Pros and cons of liquid biopsy: Ready to replace tissue?

Transcription

1 Pros and cons of liquid biopsy: Ready to replace tissue? 2-Day Molecular Biologists Symposium: Liquid biopsies Federico Rojo

2 Enterprise Interest No disclosures.

3 Biological limitations for molecular testing: Spatial and temporal (dynamic) molecular heterogeneity in cancer

4 Biological limitations for molecular testing: Feasibility (and opportunity) for re-biopsy in disseminated disease Waiting time Anatomical location is difficult for biopsy Sense of risk involved in re-biopsy Patient poor performance status Failure up to 20% of patients Yoon, et al. Radiology 2012 Yu, et al. Clin Cancer Res 2013 Chouaid, et al. Lung Cancer 2014 Redig, et al. JAMA Oncol Campo et al. J Clin Oncol 2016

5 Circumvent biological limitations of molecular testing by circulating biomarkers: Liquid biopsy Often tissue is not enough: Liquid biopsy Main advantages: Rapid Easy and accepted by patients Repeatable Avoid issues relater to tumor heterogeneity Main disadvantage: Sensitivity Targets CTCs cfdna cfrna Platelets Exosomes Origins Selected viable tumor cells leaving actively primary and/or metastasis Analysis of therapeutic targets and drug resistance conferring gene mutations on peripheral blood samples: Understanding metastatic development Estimation of risk for metastatic relapse or progression Prediction of targeted therapy response Monitoring (minimal residual) disease Tracking secondary ( acquired ) resistance Assessing intratumor heterogeneity Necrotic and apoptotic tumor cells Necrotic and apoptotic tumor cells Tumor Active incorporation of exosomes Active secretion of encapsulated particles by tumor cells Definition Tumor cells Fragmented genomes released from dying tumor cells of primary and/or metastasis Fragmented RNA released from dying tumor cells Circulating platelets Circulating encapsulated particles Analytes DNA, RNA (mrna, mirna), protein DNA RNA RNA (mrna, mirna) RNA (mrna, mirna), protein

6 Survey of ctdna in human cancer by tumor type and stage Cases with detectable cdna, Stage IV Cases with detectable cdna, localized vs metastatic Bettegowda et al, Sci Tran Med Feb 2014

7 Liquid biopsy: Pros

8 Diagnostic applications of blood-based molecular testing

9 Diagnostic applications of blood-based molecular testing Early Stage Early Diagnosis

10 Early stage: Early detection Liquid biopsy direct detection of early stage cancer CancerSEEK evaluates 8 proteins and mutations in 1933 distinct genomic positions from 16 genes Sensitivity: 69-98% for the detection of five cancer types (ovary, liver, stomach, pancreas, and esophagus) Specificity: >99% N=1005, non-metastatic ovary, liver, stomach, pancreas, esophagus, colorectum, lung and breast tumors

11 Diagnostic applications of blood-based molecular testing Early Stage Prognosis

12 Early stage: Prognosis Prediction of relapse in early breast cancer ChemoNEAR study design García-Murillas, I et al. Science Trans Med 2015 García-Murillas, I et al. SABCS 2016

13 Early stage: Prognosis Prediction of relapse in early breast cancer García-Murillas, I et al. Science Trans Med 2015 García-Murillas, I et al. SABCS 2016

14 Early stage: Prognosis Role of liquid biopsy in predicting post-operative recurrence in NSCLC 5 studies, 353 patients DFS in surgical NSCLC Ling, H et al. J Thorac Dis 2018

15 Diagnostic applications of blood-based molecular testing Early Stage Residual Disease

16 Early stage: Minimal residual disease ctdna as prognostic marker for colorectal cancer in early stage RFS in stage II colorectal cancer N=250 stage II CRC Post-surgery plasma Post-chemo plasma Clinical risk Tie, J et al. Sci Trans Med 2016

