| Literature DB >> 35181986 |
Pauline A J Mendelaar1, Debbie G J Robbrecht1, Maud Rijnders1, Ronald de Wit1, Vanja de Weerd1, Teoman Deger1, Hans M Westgeest2, Maureen J B Aarts3, Jens Voortman4, John W M Martens1, Astrid A M van der Veldt1,5, José Alberto Nakauma-González1,6,7, Saskia M Wilting1, Martijn Lolkema1.
Abstract
Second-line treatment with immune checkpoint inhibition in patients with metastatic urothelial cancer (mUC) has a low success rate (~ 20%). Circulating tumour-derived DNA (ctDNA) levels may guide patient stratification, provided that an affordable and robust assay is available. Here, we investigate whether the modified fast aneuploidy screening test-sequencing system (mFast-SeqS) may provide such an assay. To this end, mFast-SeqS was performed on cell-free DNA (cfDNA) from 74 patients with mUC prior to treatment with pembrolizumab. Results were associated with corresponding tissue-based profiles, plasma-based variant allele frequencies (VAFs) and clinical response. We found that plasma-derived mFast-SeqS-based aneuploidy scores significantly correlated with those observed in the corresponding tumour tissue as well as with the ctDNA level in the plasma. In multivariate logistic regression analysis, a high aneuploidy score was independently associated with lack of clinical benefit from treatment with pembrolizumab. In conclusion, mFast-SeqS provides a patient-friendly, high-throughput and affordable method to estimate ctDNA level. Following independent validation, this test could be used to stratify mUC patients for response prior to the initiation of treatment with pembrolizumab.Entities:
Keywords: advanced urothelial carcinoma; biomarker; chromosomal instability; ctDNA; liquid biopsies; pembrolizumab
Mesh:
Substances:
Year: 2022 PMID: 35181986 PMCID: PMC9120908 DOI: 10.1002/1878-0261.13196
Source DB: PubMed Journal: Mol Oncol ISSN: 1574-7891 Impact factor: 7.449
Fig. 1Cohort description. Description of the number of included patients per method of analysis. Per method, the number of excluded patients and the reason of exclusion of samples or patients is mentioned.
Fig. 2mFast‐SeqS detected aneuploidy in the blood is tumor‐derived and reflects the ctDNA level. (A) 13 patients with aneuploidy score ≥ 5. Spearman correlation coefficient was estimated per chromosomal arm between copy number alterations (CNAs) from WGS data and Z‐score from mFast‐SeqS performed on ctDNA. The relative deviation of CN from the expected normal CN was calculated and log2 transformed. (B) 17 patients in which a mutation covered by the Oncomine™ Colon cfDNA Assay was successfully detected. Spearman correlation between the maximal VAF and aneuploidy score per patient. Values were square‐root transformed to reduce skewness in the data distribution.
Overview of the observed mutations in tissue‐based WGS data and the corresponding Oncomine NGS results in plasma samples. HGVS.c, Human Genome Variation Society coding mutation nomenclature; VAF, variant allele frequency.
| Subject | Gene | HGVS.c | Protein | VAF in tissue | VAF in plasma | Aneuploidy score |
|---|---|---|---|---|---|---|
| 2 | TP53 | c.659A > G | Y220C | 52.38 | Failed | 1.49 |
| 3 | ERBB2 | c.2264T > C | L755S | 53.41 | 19.53 | 7.7 |
| 7 | TP53 | c.743G > A | R248Q | 39.24 | Failed | 1.06 |
| 7 | ERBB2 | c.929C > T | S310F | 27.69 | Failed | 1.06 |
| 10 | TP53 | c.517G > A | V173M | 46.67 | Failed | 1.22 |
| 11 | CTNNB1 | c.134C > T | S45F | 36.36 | 0 | 1.99 |
| 18 | PIK3CA | c.1633G > A | E545K | 20.79 | Failed | 1.24 |
| 23 | TP53 | c.742C > T | R248W | 86.84 | 24.28 | 25.35 |
| 29 | FBXW7 | c.1514G > A | R505H | 30.39 | 19.61 | 7.54 |
| 32 | TP53 | c.853G > A | E285K | 47.87 | 41.3 | 69.89 |
| 33 | PIK3CA | c.3140A > G | H1047R | 30.07 | 0.87 | 2.43 |
| 33 | TP53 | c.659A > G | Y220C | 30.56 | 0.9 | 2.43 |
| 41 | PIK3CA | c.1633G > A | E545K | 31.36 | 4.83 | 1.72 |
| 41 | CTNNB1 | c.134C > T | S45F | 30.77 | 3.7 | 1.72 |
| 43 | TP53 | c.574C > T | Q192Ter | 26.60 | 10.24 | 9.22 |
| 45 | FBXW7 | c.1513C > G | R505G | 38.52 | 0 | 0.65 |
| 45 | PIK3CA | c.1633G > A | E545K | 16.54 | 0 | 0.65 |
| 47 | FBXW7 | c.1513C > G | R505G | 48.98 | 0 | 2.23 |
| 48 | TP53 | c.742C > T | R248W | 61.33 | 2.94 | 1.75 |
| 53 | CTNNB1 | c.110C > G | S37C | 38.10 | 2.69 | 0.74 |
| 53 | TP53 | c.589G > A | V197M | 55.52 | 3.693 | 0.74 |
| 55 | TP53 | c.532dup | H178PfsTer3 | 53.85 | 0 | 5.81 |
| 60 | PIK3CA | c.1624G > C | E542Q | 27.73 | 4.88 | 5.11 |
| 60 | PIK3CA | c.1633G > A | E545K | 26.92 | 4.878 | 5.11 |
| 68 | TP53 | c.517G > A | V173M | 47.58 | 0.6 | 2.24 |
| 70 | TP53 | c.586C > T | R196Ter | 12.64 | 5.17 | 8.54 |
| 78 | PIK3CA | c.1624G > A | E542K | 10.99 | 3.21 | 2.59 |
Fig. 3Prediction of response by aneuploidy score and PD‐L1. (A) The proportion of aneuploidy high and low patients was shown for responders, non‐responders, and the total cohort. The Chi‐square test was used to determine statistical significance. (B) The proportion of PD‐L1 positive and negative patients was shown for responders, non‐responders, and the total cohort. The Chi‐square test was used to determine statistical significance. (C) Kaplan–Meier curve is shown for time on pembrolizumab treatment in aneuploidy positive and negative patients. The obtained curves were compared using the log‐rank test. (D) Kaplan–Meier curve is shown for time on pembrolizumab treatment in PD‐L1 positive and negative patients. The obtained curves were compared using the log‐rank test.
