Cell-free DNA comparative analysis of genomic landscape of first-line hormone-receptor positive metastatic breast cancer from US and China

doi:10.21203/rs.3.rs-120555/v2

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Cell-free DNA comparative analysis of genomic landscape of first-line hormone-receptor positive metastatic breast cancer from US and China

https://doi.org/10.21203/rs.3.rs-120555/v2

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published 31 Aug, 2021

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Purpose: Comparison of mutation landscape across ethnics using the identical detecting platform is important. We explored the differential genomic landscape of patients with hormone-receptor positive (HR+), HER2-negative MBC of first line recurrence or Stage IV at diagnosis from the United States (US) and China (CN).

Methods: Twenty-seven US patients and 65 CN patients had circulating tumor DNA (ctDNA) sequencing from plasma using the harmonized CLIA-certified, 152-gene PredicineCare^TM liquid biopsy assay. Clinical outcomes were correlated with ctDNA variants. Progression-free survival (PFS) was performed for patients and compared using log-rank test.

Results: All patients from CN cohort received chemotherapy and/or hormonal therapy, while 85.2% (23/27) patients of US cohort hormonal plus CDK4/6 inhibitor. Mutations were detected in 23 of 27 (85%) US patients and 54 of 65 (83%) CN patients. Prevalence of AKT1(18.5% vs. 3.1%, P = 0.008) and CDH1 were higher in US cohort (18.5% vs. 1.5%, P = 0.021), and gain of FGFR1 was higher in the CN cohort (7.4% vs. 24.6%, P = 0.048). PTEN deletion (5.7 months vs. 13.2 months, P = 0.03) and ESR1 alterations (9.0 months vs. 13.2 months, P = 0.02) were associated with significantly shorter PFS in CN cohort. However, the similar result was not found in US cohort.

Conclusions: Differential prevalence of FGFR1, AKT1, and CDH1 in HR+ MBC were found between US and CN, which indicates a slight difference in a genomic setting. Meanwhile, certain genes such as PTEN and ESR1 shows varied predictive value across US and CN cohort regarding PFS.

Cancer Biology

Oncology

HR-positive advanced breast cancer

circulating tumor DNA

next generation sequencing

Metastatic breast cancer (MBC) is a heterogeneous disease with increased genomic complexity compared to primary breast cancer and is associated with known somatic mutations of variable biological value in different subtypes[1]. Hormone-receptor positive (HR+), HER2- breast cancer (BC) accounts for over 70% percent of breast cancer [2, 3]. Currently, endocrine therapy, CDK4/6 inhibitors, and PI3K/AKT/mTOR pathway inhibitors are being used in the clinic with several novel endocrine, targeted, and chemotherapy-based treatments in clinical development [4, 5].

Liquid biopsies, including cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), cell-free RNA, circulating tumor cells, exosomes, and protein have emerged as clinically relevant tools for prognosis, genomic characterization, and disease response in MBC. For MBC patients with metastasis in lung, liver, or bone, acquiring biopsies, particularly at serial timepoints, can be difficult and invasive [6]. Further, tissue biopsies may only reflect a spatially and temporally limited snapshot of disease biology [7]. In contrast, cfDNA assays have potential advantages with respect to tissue as non-invasive tools to reflect tumor heterogeneity that is feasible for facilitating serial disease monitoring. In multiple clinical trials for patients with MBC, ctDNA assays have been used for incorporating mutational profiling in drug development to identify potential predictive biomarkers [8]. For example, ESR1 mutations were present in 37% of baseline samples and were enriched in patients with luminal A and PIK3CA-mutated tumors [9]. Another study using archived baseline plasma from SoFEA and PALOMA3 reported that ESR1 mutations were present in 39.1% of patients in SoFEA and 25.3% in PALOMA-3. Analysis of cfDNA from the BOLERO-2 trial using droplet digital PCR (ddPCR) showed that 28.8% of patients had either D538G or Y537S mutations in ESR1 [10] and 43.3% of the patients harbored H1047R, E545K, or E542K mutations in PIK3CA [11]. There was also a study using exome sequencing of plasma DNA from the PALOMA-3 study, which showed the dynamic changes in PIK3CA and ESR1 mutations after treatment, demonstrating the utility of serial monitoring in MBC [12, 13].

Despite diagnostic and therapeutic advances for patients with MBC, breast cancer continues to have dramatic differences in terms of disease onset, management, and clinical outcomes between CN and western countries. For instance, age of breast cancer diagnosis is almost 10 years younger in Chinese patient populations as compared with patients in the United States (US) and the European Union (EU) [14]. Genomic profiling of breast cancer patients in the US and CN has reported controversial results. Studies across different tumor types report significant differences in certain gene pathways and molecular subtypes [15-19], while others showed similar genetic landscape [20, 21].