17 Diagnostic applications of blood-based molecular testing Advanced Stage Treatment selection

18 Advanced stage: Treatment selection ctdna EGFR testing predicts TKI benefit in NSCLC Plasma EGFR mut+ Tissue EGFR mut+ Plasma EGFR mut- Mok, T et al. Clin Cancer Res 2015 Maemondo, M et al. NEJM 2010

19 Advanced stage: Treatment selection Statement paper from IASLC: role of liquid biopsy in advanced NSCLC Rolfo, C et al. J Thorac Oncol 2018

20 Biological limitations for molecular testing: Spatial and temporal (dynamic) molecular heterogeneity in cancer Ichihara, E & Lovely, CM. Cancer Discov 2015

21 Advanced stage: Treatment selection T790M plasma detection and clinical response to osimertinib BEAMing dpcr plasma analysis (AURA trial, n=271 patients) for T790M, Del19, & L858R Tumor T790M+ 62% ORR 9.7m PFS PlasmaT790M+ 63% ORR 9.7m PFS Plasma T790M positive predicts for a high ORR and a prolonged PFS, identical to that predicted by a tumor T790M positive result (Cobas) Oxnard, GR et al. J Clin Oncol 2016

22 Advanced stage: Treatment selection Statement paper from IASLC: role of liquid biopsy in NSCLC progression during treatment with TKI Rolfo, C et al. J Thorac Oncol 2018

23 Advanced stage: Treatment selection ESMO guidelines: role of liquid biopsy in NSCLC progression during treatment with TKI Novello, S et al. Ann Oncol 2016

24 Advanced stage: Treatment selection Tumor Mutational Burden in Blood and Atezolizumab efficacy in 2L+ NSCLC Gandara, DR et al. Nat Med 2018

25 Diagnostic applications of blood-based molecular testing Advanced Stage Monitoring Response

26 Advanced stage: Prognosis ctdna as prognostic marker for CRC in advanced stage PLACOL study ctdna concentration at baseline ctdna variation during follow-up Garlan, F et al. Clin Cancer Res 2017

27 Advanced stage: Prediction of benefit Early ctdna dynamics and clonal selection with palbociclib for breast cancer PALOMA-3 phase III trial in metastatic luminal breast cancer with progression to AI Relative change in PIK3CA and ESR1 after 15 days of treatment predicts PFS on palbociclib+fulvestrant O Leary, B et al. Nat Comm 2018

28 Diagnostic applications of blood-based molecular testing Advanced Stage Clonal Evolution: Acquired Resistance

29 Advanced stage: Secondary mutations ESR1 mutations in metastatic luminal breast cancer after AI Tot, W et al. Nat Genetics 2013 Robinson, DR et al. Nat Genetics 2013 Schiavon, G et al. Science Trans Med 2015

30 Advanced stage: Secondary mutations ESR1 mutations in metastatic luminal breast cancer after AI Luminal breast cancer Prior sensitivity to nonsteroidal aromatase inhibitor N=723 SoFEA Fulvestrant 250mg + Placebo Fulvestrant 250mg + Anastrozole Exemestane Fribbens, C et al. J Clin Oncol 2016

31 Advanced stage: Secondary mutations Emergence of secondary mutations in mcrc after anti-egfr mab therapy Bettegowda et al, Sci Tran Med Feb 2014

32 Advanced stage: Mutation tracking Monitoring ctdna levels in NSCLC treated with anti-egfr TKI therapy Chabon, JJ et al. Nat Communications 2016 Thomson, JC et al. Clin Cancer Res 2016

33 Liquid biopsy: Cons

34 Liquid biopsy: Limitations Driver mutations in non-cancerous persons Low frequency TP53 mutations were also found in 100% of peripheral blood samples from 17 women with and without ovarian cancer (none with hematologic disorder) Clonal hematopoiesis with somatic mutations in 10% of persons older than 65 years of age and in 1% younger than 50 years Krimmel, JD et al. Proc Natl Acad Sci 2016 Fernandez-Cuesta, L et al. EBioMedicine 2016 Genovese, G et al. N Engl J Med 2014

