Finding Waldo: The Evolving Paradigm of Circulating Tumor DNA (ctDNA)—Guided Minimal Residual Disease (MRD) Assessment in Colorectal Cancer (CRC)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Targeting MRD: Rationale and Evidence Supporting the Strategy
3. Biology of Cell-Free DNA
4. ctDNA Assays
ctDNA Assay | Tumor-Informed | Assay Description | Target Alterations in Plasma DNA | Turnaround Time | Comments |
---|---|---|---|---|---|
Guardant REVEAL [28] | No | Plasma-only NGS-based test that integrates somatic alterations and epigenomic cancer signatures. | Somatic and epigenetic aberrations | 2 weeks | Integrating epigenomic signatures increased sensitivity by 25–36% versus genomic alterations alone. Fastest turnaround time as tumor sequencing is not required. |
Safe-seqS [55] | Yes | Tumor sequencing followed by deep sequencing of plasma DNA with unique molecular barcoding to detect tumor-specific mutations. | One tumor-specific mutation in each patient | 2 weeks * | ctDNA result is classified as detectable (ctDNA-positive) or undetectable |
Signatera [29] | Yes | A personalized, tumor-informed, multiplex PCR-based NGS assay. Sixteen patient-specific, somatic SNVs are selected for each patient based on the whole-exome sequencing of the tumor for interrogation in the cfDNA. Plasma samples with at least two tumor-specific SNVs are defined as ctDNA-positive. | 16 somatic variants | 7–10 days * | Limit of detection 0.01% variant allele frequency. Provides ctDNA level expressed as mean tumor molecules (MTM)/mL of plasma |
ddPCR [58] | Yes | Targeted sequencing of the primary tumor for a predefined panel of 29 genes followed by an interrogation of plasma cfDNA by ddPCR to search for the tumor-specific mutations (1–2 mutations). | 1 to 2 alterations selected by tumor sequencing | 2–5 days * | Tracking at least two variants in plasma increased the ability to identify MRD to 87.5%. |
5. ctDNA-Guided MRD Assessment: Studies in Colorectal Cancer
6. ctDNA-Guided Surveillance
7. ctDNA-Guided Clinical Trials
8. Future Perspective
9. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Study | Patient Population | n | ctDNA Assay | ctDNA Testing Time Points | Major Findings | Comments |
---|---|---|---|---|---|---|
Tie et al., 2016 [55] | Stage II CC | 230 | Safe-SeqS | 4–10 weeks post-op and every 3 months for 2 years | Cohort not receiving ACT If ctDNA-+ve post-op: HR for cancer recurrence—18 (95% CI, 7.9 to 40). Cohort receiving ACT If ctDNA-+ve post-ACT: HR for recurrence—11 (95% CI, 1.8 to 68). | ctDNA detection preceded radiologic recurrence by a median of 5.5 months. |
Reinert et al., 2019 [29] | Stages I to III CRC | 130 | Signatera | Preop, post-op day 30, and every 3 months for up to 3 years. | HR for cancer recurrence with positive ctDNA:
| Serial ctDNA analyses revealed disease recurrence up to 16.5 months ahead of radiologic imaging (mean, 8.7 months; range, 0.8–16.5 months). |
Tie et al., 2019 [32] | Stage III CC | 96 | Safe-SeqS | 4–10 weeks post-op and within 6 weeks of ACT completion | HR for cancer recurrence with positive ctDNA:
| RFS at 3 years in patients who are ctDNA-positive vs. -negative: post-op 47% vs. 76%, post-ACT 30% vs. 77%. |
Tarazona et al., 2019 [30] | Stages I to III CC | 150 | Tumor-informed ddPCR | Preop, 6–8 weeks post-op and every 4 months up to 5 years. | HR for recurrence with positive ctDNA:
| ctDNA detection during surveillance preceded radiological recurrence by a median of 11.5 months. |
Henriksen et al., 2022 [27] | Stage III CRC | 168 | Signatera | 2–4 weeks post-op and every 3 months thereafter | Detection of ctDNA was a strong recurrence predictor post-o (HR = 7.0; 95% CI, 3.7–13.5) and immediately after ACT (HR = 50.76; 95% CI, 15.4–167). | ctDNA detected recurrence with a median lead-time of 9.8 months compared with radiologic studies. |
Parikh et al., 2021 [28] | Stages I–IV CRC | 103 | Tumor-uninformed assay (REVEAL) | Post-op, post-ACT, and longitudinally in some patients | HR for recurrence when +ve for ctDNA post definitive therapy and with >1 year of follow-up: 11.28. | Integrating epigenomic signatures increased sensitivity by 25–36% versus genomic alterations alone. |
Tie et al., 2019 [33] | Locally advanced rectal carcinoma | 159 | Safe-SeqS | Pretreatment, post CRT, and 4–10 weeks after surgery. | Significantly worse RFS if ctDNA was detectable after CRT (HR, 6.6; p < 0.001) or after surgery (HR, 13.0; p < 0.001). | The estimated 3-year RFS was 33% for the post-op ctDNA-positive patients and 87% for the post-op ctDNA-negative patients. |
McDuff et al., 2021 [59] | Locally advanced rectal carcinoma | 29 | ddPCR | Baseline, preop, and post-op | At a median follow-up of 20 months, patients with detectable post-op ctDNA experienced poorer RFS (HR, 11.56; p = 0.007). | All patients (4 of 4) with detectable post-op ctDNA recurred, whereas only 2 of 15 patients with undetectable ctDNA recurred (negative predictive value = 87%). |
Tie et al., 2021 [60] | CRC with liver metastasis | 54 | Safe-SeqS | Preop and post-op samples, serial samples during pre- or post-op chemotherapy, and follow-up | Detectable post-op ctDNA predicted a significantly lower RFS (HR, 6.3; 95% CI, 2.58 to 15.2; p < 0.001) and OS (HR, 4.2; 95% CI, 1.5 to 11.8; p < 0.001) | End-of-treatment (surgery +/− ACT) ctDNA detection was associated with a 5-year RFS of 0% compared to 75.6% for patients with an undetectable end-of-treatment ctDNA (HR, 14.9; 95% CI, 4.94 to 44.7; p < 0.001). |
Loupakis et al., 2021 [61] | CRC undergoing liver resection | 112 | Signatera | Post-op, at the time of radiologic relapse or last follow-up. | ctDNA-positive status was also associated with an inferior overall survival: HR: 16.0; 95% CI, 3.9 to 68.0; p < 0.001. | ctDNA was detectable in the post-op sample in 54.4% (61 of 112) of patients, of which 96.7% (59 of 61) progressed at the time of data cutoff (HR: 5.8; 95% CI, 3.5 to 9.7; p < 0.001). |
Kotaka et al., 2022 (Galaxy study) [62] | Stages I–IV CRC patients | 1365 | Signatera | Before surgery, 1-month post-op and every 3 months thereafter for 2 years | Six-month DFS rate was significantly higher in patients whose ctDNA was converted with ACT compared to patients who remained positive after ACT with an HR of 52.3 (95% CI: 7.2–380.5; p < 0.001), after a median follow-up of 6.6 months. | Cumulative incidence of ctDNA clearance was significantly higher with ACT vs. non-ACT (67% vs. 7% by 24 weeks; cumulative HR = 17.1; 95% CI: 6.7–43.4, p < 0.001). |