Few studies have explored the differences in genomic features of tumors, particularly based on ctDNA assessment, across populations. In this study, we used a harmonized ctDNA liquid biopsy test to systematically compare the genomic landscape of patients with HR+ MBC at the time of first recurrence or de-novo metastatic diagnosis in the US and CN.

Patients

Two cohorts with HR+ and HER2- BC at the time of first line relapse or de-novo metastatic pathological diagnosis from the US (February 2017 - October 2019) and CN (March 2018 - March 2019) participated in this study. The enrollment criteria were: 1). The patients had HR+ and HER2- relapse after surgery or de-novo MBC. HR+ was defined as ≥1% for estrogen receptor (ER) and / or progesterone receptor (PR) positive; 2). Patients signed informed consent for additional blood to be collected for gene testing; 3). Age between 18 and 85 years; 4). At least one measurable lesion according to the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1; 5). Patients had a performance status score of Eastern Cooperative Oncology Group (ECOG) ≤ 1; 6). Patients had a life expectancy of at least 12 weeks, and adequate hematologic, hepatic, and renal function. Plasma samples were prospectively collected, 10 mL from each patient, before any treatment was initiated in the metastatic setting. Institutional Review Boards at each site approved the study in US (ethic No. NU16B06) and CN (ethic No. 2016KT75) .

Plasma cfDNA NGS testing

cfDNA testing was performed using the harmonized 152-gene PredicineCARE assay in two College of American Pathologist (CAP)-accredited laboratories separately, one was in the US (Predicine Inc.) and another one was located in CN (Huidu Shanghai Medical Sciences Ltd.).

Plasma cfDNA extraction

cfDNA was extracted using QIAamp circulating nucleic acid kit from plasma samples. Quantity and quality of the purified cfDNA were checked using Qubit fluorimeter and Bioanalyzer 2100.

Library preparation, capture and sequencing

5 to 20ng of extracted cfDNA was prepared for library construction including end-repair, dA-tailing, adapter ligation, and PCR amplification. The amplified DNA libraries with sufficient yields proceeded to hybrid capture. In brief, the library was hybridized overnight with the panel probes. Unbound fragments were then washed away. The purified libraries were QCed with Bioanalyzer 2100 and then paired-end 2x150bp sequenced using the Illumina sequencing platform.

Variant calling

Variants were called using a Predicine in-house developed analysis pipeline, starting from the raw sequencing data to the final mutation calls, which has been described in previous publications [22, 23]. Briefly, the pipeline first performed adapter trimming, barcode checking, and correction. Cleaned paired FASTQ files were outputted by the in-house pipeline and further aligned to the human reference genome build hg19 using BWA (version 0.7.15) alignment tool. Consensus bam files were then derived by merging paired-end reads originated from the same molecules (based on mapping location and unique molecular identifiers) as single strand fragments. Single strand fragments from the same double strand DNA molecules were further merged as double stranded. Both sequencing and PCR errors were deeply suppressed during this process. Candidate variants, consisting of point mutations, small insertions, and deletions, were identified across the targeted regions covered in the panel. Copy number variations were estimated at the gene level. The pipeline calculated the on-target unique fragment coverage, which was first corrected for GC bias, and was then adjusted to the probe level bias (estimated from a pooled reference).

Statistical analysis

Fisher’s exact test was performed to compare the mutational prevalence between CN and US cohorts. The basic clinical characteristic comparison of the two cohorts were carried out using a t-test. Kaplan-Meier survival analysis was performed to analyze the correlation between genomic alterations and progression-free survival (PFS), and p-values were calculated using the log-rank test by comparing the patients with and without a particular genomic alteration. R (version 3.5) was used for statistic analysis. Survival and surminer R packages were used for survival analysis.

Baseline patient characteristics

In total, there were 27 US patient at Northwestern University and 65 Chinese patients at Peking University Cancer Hospital enrolled in this study based on the inclusion criteria (see Materials and Methods). All were female. Median age of diagnosis was 51 years (range: 30–79) in the US cohort and 49 years (range: 27–82) years in the CN cohort. 87% of US patients and 82% of Chinese patients had received adjuvant therapy for primary BC, including chemotherapy and/or endocrine therapy. The sites of metastasis in decreasing order of frequency were liver, lung, and bone in the US cohort and lung, liver, and bone in the CN cohort. There were no significant differences found between US and Chinese samples with respect to age (median age was 51 in US and 49 years in CN) and primary tumor stages (mostly stage II or above in US and Chinese patients, 91.3% and 75.0%, respectively). Patients’ clinical and pathological characteristics are summarized in Table 1.