Logistic regression model for prediction of clinical benefit. TFI, treatment free interval following first line chemotherapy (at least 4 cycles of cisplatin/gemcitabine or carboplatin/gemcitabine).
| Univariate analysis | Multivariate analysis | |||||
|---|---|---|---|---|---|---|
| OR | 95% CI |
| OR | 95% CI |
| |
| Clinical variables | ||||||
| Gender | 0.36 | 0.09–1.15 | 0.105 | |||
| Visceral metastases present | 0.62 | 0.23–1.62 | 0.332 | |||
| CPS PD‐L1 ≥ 10 | 2.92 | 1.10–8.05 | 0.034 | 2.80 | 0.93–8.92 | 0.072 |
| Albumin (mg·L−1) | 1.12 | 1.00–1.27 | 0.065 | |||
| LDH (U·L−1) | 0.99 | 0.98–1.00 | 0.183 | |||
| Platelets (×10^9·L−1) | 1.00 | 0.99–1.00 | 0.115 | |||
| Hb (mmol·L−1) | 1.15 | 0.74–1.80 | 0.528 | |||
| TFI < 3 months | 0.17 | 0.025–0.66 | 0.025 | 0.12 | 0.02–0.52 | 0.011 |
| Response to first line chemotherapy | 1.49 | 0.74–3.22 | 0.275 | |||
| mFast‐SeqS variables | ||||||
| cfDNA concentration (ng·mL−1) | 0.97 | 0.93–1.00 | 0.143 | |||
| Aneuploidy score ≥ 5 | 0.13 | 0.02–0.50 | 0.009 | 0.11 | 0.02–0.46 | 0.007 |
| Aneuploidy score continuous | 0.89 | 0.77–0.98 | 0.066 | |||
Logistic regression model for prediction of overall survival (OS) at 6 months (deceased vs alive). TFI, treatment free interval following first line chemotherapy (at least 4 cycles of cisplatin/gemcitabine or carboplatin/gemcitabine).
| Univariate analysis | Multivariate analysis | |||||
|---|---|---|---|---|---|---|
| OR | 95% CI |
| OR | 95% CI |
| |
| Clinical variables | ||||||
| Gender | 0.36 | 0.12–1.07 | 0.071 | |||
| Visceral metastases present | 0.29 | 0.10–0.78 | 0.017 | 1.43 | 0.30–7.65 | 0.660 |
| CPS PD‐L1 ≥ 10 | 1.93 | 0.73–5.31 | 0.193 | |||
| Albumin (mg·L−1) | 1.14 | 1.03–1.29 | 0.023 | 1.10 | 0.93–1.34 | 0.300 |
| LDH (U·L−1) | 1.00 | 0.99–1.00 | 0.256 | |||
| Platelets (×10^9·L−1) | 1.00 | 0.99–1.00 | 0.382 | |||
| Hb (mmol·L−1) | 1.44 | 0.91–2.34 | 0.129 | |||
| TFI < 3 months | 0.19 | 0.05–0.66 | 0.013 | 0.11 | 0.01–0.65 | 0.027 |
| Response to first line chemotherapy | 1.90 | 0.95–4.01 | 0.076 | |||
| mFast‐SeqS variables | ||||||
| cfDNA concentration (ng·mL−1) | 0.94 | 0.89–0.98 | 0.016 | 0.92 | 0.84–0.99 | 0.056 |
| Aneuploidy score ≥ 5 | 0.13 | 0.03–0.41 | 0.001 | 0.04 | 0.003–0.26 | 0.003 |
| Aneuploidy score continuous | 0.79 | 0.66–0.91 | 0.005 | |||