Tie et al., 2022 (DYNAMIC) [63] | Stage II CC | 455 | SafeSeqS | 4 and 7 weeks post-surgery | Adjuvant therapy guided by ctDNA resulted in chemotherapy administration in lower proportion of patients without any detriment to 2-year RFS. | DYNAMIC is the first reported prospective randomized study supporting the ctDNA-guided adjuvant therapy approach in stage II colon cancer. |
Study Identifier | Study Phase | Study Population | n | ctDNA Assay | Study Description | Primary Endpoint |
---|---|---|---|---|---|---|
NCT04068103 (COBRA) | II/III | Stage II CC without high-risk features | 1408 | LUNAR-1 (Guardant Health) | Arm A: active surveillance. Arm B: ctDNA directed therapy (ctDNA-positive → FOLFOX/CAPOX for 6 months, ctDNA-negative → active surveillance) | Clearance of ctDNA with ACT (phase II) and RFS (phase III) |
NCT05174169 (CIRCULATE-US) | II/III | Stage II and III CC | 1912 | Signatera | Cohort A: Arm 1—ctDNA-negative treated with FOLFOX 3–6 months/CAPOX 3 months. Arm 2—ctDNA-negative undergoing serial ctDNA monitoring and no treatment. Cohort B: Arm 3—ctDNA-+ve treated with FOLFOX/CAPOX for 6 months. Arm 4—ctDNA-+ve treated with mFOLFIRINOX | TTPos (time from randomization until ctDNA-positive event), DFS |
NCT04120701 (CIRCULATE-PRODIGE 70) | III | Resected Stage II CC | 1980 | ddPCR | ctDNA-positive → randomized (2:1) to receive ACT or no ACT. ctDNA-negative → surveillance. | 3-year DFS in ctDNA-positive patients. |
ACTRN12615000381583 (DYNAMIC-II) | III | Stage II CC | 450 | Safe-SeqS | Arm A: positive for ctDNA → ACT, negative for ctDNA → surveillance. Arm B: treated at the discretion of the clinicians. | RFS |
ACTRN12617001566325 (DYNAMIC-III) | II/III | Stage III CC | 1000 | Safe-SeqS | Arm A: standard of care. Arm B: ctDNA-informed (ctDNA-negative → therapy de-escalation; ctDNA-positive → therapy escalation) | RFS |
GALAXY (UMIN000039205) | Prospective observational | Stages II∓IV CRC | 2500 | Signatera | Serial ctDNA monitoring after surgery. If ctDNA-negative--> VEGA trial (therapy de-escalation). If ctDNA-+ve → ALTAIR trial. | DFS |
VEGA (jRCT1031200006) | III | High-risk stage II or low-risk stage III CC | 1240 | Signatera | Designed to compare adjuvant CAPOX for 3 months vs. observation for GALAXY patients with negative ctDNA at week 4 after surgery. | DFS |
NCT04089631 (CIRCULATE AIO-KRK-0217) | III | Stage II CC | 4812 | NGS | Patients positive for ctDNA post-resection are randomized to observation vs. capecitabine or CAPOX (investigator’s choice) × 6 months | DFS |
MEDOCC-CrEATE (NL6281/NTR6455) | III | Stage II CC | 1320 | PGDx elio™ | Standard of care surveillance vs. ctDNA-guided ACT (ctDNA-positive: 6 months of CAPOX; ctDNA-negative: surveillance) | The proportion of patients receiving ACT after surgery if ctDNA-positive. |
NCT03748680 (IMPROVE-IT) | II | Stage I and II CRC | 64 | ddPCR, NGS | ctDNA-positive patients randomized to observation vs.FOLFOX or CAPOX for 6 months. | DFS |
NCT04264702 (BESPOKE) | Prospective Observational | Stage II and III CRC | 1000 | Signatera | Serial ctDNA testing following surgery and ACT vs. observation at the discretion of the treating clinician. Control arm-matched stage II and III patients with a minimum 2 years of follow-up data. | 1. Impact of ctDNA on adjuvant treatment decisions. 2. Rate of ctDNA detected recurrence while asymptomatic. |