Table 1

Comparison of baseline clinical characteristics between US and CN (n = 90)
Clinical characteristics	US (n = 27)	CN (n = 65)	P
Age at diagnosis			0.400
≤45 years	10 (37.0%)	21 (31.7%)
༞45 years	17 (63.0%)	44 (68.3%)
HR intensity of primary tumor			0.005
≤25%	9 (33.3%)	7 (9.5%)
༞25%	18 (66.7%)	58 (90.5%)
Tumor grade of primary tumor			0.306
I	2 (7.4%)	4 (6.2%)
II	13 (48.1%)	32 (49.2%)
III	8 (29.6%)	10 (15.4%)
Unknown	4(14.8%)	19(29.2%)
T stage of primary tumor			0.013
T1/2	15 (55.6%)	52 (80.0%)
T3/4	10 (37.0%)	7 (10.8%)
Unknown	2 (7.4%)	6 (9.2%)
N stage of primary tumor			0.776
N0/1	14 (51.6%)	33 (50.8%)
N2/3	12 (44.4%)	27 (41.5%)
Unknown	1 (3.7%)	5 (7.7%)
Previous neoadjuvant chemotherapy			0.022
No	11 (40.8%)	54 (83.1%)
Yes	9 (33.3%)	11 (16.9%)
Unknown	7 (25.9%)	0 (0.0%)
Previous adjuvant chemotherapy			0.987
No	8 (29.6%)	24 (36.9%)
Yes	15 (55.5%)	39 (60.0%)
Unknown	4 (14.8%)	2 (3.1%)
Previous adjuvant endocrine therapy			༜0.001
No	1 (3.7%)	20 (30.8%)
SERM^a	8 (29.6%)	33 (50.8%)
AI^b	8 (29.6%)	10 (15.4%)
SERM + AI	5 (18.5%)	1 (1.5%)
Unknown	5 (18.5%)	1 (1.5%)
Disease free survival			0.119
≤6.0 months	9 (33.3%)	37 (56.9%)
༞6.0 months	10 (37.0%)	15 (23.1%)
Unknown	8 (29.6%)	13 (20.0%)
Liver metastasis			0.129
No	24 (88.9%)	50 (75.8%)
Yes	3 (11.1%)	15 (24.2%)
Lung metastasis			0.021
No	23 (85.2%)	40 (61.3%)
Yes	4 (14.8%)	25 (38.7%)
Brain metastasis			0.217
No	25 (92.6%)	64 (98.4%)
Yes	2 (7.4%)	1 (1.6%)
Bone metastasis			0.538
No	10 (37.0%)	25 (38.7%)
Yes	17 (63.0%)	40 (61.3%)
Lymph metastasis			0.078
No	16 (59.3%)	27 (40.3%)
Yes	11 (40.7%)	38 (59.7%)
Chest metastasis			0.156
No	27 (100.0%)	60 (91.9%)
Yes	0 (0.0%)	5 (8.1%)
Other metastasis			0.386
No	19 (70.4%)	48 (75.8%)
Yes	8 (29.6%)	17 (24.2%)
Previous neoadjuvant and/or adjuvant chemotherapy			0.017
No	0 (0.0%)	18 (27.7%)
Yes	20 (74.1%)	45 (69.2%)
Unknown	7(25.9%)	2 (3.1%)
Liver and/or lung metastasis			0.021
No	20 (74.1%)	31 (48.4%)
Yes	7 (25.9%)	34 (51.6%)
First-line therapeutic regimen			0.000
Chemotherapy	0 (0.0%)	22 (33.8%)
Hormonal therapy	3 (11.1%)	15 (23.1%)
Chemotherapy followed by hormonal therapy	0 (0.0%)	28 (43.1%)
Hormonal plus CDK4/6 inhibitor	23 (85.2%)	0 (0.0%)
Unknown	1 (3.7%)	0 (0.0%)
^aSERM: tamoxifen/toremifene ^bAI: anastrozole/exemestane/letrozole

