Next-generation sequencing (NGS) allows sequencing of a high number of nucleotides in a short time frame at an affordable cost. While this technology has been widely implemented, there are no ...recommendations from scientific societies about its use in oncology practice. The European Society for Medical Oncology (ESMO) is proposing three levels of recommendations for the use of NGS. Based on the current evidence, ESMO recommends routine use of NGS on tumour samples in advanced non-squamous non-small-cell lung cancer (NSCLC), prostate cancers, ovarian cancers and cholangiocarcinoma. In these tumours, large multigene panels could be used if they add acceptable extra cost compared with small panels. In colon cancers, NGS could be an alternative to PCR. In addition, based on the KN158 trial and considering that patients with endometrial and small-cell lung cancers should have broad access to anti-programmed cell death 1 (anti-PD1) antibodies, it is recommended to test tumour mutational burden (TMB) in cervical cancers, well- and moderately-differentiated neuroendocrine tumours, salivary cancers, thyroid cancers and vulvar cancers, as TMB-high predicted response to pembrolizumab in these cancers.
Outside the indications of multigene panels, and considering that the use of large panels of genes could lead to few clinically meaningful responders, ESMO acknowledges that a patient and a doctor could decide together to order a large panel of genes, pending no extra cost for the public health care system and if the patient is informed about the low likelihood of benefit. ESMO recommends that the use of off-label drugs matched to genomics is done only if an access programme and a procedure of decision has been developed at the national or regional level. Finally, ESMO recommends that clinical research centres develop multigene sequencing as a tool to screen patients eligible for clinical trials and to accelerate drug development, and prospectively capture the data that could further inform how to optimise the use of this technology.
•ESMO recommends the use of tumour multigene NGS in NSCLC, cholangiocarcinoma, prostate and ovarian cancers.•It is recommended to test TMB in well- and moderately-differentiated neuroendocrine tumours (NETs), cervical, salivary, thyroid and vulvar cancers.•Academic research centres should perform multigene NGS as part of their missions to enable access to innovative treatments.•A large panel of genes could be ordered, considering the benefit for the patient and the cost for the public health care system.
α-Selective phosphatidylinositol 3-kinase (PI3K) inhibitors improve outcome in patients with PIK3CA-mutated, hormone receptor-positive (HR+)/Her2− metastatic breast cancer (mBC). Nevertheless, it is ...still unclear how to integrate this new drug family in the treatment landscape.
A total of 649 patients with mBC from the SAFIR02 trial (NCT02299999), with available mutational profiles were selected for outcome analysis. PIK3CA mutations were prospectively determined by next-generation sequencing on metastatic samples. The mutational landscape of PIK3CA-mutated mBC was assessed by whole-exome sequencing (n = 617). Finally, the prognostic value of PIK3CA mutations during chemotherapy was assessed in plasma samples (n = 44) by next-generation sequencing and digital PCR.
Some 28% (104/364) of HR+/Her2− tumors and 10% (27/255) of triple-negative breast cancer (TNBC) presented a PIK3CA mutation (P < 0.001). PIK3CA-mutated HR+/Her2− mBC was less sensitive to chemotherapy adjusted odds ratio: 0.40; 95% confidence interval (0.22–0.71); P = 0.002, and presented a worse overall survival (OS) compared with PIK3CA wild-type adjusted hazard ratio: 1.44; 95% confidence interval (1.02–2.03); P = 0.04. PIK3CA-mutated HR+/Her2− mBC was enriched in MAP3K1 mutations (15% versus 5%, P = 0.0005). In metastatic TNBC (mTNBC), the median OS in patients with PIK3CA mutation was 24 versus 14 months for PIK3CA wild-type (P = 0.03). We further looked at the distribution of PIK3CA mutation in mTNBC according to HR expression on the primary tumor. Some 6% (9/138) of patients without HR expression on the primary and 36% (14/39) of patients with HR+ on the primary presented PIK3CA mutation (P < 0.001). The level of residual PIK3CA mutations in plasma after one to three cycles of chemotherapy was associated with a poor OS continuous variable, hazard ratio: 1.03, 95% confidence interval (1.01–1.05), P = 0.007.
PIK3CA-mutated HR+/Her2− mBC patients present a poor outcome and resistance to chemotherapy. Patients with PIK3CA-mutated TNBC present a better OS. This could be explained by an enrichment of PIK3CA mutations in luminal BC which lost HR expression in the metastatic setting.
