With a half-life of minutes to hours, circulating tumor DNA (ctDNA) is in fixed flux, rendering its analysis extremely helpful in metastatic breast most cancers administration offered that it’s utilized appropriately, in response to Pedram Razavi, MD, PhD, who added that ongoing analysis continues to unfold concerning the expertise’s capability to offer a complete evaluation of the genomic underpinnings of the illness with enough sensitivity and specificity.
“Estimating the ctDNA fraction is required for correct interpretation of the ctDNA outcomes,” Razavi mentioned throughout a presentation on the twenty third Annual Worldwide Congress on the Way forward for Breast Most cancers® East.1 “Incorporating ctDNA fraction evaluation assessed by the identical assay or orthogonal checks [is needed, and it’s] essential to interpret leads to the context of ctDNA fraction and to incorporate ctDNA fraction as an important a part of the report.”
Razavi added that regardless of its sooner turnaround time and higher feasibility, ctDNA profiling nonetheless lacks the sensitivity and specificity required to detect sure alterations. Furthermore, he added that ctDNA shouldn’t be used as a catch-all instrument given the low abundance and fragmented nature of sure courses of genomic alterations together with structural variants, giant insertion-deletions (indels), and replica quantity alterations. In consequence, Razavi beneficial reaching for each ctDNA and tissue profiling in first-line metastatic breast most cancers, and, upon development, beginning with ctDNA and reflexing to tissue in subsequent settings.
Razavi is the director of the Breast Translational Program and Breast Molecular Tumor Board, and director of Liquid Biopsy and Genomics throughout the MSK International Biomarker Improvement Program at Memorial Sloan Kettering Most cancers Heart (MSK) in New York, New York.
Going Past Genotyping: Utilizing ctDNA to Research Spatial Tumor Heterogeneity
The usage of broad-based genomic evaluation in breast most cancers has helped outline the germline and somatic alterations which might be present in every molecularly distinct subgroup. Nevertheless, much less is understood in regards to the genomic make-up of metastatic tumors. As such, investigators at MSK launched a big genomic dataset of sufferers with metastatic most cancers, from which they extracted knowledge on sufferers with the most important breast most cancers subset: hormone receptor (HR)–constructive illness. Potential focused sequencing was carried out on 1,918 tumors from 1,756 sufferers with breast most cancers. Tumors and matched regular DNA had been evaluated with the MSK-Built-in Mutation Profiling of Actionable Most cancers Targets platform, which might determine somatic mutations, DNA copy-number alterations, and choose rearrangements in as much as 468 cancer-associated genes. Sequencing was carried out with excessive protection depth, permitting for higher sensitivity vs widespread broader-scale sequencing approaches for subclonal mutational occasions.2
Outcomes confirmed that, general, mutations in 32 genes had been considerably extra widespread in metastases in contrast with main tumors (Q < .05). Moreover, a case examine of a 60-year-old feminine with metastatic HR-positive, HER2-negative breast most cancers who participated within the examine was shared throughout the assembly. Razavi defined that a number of alterations had been discovered on this affected person at varied metastatic websites, together with TP53, CDH1, ERBB3, ERBB2, PIK3CA, and ESR1. This additional signifies the intensive spatial heterogeneity in superior tumor samples and ensuing polyclonal resistance by convergent evolution.
“We had premortem samples from the post-mortem from that affected person and we analyzed the cell-free DNA [cfDNA]. Very curiously we discovered that cfDNA can determine many of the alterations that we present in a number of tumor websites,” Razavi mentioned. “This offers one other alternative for us to doubtlessly design scientific trials that tackle the polyclonal resistance.”
Of word, the ctDNA stage for every mutation was related to the variant allele fraction (VAF) of the tumor and the variety of websites harboring the mutation, in response to Razavi. “Most significantly, identification and stage of the mutations within the bloodstream was [highly] related to how most of the illness websites had that mutation. So, the upper the variety of websites that had it, the upper the probability and the upper the extent of ctDNA,” Razavi mentioned.