Mutational And Cnv Landscape

The samples were tested by a harmonized NGS-based 152-gene PredicineCARE™ assay by Predicine Inc. in the US and by Huidu (Shanghai) in CN. SNV/Indel mutations were detected in 23 of 27 (85%) US patients and 54 of 65 (83%) Chinese patients. The number of mutations detected in each patient ranged from 0 to 9 in US patients and 0 to 9 in Chinese patients. CNVs, including both copy number gain and loss, were also detected in 13 of 27 (48%) US patients and 32 of 65 (51%) Chinese patients. The number of CNVs detected in each patient ranged from 0 to 19 in US patients and 0 to 24 in Chinese patients. The top SNV/Indel mutations detected similarly included TP53 (44.6%), PIK3CA (25.9%), ESR1(11.1%) and BRCA2 (11.1%) in US patients, and TP53(33.8%), PIK3CA (44.6%), ESR1(12.3%) and BRCA2 (9.2%) in Chinese patients. Alterations in CDH1(18.5% vs. 1.5%, P = 0.008) and AKT1 (18.5% vs. 3.1%, P = 0.021) were significantly higher in the US cohort than in the Chinese cohort. The top CNV detected included copy number gain in the US vs. CN populations were the following: CCND1 11.1% vs 16.9, CCND2 14.8% vs 12.3, CCND3 14.8% 3.1%, and MYC 11.1% vs 13.8, respectively. There were no statistically significant differences in these genomic alterations. In contrast, FGFR1 gain was significantly different between the US 7.4% and CN 24.6% (P = 0.048), while CDK4 gain not significantly different between the US 7.4% and CN 1.5% populations (P = 0.205). For copy number loss, US vs CN were ATM loss 0 vs 16.9% (P = 0.017), RB1 loss 3.7% vs 13.8% (P = 0.145), BRCA2 0 vs 7.7% (P = 0.168), PTEN 7.4% vs 4.6%, (P = 0.460), BRCA1 0 vs 1.5% (P = 0.707). (Fig. 1A-C).

Survival Analysis

The first-line treatment regimens for US and CN patients were different. The majority of patients (85.2%) in the US cohort were treated with standard of care single hormonal therapy plus CDK4/6 inhibitor treatment, while no patients in the Chinese cohort received upfront CDK4/6 inhibitors. For the US cohort, patients who received hormonal therapy plus CDK4/6 inhibitors were set up as group and their PFS was compared to the CN group. The result showed that US patients using hormonal plus CDK4/6 inhibitors had longer median PFS as compared to CN patients (26.9 months vs. 11.3 months, P = 0.025) (Fig. 2A). We also carried out survival analysis for patients with any AKT activating or PTEN inactivating, or DDR deficiency mutations, in Chinese and US patients (Supplementary Fig. 1, and data not shown). PTEN deletion was associated with shorter PFS of HR + MBC patients in CN (5.7 months vs. 13.2 months, P = 0.03) (Fig. 2B). This result was not encountered in US patients (5.4 months vs. 16.5 months, P = 0.65) (Fig. 2B). Meanwhile, patients with cfDNA-based ESR1 alterations had shorter PFS compared to the other patients in the first-line treatment after relapse in the CN patient cohort (9.0 months vs. 13.2 months, P = 0.02) (Fig. 2C). These data was not statistically significant in US patients (11.2 months vs. 26.9 months, P = 0.62) (Fig. 2C). Literature shows that cfDNA yield have been reported as a prognostic biomarker related to patient disease progression and prognosis [24]. However, there was no significant difference in cfDNA yield between Chinese and US patients from this study. (Supplementary Fig. 2). In addition to mutational aspect, we also found that patients with liver or lung metastasis tend to have shorter PFS (14.3 months vs. 10.5 months, P = 0.15). This trend was also observed in CN cohort (14.3 months vs. 10.3 months, P = 0.18) but not in US cohort (13.5 months vs. 16.5 months, P = 0.80).(Data not showed)

In this retrospective study, the gene mutation landscape in metastatic breast cancer was compared across two different populations. The results of the mutational analysis and prevalence varied for particular alterations between the two Ethnic groups. Currently, cfDNA-derived gene mutational assays have gained much attention in breast cancer (Fig. 3A and B). In prior work, the cfDNA-derived mutations were detected using next-generation sequencing (NGS) platforms in almost all of the studies. However, the means of extracting, processing and analyzing cfDNA samples were different, which can lead to a limited ability to compare differences across populations.

This retrospective, multicenter study is the first proof-of-concept study to report on the use of a single harmonized ctDNA assay in clinically uniform populations of HR + MBC from two institutions in the US and CN. The populations analyzed included newly recurred and de-novo MBC patients who had not been exposed to treatment in the advanced setting, but who had received adjuvant endocrine therapy in similar proportion following standard-of-care guidelines. The study demonstrates that cfDNA analysis can provide a reliable real-world assessment of the molecular landscape of luminal breast cancer and identify differences in genomic abnormalities between patients in the US and CN.

For cancer variants that were known to interfere with endocrine therapy combined with or without PI3K/AKT/mTOR or CDK4/6 inhibitors, such as PTEN gene deletion (i.e., copy number loss) or ESR1 activating mutations and copy number gain were evaluated in the present study. Previous studies have shown that PIK3CA was mutated in 18–40% BC patients [25]. Some studies using cfDNA showed that PIK3CA mutations were present in 43.3%[12] and 25%[26] MBC patients in different studies. A recent study with cfDNA on a small cohort in CN observed that PIK3CA mutations were present in 29.4% (5/17) MBC patients [17]. In this study, we found significant difference of prevalence for AKT1 (18.5% vs. 3.1%, P = 0.008) between US and CN patients, respectively. While the percentage was all within the previously reported ranges in other studies, the difference in PIK3CA detection in our study may have been secondary to differences in features of the study populations and raise the hypothesis of differential molecular pathways of endocrine resistance when comparing Ethnic groups treated with similar therapies.