NCT04259944 (PEGASUS) | II | Resected MSS stage III and high-risk stage II (T4N0) CC | 140 | LUNAR-1 (Guardant Health) | ctDNA-guided ACT. (i) ctDNA-positive → CAPOX for 3 months; (ii) ctDNA-negative → capecitabine for 6 months but will be retested after 1 cycle, and if found ctDNA-positive, will be switched to CAPOX. | The number of patients negative for ctDNA post-op and post ACT later turning ctDNA-positive or developing radiographic relapse. |
NCT04084249 (IMPROVE-IT2) | III | Stage III or high-risk stage II CRC | 254 | ddPCR, NGS | Patients were randomized to ctDNA-guided post-operative surveillance or standard-of-care CT-scan surveillance. | Fraction of patients with relapse receiving curative resection or local treatment |
NCT03803553 (ACT-3) | III | Stage III CC | 500 | LUNAR-1 (Guardant Health) | ctDNA-enriched second-line adjuvant therapy: patients are distributed post-ACT as follows- 1. ctDNA-negative: active surveillance; 2. ctDNA-positive: (a) MSS patients- 6 months of FOLFIRI vs. active surveillance, (b) MSI high-6 months of nivolumab, (c) BRAF mutant and MSS-6 months of BRAF directed therapy. | DFS, ctDNA clearance rate |
NCT04457297 (ALTAIR) | III | Stage II∓IV CRC | 240 | Signatera | TAS-102 for 6 months vs. placebo for patients positive for ctDNA following completion of standard ACT and no evidence of relapse radiologically in the GALAXY study | DFS |
NCT03436563 | Ib/II | Stage IV CRC | 74 | Signatera | Patients with metastatic CRC positive for ctDNA following resection of all metastases will receive M7824 (anti-PDL1/TGFbetaRII fusion protein) for 6 doses | ctDNA clearance rate |
NCT04589468 | Ia/b | CRC, breast, and prostate cancer stage I–III | 70 | Signatera | Patients with primary breast, prostate, or colorectal cancer and detectable ctDNA (n = 50) post definitive treatment will perform one of five escalating dose levels of exercise. | RP2D of exercise |
NCT04853017 (Amplify-201) | I/II | Solid tumors, including CRC with RAS mutation | 18 | Signatera | Patients with tumors harboring RAS mutation and minimal residual disease with detection of ctDNA receive different dose levels of ELI-002, a RAS targeting vaccine. | 1. MTD of ELI-002 and the RP2D 2. Safety |
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Chakrabarti, S.; Kasi, A.K.; Parikh, A.R.; Mahipal, A. Finding Waldo: The Evolving Paradigm of Circulating Tumor DNA (ctDNA)—Guided Minimal Residual Disease (MRD) Assessment in Colorectal Cancer (CRC). Cancers 2022, 14, 3078. https://doi.org/10.3390/cancers14133078
Chakrabarti S, Kasi AK, Parikh AR, Mahipal A. Finding Waldo: The Evolving Paradigm of Circulating Tumor DNA (ctDNA)—Guided Minimal Residual Disease (MRD) Assessment in Colorectal Cancer (CRC). Cancers. 2022; 14(13):3078. https://doi.org/10.3390/cancers14133078
Chicago/Turabian StyleChakrabarti, Sakti, Anup Kumar Kasi, Aparna R. Parikh, and Amit Mahipal. 2022. "Finding Waldo: The Evolving Paradigm of Circulating Tumor DNA (ctDNA)—Guided Minimal Residual Disease (MRD) Assessment in Colorectal Cancer (CRC)" Cancers 14, no. 13: 3078. https://doi.org/10.3390/cancers14133078
APA StyleChakrabarti, S., Kasi, A. K., Parikh, A. R., & Mahipal, A. (2022). Finding Waldo: The Evolving Paradigm of Circulating Tumor DNA (ctDNA)—Guided Minimal Residual Disease (MRD) Assessment in Colorectal Cancer (CRC). Cancers, 14(13), 3078. https://doi.org/10.3390/cancers14133078