Findings printed in Nature Drugs in 2019 additional illustrated that using a high-intensity sequencing assay of cfDNA and matched white blood cell DNA spanning 508 genes might determine tumor-derived mutations with excessive sensitivity and specificity. Furthermore, investigators discovered that 53.2% of mutations recognized in 124 sufferers with metastatic most cancers by cfDNA had clonal hematopoiesis commonalities, additional illustrating the significance of a sequencing instrument able to correct variant interpretation.3
Taking this expertise one step additional, investigators evaluated pretreatment and posttreatment ctDNA samples of sufferers who acquired alpelisib (Piqray) plus aromatase inhibitors in a section 1/2 trial (NCT01870505). Outcomes from the longitudinal evaluation demonstrated that loss-of-function PTEN mutations occurred in 25% of sufferers with resistance and that ESR1 activating mutations, along with correlating with resistance, additionally expanded in quantity and allele fraction throughout remedy.4
“We will [also] doubtlessly be taught from the PADA-1 [NCT03079011] expertise going after the resistant clone early and attempting to handle polyclonal resistance, which is a serious downside and one of many causes you can not remedy metastatic illness in breast most cancers,” Razavi mentioned.
Concerns for MRD ctDNA Assays
The following section of growth that investigators imagine might take ctDNA from bench to bedside is proof of their utility in detecting clones beneath present thresholds, which is the place minimal residual illness (MRD)–knowledgeable assays could come into play, defined Rizavi.
“One other downside is [the resistant clones] are inclined to [occur] even sooner than the genotyping thresholds that we have now. The genotype threshold that we have now now with many of the assays is round 0.05% to 0.1%, however now have a number of assays that may go beneath that… ctDNA modifications can occur a lot sooner than what we are able to determine with these genotyping assays, [so we get] false negatives within the present paradigm utilizing some of these assays. However we have now been creating a number of MRD assays, and these MRD assays permit us to determine ctDNA at an especially low stage,” Razavi mentioned.
For instance, findings from a examine offered at the 2024 ASCO Annual Assembly demonstrated the feasibility of utilizing an ultra-sensitive, whole-genome sequencing–primarily based, tumor-informed ctDNA platform to determine sufferers at excessive danger of relapse. A complete of 598 plasma samples had been evaluated from 76 sufferers with early breast most cancers together with triple-negative (n = 23), HER2-positive (n = 33), and HR-positive illness (n = 16). Samples had been collected at baseline, cycle 2 of neoadjuvant chemotherapy, post-surgery, and each 3 months throughout follow-up for the primary yr, and each 6 months thereafter for as much as 5 years.5
Outcomes confirmed a variety of ctDNA ranges, with a median worth of 336 elements per million (PPM; vary, 3.73-112,011). Notably, 39% of all ctDNA detections fell into the ultra-low vary of lower than 100 PPM (beneath roughly 0.01% tumor fractions). Relating to the correlation with outcomes, at a median follow-up of 76 months (vary 5-113), the presence of ctDNA was related to excessive danger of future relapse (P <.001) and shortened general survival (P <.001). Notably, the median lead-time from ctDNA detection to scientific relapse was 15 months (vary, 4-41), showcasing the potential utility of utilizing the expertise to watch illness burden and intercept resistance earlier than it may be genotyped.5
Present Me the Information: ctDNA Monitoring in First-Line HR-Constructive Metastatic Breast Most cancers
Extra knowledge from the 2024 ASCO Annual Assembly offered by Jesus Fuentes Antras, MD, of Princess Margaret Most cancers Centre, and colleagues reinforce earlier findings exhibiting the advantage of longitudinal ctDNA analysis. On this particular examine, investigators used a tumor-informed ctDNA assay that tracked patient-specific variants recognized by tumor sequencing. Eligible sufferers included these with HR-positive, HER2-negative metastatic breast most cancers receiving normal endocrine remedy together with a CDK4/6 inhibitor. Plasma samples had been collected at baseline, inside 30 days, and roughly each 3 months with restaging scans. Archival tumor whole-genome sequencing was used to create individualized panels for ctDNA monitoring.6
A complete of 51 sufferers had been analyzed. Sufferers had a median age of 60 years (vary, 38-88) and most had been receiving frontline remedy (75%) versus second-line remedy (20%). Most sufferers had visceral illness (67%) and the breakdown of CDK4/6 inhibitor use was as follows: palbociclib (Ibrance; 76%), ribociclib (Kisqali; 22%), and abemaciclib (Verzenio; 2%).