In prior work, a mutational frequency of 0.4% was observed for ATM in 7,675 BRCA1 & 2-negative breast cancer patients in a Chinese population [27, 28] and a mutational frequency range from 0.45 to 1.0% was found in the US and Europe [29, 30]. However, no available data regarding ctDNA based comparison between US and CN have been reported. Here, we found that ATM loss was more frequently observed in CN patients with HR+/HER2- mBC as compared to US (16.9% vs. 0.0%, P = 0.017). Similar to previous studies[31] [21], our data showed that the mutational prevalence of CDH1 detected using plasma of HR+/HER2- patients was higher in US than CN(18.5% vs. 1.5%). Our data also showed the CNV mutation prevalence of FGFR1 gain was higher in CN patients when comparing to US (24.6% vs. 7.4%, P = 0.048). This result was in line with previous reports found in HR+/HER2- cohort of US (1.0 ~ 8.0%) and CN (13.0%) [12, 21, 31].

PTEN exerts its function in multiple ways including repressing tumor cell growth and cell survival. The nuclear PTEN exhibit phosphatase-independent tumor suppressive function such as regulation of chromosome stability, DNA repair, and apoptosis [32, 33]. PTEN loss has been identified in cfDNA of 25% mBC patients [26]. Here, we found that the difference of PTEN mutation frequency between the US and CN did not reach statistical significance (11.1% vs. 3.1%, P = 0.15). However, PTEN deletion, an agonist of PIK3CA/AKT pathway, was associated with shorter PFS of HR + MBC patients in CN (P = 0.03), but not in US (P = 0.65) .

On the other hand, circulating ESR1 mutation is a poor prognostic factor in ER + MBC[34], Chandarlapaty et al reported that cfDNA ESR1 mutations were associated with shorter OS of MBC patients from the BOLERO-2 study [10]. A recent meta-analysis by Zhang et al. demonstrated that plasma ESR1 mutation carriers had significantly worse PFS compared to wild-type ESR1[35]. In the present study, the ESR1 mutation prevalence between the US and CN was not significantly different. Patients with cfDNA-based ESR1 copy number gain or mutation had shorter PFS compared to the other patients in the first-line treatment after relapse in the CN patient cohort (P = 0.023). However, this finding was not observed in US patients (P = 0.62). The predictive value of ESR1 mutation together with the PTEN deletion found in our study raised a hypothesis: when patient who received CDK4/6 inhibitor based regimen(US cohort in present study), the ESR1 or PTEN variation may have less effect on the PFS. In opposite, patient received hormonal therapy and/or chemotherapy seemed to be more affected by ESR1 or PTEN variation, as found in CN cohort. Additionally, there is a trend that patients with liver or lung metastasis tend to have shorter PFS (P = 0.18) in CN cohort, which is not found in US cohort (P = 0.80). This may partly due to the massive application of CDK4/6 inhibitor in US patients, and this hypothesis need to be further demonstrated in larger cohort. Besides, we also noted that lung metastatic rate was higher in CN group as compared to US group (P = 0.021). previous study demonstrated that HR-positive patients with non-visceral metastases had a better prognosis than those with visceral metastases[36]. Thus, we believe the higher lung metastatic rate of CN group may contributes to the shorten PFS. This study has several limitations. Firstly, this is a retrospective study, with the limitations associated with this type of study. Secondly, the number of study cohort for each center is relatively small, a larger study is required to more conclusively confirm our finding.

Collectively, our data revealed the differential prevalence of FGFR1, AKT1 and CDH1 in HR + positive MBC between US and CN, which indicates a slightly different biological features of two ethnics. Moreover, the ESR1 nor PTEN variation seems to have less effect on PFS of patients received CDK4/6 inhibitor based regimen.

Acknowledgements

The authors wish to thank the participated patients from US and CN, whom willing to enrolled for present study.

Authors’ contributions

Xiaoran Liu and Feng Xie did all the statistical analyses and constructed the tables and figures. Xiaoran Liu and Andrew A. Davis were also the main author of the manuscript. Huiping Li and Massimo Cristofanilli supervised the project. Huiping Li and Lorenzo Gerratana supervised the pathological evaluation. Huiping Li, Amir Behdad and Firas Wehbe evaluated the inclusion criteria of TMA and revised the manuscript. Xinyu Gui, Yifei Chen, Xiaoran Liu, Youbin Zhang and Qiang Zhang collected the raw clinical data. Huiping Li and Ami N. Shah provided the information on molecular subtypes and revised the manuscript. Yong Huang, Jianjun Yu, Pan Du and Shidong Jia provided the technology support of ctDNA sequencing and analyzing. All authors read and approved the final manuscript.