35 n future include sampling of ctdna originating from multiple micrometastatic tumours each too small to be apparent on CT imaging but with a combined burden sufficient to result in detectable levels of ctdna and/or a shift in tumour cell death dynamics towards a biology that is more conducive to ctdna release in the metastatic setting. stage IV lung cancers were diagnosed in the LDCT group, suggesting that LDCT generally enabled the identification of lung cancers at an earlier stage than was possible with chest radiography (resulting in stage shifts), increasing the feasibility of cure44. This finding suggests that, in order to demonstrate superior sensitivity to chest Liquid biopsy: Limitations e burden ell-free ology ning z et al.41 pycer and uivalent Correlation between abundance of ctdna and tumor stage utant um. of ctdna also early 42,43. ogical through with the ons PCR he MAFs umour ur ship stimation mean Fig. 3 The correlation between the abundance of ctdna, tumour volume, tumour diameter, and 0.008% T stage. This figure demonstrates the correlation between estimated mean clonal mutant allele freuse Abbosh, C et al. Nat Rev 2018 quency (MAF) in circulating tumour DNA (ctdna) isolated from plasma, tumour volume, and predicted

36 Liquid biopsy: Limitations Proportion of advanced cancer patients with less than 2% of VAF in cfdna Pecuchet, N et al. Clin Chem 2016

37 Liquid biopsy: Limitations Correlation between abundance of ctdna and sensivity of the test Liquid biopsy has lower sensitivity than tumor biopsy for rare variants: - detection of alterations in peripheral fluids rather than the tumor itself (volume dilution) - background of non-altered cfdna from cellular sources other than tumor (other comorbidities such as sepsis, abundant cfdna may be circulating that is derived from noncancerous cell compartments) Abbosh, C et al. Nat Rev 2018

38 Liquid biopsy: Limitations Low abundance of ctdna in certain clinical situations Very low release of tumor DNA into plasma in some patients with cancer: - some lesions, e.g., brain metastases, may shed little to no ctdna into the circulation - particularly frequent in cancers of the central nervous system, potentially because the blood-brain barrier blocks release of tumor DNA into the systemic circulation García-Murillas, I et al. Science Trans Med 2015 García-Murillas, I et al. SABCS 2016 Chetan Bettegowda, C et al. Sci Transl Med 2014

39 Advanced stage: Limitations Clinical impact of false positive T790M Plasma plasma EGFR detection T790M Plasma from AURA trial sent for BEAMing Paired tumor and plasma available for 216 patients 16.5mos mpfs 47 T790M+ in tumor, not plasma T790M+ in tumor: 62% RR, 10m PFS 111 T790M+ in tumor and plasma 9.2mos mpfs 40 patients T790M- tumor and plasma 2.8mos mpfs 18 T790M+ in plasma, not tumor 4.3mos mpfs T790M+ in plasma: 63% RR, 10m PFS Oxnard, J et al. J Clin Oncol 2016

40 Liquid biopsy: Limitations Standardization and clinical utility Efficiency and reproducibility of pre-analytical and analytical steps are critical to allow reliable quantitation of variant ctdna Lack of standardization: The best unit for quantifying DNA burden is not established Definition of clinically-relevant threshold in each tumor type and clinical setting ctdna responses do not always parallel imaging-based responses Clinical utility has not been established: no evidence that treatment on the basis of the detection of ctdna improves outcome. Prospective randomized trials have failed to demonstrate survival benefits from screening for occult recurrences in breast and ovary cancers, although there are data to suggest they are helpful in colorectal and prostate cancers Reinert, T et al. Gut 2016 Diehl, F et al. Nat Med 2008 Garcia-Saenz, JA et al. BMC Cancer 2017 Bardelli, A & Pantel, K. Cancer Cell 2017