Outcomes confirmed that larger estimated VAF at baseline was related to shorter time to remedy failure (TTF; hazard ratio, 1.14; 95% CI, 1.05-1.23; P <.01). Nevertheless, early will increase above baseline didn’t considerably correlate with TTF, with 3 of 8 circumstances exhibiting extended responses. Extra findings demonstrated that ctDNA clearance was related to longer TTF (hazard ratio, 0.06; 95% CI, 0.01-0.45; P < .01), with a median worth that was not reached vs 14.5 months for sufferers with and with out ctDNA clearance, respectively.
“There’s a position for doing ctDNA-guided vs image-guided monitoring in metastatic illness and these are the forms of scientific trials that we must always do. I’m not saying that we must always utterly abandon imaging in sufferers, however there’s the potential for us to watch sufferers with ctDNA and have ctDNA-triggered imaging in sufferers,” Razavi concluded.
Disclosures: Dr Razavi reported institutional grant/funding from the Nationwide Institutes of Well being, Komen, Breast Most cancers Alliance, Grail, Illumina, Novartis, AstraZeneca, Epic Sciences, Invitae/ArcherDx, Biotheranostics, Tempus, Inivata, Biovica, Guardant, Personalis, Myriad, Foresight; and serving as a guide/advisory board advisor for Novartis, AstraZeneca, Pfizer, Lilly/Loxo, Prelude Therapeutics, Epic Sciences, Basis Drugs, Inivata, Natera, Tempus, SAGA Diagnostics, Paige.ai, Guardant, and Myriad.
References
- Razavi P, et al. Understanding ctDNA leads to metastatic breast most cancers exploring potential utilities in scientific observe and trial design. Offered at: twenty third Annual Worldwide Congress on the Way forward for Breast Most cancers East; July 19-20, 2024; New York, NY.
- Razavi P, Chang MT, Xu G, et al. The genomic panorama of endocrine-resistant superior breast cancers. Most cancers Cell. 2018;34(3):427-438.e6. doi:10.1016/j.ccell.2018.08.008
- Razavi P, Li BT, Brown DN, et al. Excessive-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants. Nat Med. 2019;25(12):1928-1937. doi:10.1038/s41591-019-0652-7
- Razavi P, Dickler MN, Shah PD, et al. Alterations in PTEN and ESR1 promote scientific resistance to alpelisib plus aromatase inhibitors. Nat Most cancers. 2020;1(4):382-393. doi:10.1038/s43018-020-0047-1
- Garcia-Murillas I, Cutts R, Abbott C, et al. Extremely-sensitive ctDNA mutation monitoring to determine molecular residual illness and predict relapse in sufferers with early breast most cancers. J Clin Oncol. 2024;42(suppl 16):1010. doi:10.1200/JCO.2024.42.16_suppl.1010
- Antras JF, Elliot M, Predominant S, et al. Characterization of molecular response and development in sufferers with metastatic HR+/HER2- breast most cancers receiving endocrine remedy and CDK4/6 inhibitors utilizing a high-sensitivity tumor-informed assay. J Clin Oncol. 2024;42(suppl 16):3052. doi:10.1200/JCO.2024.42.16_suppl.3052