Funding

The present study was supported by the National Natural Science Foundation of China, and the Grant No. was 81502269.

Availability of supporting data

All data in the main text are publicly available after its publication. The supporting data of this study are available on request from the corresponding author (Huiping Li).

Ethics approval and consent to participate

The present study were approved by the medical ethics committee of Beijing cancer hospital (ethic No. 2016KT75) and of Lurie Comprehensive Cancer Center (ethic No. NU16B06). Written informed consent was obtained from all study participants at enrolled.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

[1] Bertucci F, Ng CKY, Patsouris A, Droin N, Piscuoglio S, Carbuccia N, Soria JC, Dien AT, Adnani Y, Kamal M, Garnier S, Meurice G, Jimenez M, Dogan S, Verret B, Chaffanet M, Bachelot T, Campone M, Lefeuvre C, Bonnefoi H, Dalenc F, Jacquet A, De Filippo MR, Babbar N, Birnbaum D, Filleron T, Le Tourneau C, Andre F. Genomic characterization of metastatic breast cancers. Nature 2019;569:560-4.

[2] Andre F, Ciruelos E, Rubovszky G, Campone M, Loibl S, Rugo HS, Iwata H, Conte P, Mayer IA, Kaufman B, Yamashita T, Lu YS, Inoue K, Takahashi M, Papai Z, Longin AS, Mills D, Wilke C, Hirawat S, Juric D, Group S-S. Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer. N Engl J Med 2019;380:1929-40.

[3] Setiawan VW, Monroe KR, Wilkens LR, Kolonel LN, Pike MC, Henderson BE. Breast cancer risk factors defined by estrogen and progesterone receptor status: the multiethnic cohort study. Am J Epidemiol 2009;169:1251-9.

[4] Tripathy D, Bardia A, Sellers WR. Ribociclib (LEE011): Mechanism of Action and Clinical Impact of This Selective Cyclin-Dependent Kinase 4/6 Inhibitor in Various Solid Tumors. Clin Cancer Res 2017;23:3251-62.

[5] Vasan N, Toska E, Scaltriti M. Overview of the relevance of PI3K pathway in HR-positive breast cancer. Ann Oncol 2019;30 Suppl 10:x3-x11.

[6] Osborne CK, Schiff R. Mechanisms of endocrine resistance in breast cancer. Annu Rev Med 2011;62:233-47.

[7] Keup C, Benyaa K, Hauch S, Sprenger-Haussels M, Tewes M, Mach P, Bittner AK, Kimmig R, Hahn P, Kasimir-Bauer S. Targeted deep sequencing revealed variants in cell-free DNA of hormone receptor-positive metastatic breast cancer patients. Cell Mol Life Sci 2020;77:497-509.

[8] Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020;97:171-223.

[9] Spoerke JM, Gendreau S, Walter K, Qiu J, Wilson TR, Savage H, Aimi J, Derynck MK, Chen M, Chan IT, Amler LC, Hampton GM, Johnston S, Krop I, Schmid P, Lackner MR. Heterogeneity and clinical significance of ESR1 mutations in ER-positive metastatic breast cancer patients receiving fulvestrant. Nat Commun 2016;7:11579.

[10] Chandarlapaty S, Chen D, He W, Sung P, Samoila A, You D, Bhatt T, Patel P, Voi M, Gnant M, Hortobagyi G, Baselga J, Moynahan ME. Prevalence of ESR1 Mutations in Cell-Free DNA and Outcomes in Metastatic Breast Cancer: A Secondary Analysis of the BOLERO-2 Clinical Trial. JAMA Oncol 2016;2:1310-5.

[11] Moynahan ME, Chen D, He W, Sung P, Samoila A, You D, Bhatt T, Patel P, Ringeisen F, Hortobagyi GN, Baselga J, Chandarlapaty S. Correlation between PIK3CA mutations in cell-free DNA and everolimus efficacy in HR(+), HER2(-) advanced breast cancer: results from BOLERO-2. Br J Cancer 2017;116:726-30.

[12] O'Leary B, Cutts RJ, Liu Y, Hrebien S, Huang X, Fenwick K, Andre F, Loibl S, Loi S, Garcia-Murillas I, Cristofanilli M, Huang Bartlett C, Turner NC. The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial. Cancer Discov 2018;8:1390-403.

