical optimization of CH-subtraction approaches to maximize utility of ctDNA as a response biomarker in patients with NSCLC. Citation Format: Chris Abbosh, Michael Kuziora, Daniel Stetson, Zhongwu Lai, Yashaswi Shrestha, Paul Labrousse, Xiaojin Shi, Helen Mann, Diana Merino Vega, Matthew D. Hellmann, Solange Peters, J. Carl Barrett, Darren Hodgson. Misclassification of clonal hematopoietic mutations as tumor-derived confound accurate ctDNA-response assessment in patients with metastatic non-small-cell lung cancer: analyses from the phase 3 MYSTIC trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2299.

Practical Application of Circulating Tumor-Related DNA of Human Papillomavirus in Liquid Biopsy to Evaluate the Molecular Response in Patients with Oropharyngeal Cancer.

Recent findings have shown that human papillomavirus (HPV) DNA is present in the blood as a tumor-specific biomarker (circulating tumor-related HPV; ctHPV) in patients with HPV-related oropharyngeal cancer (HPV-related OPC). The molecular response (MR) in patients with HPV-related OPC can be defined as the change in the number of ctHPV copies in relation to its initial quantity. The optimal model for assessing the MR using a liquid biopsy (LB) should be based on the E6/E7 sequences of the viral genome. MR assessment can help to evaluate the intensity of ongoing treatments in relation to the tumor response. The evaluation of the residual disease at the end of therapy may also be performed by MR assessment. If a partial MR (pMR) is found, caution is indicated and a subsequent LB should be considered, due to the likelihood of disease progression. Complete radiological and clinical responses together with a complete MR (cMR) convincingly indicate a low risk of treatment failure. Moreover, molecular recurrence (Mrec) during a follow-up, confirmed in two consecutive assays, even despite the lack of any other clinical or radiological symptoms of progression, indicates patients at high risk of disease recurrence. In conclusion, MR by ctHPV assessment may hasten the early detection of disease progression, at any stage of the management of the patient with HPV-related OPC.

Molecular Response Assessment in Patients with Chronic Myeloid Leukemia; Clinicopathological Retrospective Research

Molecular Response Assessment in Patients with Chronic Myeloid Leukemia; Clinicopathological Retrospective Research

Clinical and Molecular Response Assessment of AML Harboring Non-Canonical FLT3 p.N676K Driver Mutations to FLT3 Inhibitor Therapies