[13] Li H, Xu Y, Zhao F, Song G, Rugo HS, Zhang Y, Yang L, Liu X, Shao B, Yang L, Liu Y, Ran R, Zhang R, Guan Y, Chang L, Yi X. Plasma PIK3CA ctDNA specific mutation detected by next generation sequencing is associated with clinical outcome in advanced breast cancer. Am J Cancer Res 2018;8:1873-86.

[14] Song QK, Li J, Huang R, Fan JH, Zheng RS, Zhang BN, Zhang B, Tang ZH, Xie XM, Yang HJ, He JJ, Li H, Li JY, Qiao YL, Chen WQ. Age of diagnosis of breast cancer in china: almost 10 years earlier than in the United States and the European union. Asian Pac J Cancer Prev 2014;15:10021-5.

[15] Chen C, Zhou Q, Wu R, Li B, Chen Q, Zhang X, Shi C. A Comprehensive Survey of Genomic Alterations in Gastric Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets. Biomed Res Int 2019;2019:2183510.

[16] Chen L, Yang L, Yao L, Kuang XY, Zuo WJ, Li S, Qiao F, Liu YR, Cao ZG, Zhou SL, Zhou XY, Yang WT, Shi JX, Huang W, Hu X, Shao ZM. Characterization of PIK3CA and PIK3R1 somatic mutations in Chinese breast cancer patients. Nat Commun 2018;9:1357.

[17] Li S, Wang X, Li Y, Lai H, Liu Y, Jin L. Non-invasive analysis of tumor mutation profiles and druggable mutations by sequencing of cell free DNA of Chinese metastatic breast cancer patients. Thorac Cancer 2019;10:807-14.

[18] Tao J, Zhang P, Liu G, Yan H, Bu X, Ma Z, Wang N, Wang G, Jia W. Cytotoxicity of Chinese motherwort (YiMuCao) aqueous ethanol extract is non-apoptotic and estrogen receptor independent on human breast cancer cells. J Ethnopharmacol 2009;122:234-9.

[19] Jiang YZ, Ma D, Suo C, Shi J, Xue M, Hu X, Xiao Y, Yu KD, Liu YR, Yu Y, Zheng Y, Li X, Zhang C, Hu P, Zhang J, Hua Q, Zhang J, Hou W, Ren L, Bao D, Li B, Yang J, Yao L, Zuo WJ, Zhao S, Gong Y, Ren YX, Zhao YX, Yang YS, Niu Z, Cao ZG, Stover DG, Verschraegen C, Kaklamani V, Daemen A, Benson JR, Takabe K, Bai F, Li DQ, Wang P, Shi L, Huang W, Shao ZM. Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies. Cancer Cell 2019;35:428-40 e5.

[20] Huang X, Dugo M, Callari M, Sandri M, De Cecco L, Valeri B, Carcangiu ML, Xue J, Bi R, Veneroni S, Daidone MG, Menard S, Tagliabue E, Shao Z, Wu J, Orlandi R. Molecular portrait of breast cancer in China reveals comprehensive transcriptomic likeness to Caucasian breast cancer and low prevalence of luminal A subtype. Cancer Med 2015;4:1016-30.

[21] Zhang G, Wang Y, Chen B, Guo L, Cao L, Ren C, Wen L, Li K, Jia M, Li C, Mok H, Chen X, Wei G, Lin J, Zhang Z, Hou T, Han-Zhang H, Liu C, Liu H, Liu J, Balch CM, Meric-Bernstam F, Liao N. Characterization of frequently mutated cancer genes in Chinese breast tumors: a comparison of Chinese and TCGA cohorts. Ann Transl Med 2019;7:179.

[22] Davis AA, Zhang Q, Gerratana L, Shah AN, Zhan Y, Qiang W, Finkelman BS, Flaum L, Behdad A, Gradishar WJ, Platanias LC, Cristofanilli M. Association of a novel circulating tumor DNA next-generating sequencing platform with circulating tumor cells (CTCs) and CTC clusters in metastatic breast cancer. Breast Cancer Res 2019;21:137.

[23] Gerratana L, Zhang Q, Shah AN, Davis AA, Zhang Y, Wehbe F, Qiang W, Flaum L, Finkelman BS, Gradishar WJ, Platanias LC, Behdad A, Cristofanilli M. Performance of a novel Next Generation Sequencing circulating tumor DNA (ctDNA) platform for the evaluation of samples from patients with metastatic breast cancer (MBC). Crit Rev Oncol Hematol 2020;145:102856.

[24] Fernandez-Garcia D, Hills A, Page K, Hastings RK, Toghill B, Goddard KS, Ion C, Ogle O, Boydell AR, Gleason K, Rutherford M, Lim A, Guttery DS, Coombes RC, Shaw JA. Plasma cell-free DNA (cfDNA) as a predictive and prognostic marker in patients with metastatic breast cancer. Breast Cancer Res 2019;21:149.

[25] Barbareschi M, Buttitta F, Felicioni L, Cotrupi S, Barassi F, Del Grammastro M, Ferro A, Dalla Palma P, Galligioni E, Marchetti A. Different prognostic roles of mutations in the helical and kinase domains of the PIK3CA gene in breast carcinomas. Clin Cancer Res 2007;13:6064-9.

[26] Razavi P, Dickler MN, Shah PD, Toy W, Brown DN, Won HH, Li BT, Shen R, Vasan N, Modi S, Jhaveri K, Caravella BA, Patil S, Selenica P, Zamora S, Cowan AM, Comen E, Singh A, Covey A, Berger MF, Hudis CA, Norton L, Nagy RJ, Odegaard JI, Lanman RB, Solit DB, Robson ME, Lacouture ME, Brogi E, Reis-Filho JS, Moynahan ME, Scaltriti M, Chandarlapaty S. Alterations in PTEN and ESR1 promote clinical resistance to alpelisib plus aromatase inhibitors. Nature Cancer 2020;1:382-93.

[27] Yang Z, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Zhang J, Xie Y. Prevalence and characterization of ATM germline mutations in Chinese BRCA1/2-negative breast cancer patients. Breast Cancer Res Treat 2019;174:639-47.

[28] Liu X, Li H, Shao B, Wu J, Kong W, Song G, Jiang H, Wang J, Wan F. Identification of recurrent BRCA1 mutation and its clinical relevance in Chinese Triple-negative breast cancer cohort. Cancer medicine 2017;6:547-54.

[29] Buys SS, Sandbach JF, Gammon A, Patel G, Kidd J, Brown KL, Sharma L, Saam J, Lancaster J, Daly MB. A study of over 35,000 women with breast cancer tested with a 25-gene panel of hereditary cancer genes. Cancer 2017;123:1721-30.

[30] Couch FJ, Shimelis H, Hu C, Hart SN, Polley EC, Na J, Hallberg E, Moore R, Thomas A, Lilyquist J, Feng B, McFarland R, Pesaran T, Huether R, LaDuca H, Chao EC, Goldgar DE, Dolinsky JS. Associations Between Cancer Predisposition Testing Panel Genes and Breast Cancer. JAMA Oncol 2017;3:1190-6.

[31] Chung JH, Pavlick D, Hartmaier R, Schrock AB, Young L, Forcier B, Ye P, Levin MK, Goldberg M, Burris H, Gay LM, Hoffman AD, Stephens PJ, Frampton GM, Lipson DM, Nguyen DM, Ganesan S, Park BH, Vahdat LT, Leyland-Jones B, Mughal TI, Pusztai L, O'Shaughnessy J, Miller VA, Ross JS, Ali SM. Hybrid capture-based genomic profiling of circulating tumor DNA from patients with estrogen receptor-positive metastatic breast cancer. Ann Oncol 2017;28:2866-73.

[32] Barroso-Sousa R, Keenan TE, Pernas S, Exman P, Jain E, Garrido-Castro AC, Hughes M, Bychkovsky B, Umeton R, Files JL, Lindeman NI, MacConaill LE, Hodi FS, Krop IE, Dillon D, Winer EP, Wagle N, Lin NU, Mittendorf EA, Van Allen EM, Tolaney SM. Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer. Clin Cancer Res 2020;26:2565-72.

[33] Dillon LM, Miller TW. Therapeutic targeting of cancers with loss of PTEN function. Curr Drug Targets 2014;15:65-79.

[34] Liao H, Huang W, Pei W, Li H. Detection of ESR1 Mutations Based on Liquid Biopsy in Estrogen Receptor-Positive Metastatic Breast Cancer: Clinical Impacts and Prospects. Front Oncol 2020;10:587671.

[35] Zhang K, Hong R, Xu F, Xia W, Kaping L, Qin G, Zheng Q, Lu Q, Shi YX, Yuan ZY, Wang S. Clinical value of circulating ESR1 mutations for patients with metastatic breast cancer: a meta-analysis. Cancer Manag Res 2018;10:2573-80.

[36] Ozawa H, Sata A, Fukui R, Bun A, Higuchi T, Fujimoto Y, Miyagawa Y, Imamura M, Miyoshi Y. A Single-centre, Retrospective, Observational Analysis of Fulvestrant for Recurrent/metastatic Breast Cancer According to Metastatic Site. Anticancer Res 2019;39:5653-62.

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Cell-free DNA comparative analysis of genomic landscape of first-line hormone-receptor positive metastatic breast cancer from US and China

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