Treatment of acute myeloid leukemia (AML) has been enhanced by the development and regulatory approval of a series of novel agents, including midostaurin and gilteritinib (FLT3 inhibitors), venetoclax (BCL2 inhibitor), ivosidenib (IDH1 inhibitor), and enasidenib (IDH2 inhibitor). A difficulty that has arisen in the era of molecular therapies, however, is determining the efficacy of these agents for patients with AML harboring atypical driver mutations. These atypical drivers were underrepresented in seminal clinical trials that led to the approval of targeted AML therapies, thereby limiting the availability of data for clinical decision making. For example, the non-canonical FLT3 p.N676K variant was initially described as an acquired resistance mechanism in patients with FLT3 internal tandem duplication (ITD) mutations who were treated with midostaurin. Follow-up studies in Ba/F3 cells demonstrated that the FLT3 N676K mutation is sensitive to midostaurin and quizartinib, but that co-occurrence of FLT3 N676K and ITD mutations confers resistance to both targeted agents. Clinical data from patients with the FLT3 N676K mutation, however, is limited to reports of two patients, both of whom developed the N676K mutation at relapse. There have been no published reports detailing the treatment of patients with the FLT3 N676K mutation with de novo disease, and limited data exist regarding the role of FLT3 inhibition for patients with the FLT3 N676K mutation in the clinical setting. To address this knowledge gap, we detail our experience caring for nine individuals with AML harboring FLT3 N676K at The University of Chicago. The patients were identified by querying the University of Chicago molecular pathology database as part of an IRB-approved retrospective analysis. Six of these patients had AML with FLT3 N676K arising as the only FLT3 variant, whereas the mutational composition of three patients carried coincident ITD or tyrosine kinase domain (TKD) mutations at some point during their clinical course. The median age at diagnosis of AML in our cohort was 41 years, with a mean presenting WBC count of 53.3 k/uL. Four of nine patients had normal cytogenetics. Additional demographic and disease-specific parameters are depicted in Table 1. One elderly patient pursued comfort care immediately after presentation. Of the remaining eight patients, six received FLT3 inhibitors at any point during their clinical trajectory. Three patients were treated with FLT3 inhibitors added to upfront standard induction therapy (midostaurin, n=2 ; sorafenib, n=1). Of those, one (patient #1) achieved a morphologic and molecular complete remission and proceeded to curative-intent allogeneic transplant. The remaining two patients (patients #5 and #6) harbored co-occuring FLT3 mutations, one with FLT3 ITD and the other with FLT3 TKD, and both experienced relapse after an initial complete remission following induction therapy. In patients for whom longitudinal next-generation sequencing data from bone marrow specimens was available, we observed dramatic reduction in measurable FLT3 N676K variant allele frequencies after FLT3 inhibitor use, regardless of line of therapy (Fig. 1). Here, we describe the largest series to date of AML patients with atypical FLT3 N676K driver mutations. Affected individuals in our cohort presented at a notably younger age and demonstrated reductions in disease burden with the use of targeted FLT3 inhibitors. The presence of concurrent canonical FLT3 mutations was associated with loss of treatment response. Longer-term follow will help evaluate the durability of FLT3 inhibitor maintenance strategies in both transplant and non-transplant clinical settings. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

BIOM-49. A PILOT STUDY OF CEREBROSPINAL FLUID EXOSOMAL SMALL RNA-SEQUENCING IN PEDIATRIC MEDULLOBLASTOMA PATIENTS ON THE NEXT CONSORTIUM “HEAD START” 4 PROTOCOL

Abstract BACKGROUND Head Start 4 is a randomized clinical trial to determine whether dose-intensive tandem consolidation, compared with a single cycle, with autologous hematopoietic progenitor cell rescue provides a survival benefit in pediatric patients with medulloblastoma or other embryonal tumors. The trial incorporates upfront molecular subgrouping and non-mandatory, prospective blood and cerebrospinal fluid (CSF) collection. This pilot study aimed to identify exosomal non-coding RNAs (exo-ncRNAs) that might serve as novel diagnostic and/or treatment response biomarkers. METHODS CSF(1-2mLs) from 11 controls (non-tumor) and 27 medulloblastoma participants including 23 obtained at baseline, 22 at the end of induction, 3 post-consolidation, and 4 relapse time points, were profiled. Exosome isolation and small RNA-sequencing were performed by System Biosciences. Differential gene expression (DGE) was performed in R (DESeq2). Variations in gene expression profiles between samples were visualized using principal component analysis. RESULTS After limiting to ncRNAs with expression of 2 counts per million in 50% or more of the samples in each comparison, ~9,500 ncRNAs were detected. DGE analyses revealed 118 ncRNAs with log2 fold change(FC) >2 and 1 ncRNA with log2FC< -2 in baseline CSF samples compared to controls. In contrast, 11 ncRNAs(log2FC >2) and 1 ncRNA(log2FC< -2) were detected in end of induction CSF samples compared to controls. Comparing end of induction to baseline CSF samples accounting for paired samples, 0 ncRNAs(log2FC >2) and 52 ncRNAs(log2FC< -2) were detected. CONCLUSIONS Overall, our data indicate that exosomal small RNA-sequencing of limited CSF volumes is feasible. Differential expression and distinct clustering between tumor baseline samples compared to non-tumor controls was observed. CSF-derived exo-ncRNAs at end of induction also demonstrated “normalization” of ncRNA profiles, signifying CSF biomarkers may serve a role in diagnosis and molecular response assessment. A comprehensive analysis including multi-marker predictive model development and molecular subgrouping will be undertaken at completion of study enrollment.