SAFIR02 trial: NCT02299999.
•Patients with HR+/Her2- mBC and PIK3CA mutation were less sensitive to chemotherapy and presented worse overall survival.•Patients with TNBC tumors and PIK3CA mutation present a better overall survival as compared with wt.•A subset of patients with PIK3CA-mutated TNBC could be luminal breast cancers that lost hormone receptor expression.•Persistant levels of cell-free circulating PIK3CA mutations on plasma during chemotherapy are indicative of a poor outcome.
Advancements in the field of precision medicine have prompted the European Society for Medical Oncology (ESMO) Precision Medicine Working Group to update the recommendations for the use of tumour ...next-generation sequencing (NGS) for patients with advanced cancers in routine practice.
The group discussed the clinical impact of tumour NGS in guiding treatment decision using the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) considering cost-effectiveness and accessibility.
As for 2020 recommendations, ESMO recommends running tumour NGS in advanced non-squamous non-small-cell lung cancer, prostate cancer, colorectal cancer, cholangiocarcinoma, and ovarian cancer. Moreover, it is recommended to carry out tumour NGS in clinical research centres and under specific circumstances discussed with patients. In this updated report, the consensus within the group has led to an expansion of the recommendations to encompass patients with advanced breast cancer and rare tumours such as gastrointestinal stromal tumours, sarcoma, thyroid cancer, and cancer of unknown primary. Finally, ESMO recommends carrying out tumour NGS to detect tumour-agnostic alterations in patients with metastatic cancers where access to matched therapies is available.
Tumour NGS is increasingly expanding its scope and application within oncology with the aim of enhancing the efficacy of precision medicine for patients with cancer.
•ESMO updates the recommendations for the use of tumour NGS in patients with advanced cancers in routine practice.•ESMO expands tumour NGS recommendation to advanced breast cancer, GIST, sarcoma, thyroid cancer, and cancer of unknown primary.•ESMO recommends tumour NGS for detecting tumour-agnostic alterations where matched therapies are accessible.•Tumour NGS should be done in clinical research centres and may be discussed under specific circumstances with patients.
Chemoradiotherapy (CRT) is the standard of care for patients diagnosed with locally advanced cervical cancer (LACC), a human papillomavirus (HPV)-related cancer that relapses in 30%-60% of patients. ...This study aimed to (i) design HPV droplet digital PCR (ddPCR) assays for blood detection (including rare genotypes) and (ii) monitor blood HPV circulating tumor DNA (HPV ctDNA) levels during CRT in patients with LACC.
We analyzed blood and tumor samples from 55 patients with HPV-positive LACC treated by CRT in a retrospective cohort (n = 41) and a prospective cohort (n = 14). HPV-ctDNA detection was carried out by genotype-specific ddPCR.
HPV ctDNA was successfully detected in 69% of patients (n = 38/55) before CRT for LACC, including nine patients with a rare genotype. HPV-ctDNA level was correlated with HPV copy number in the tumor (r = 0.41, P < 0.001). HPV-ctDNA positivity for HPV18 (20%, n = 2/10) was significantly lower than for HPV16 (77%, n = 27/35) or other types (90%, n = 9/10, P = 0.002). HPV-ctDNA detection (positive versus negative) before CRT was associated with tumor stage (P = 0.037) and lymph node status (P = 0.02). Taking into account all samples from the end of CRT and during follow-up in the prospective cohort, positive HPV-ctDNA detection was associated with lower disease-free survival (DFS) (P = 0.048) and overall survival (OS) (P = 0.0013).
This is one of the largest studies to report HPV-ctDNA detection before CRT and showed clearance of HPV ctDNA at the end of treatment in most patients. Residual HPV ctDNA at the end of CRT or during follow-up could help to identify patients more likely to experience subsequent relapse.
•HPV ctDNA can be detected before CRT in patients with LACC (69%).•HPV-ctDNA detection was associated with tumor stage and lymph node status.•A lower detection rate of HPV ctDNA was observed for HPV18 genotype.•Residual ctDNA levels after CRT and during follow-up had a prognostic impact.
The current histoclinical breast cancer classification is simple but imprecise. Several molecular classifications of breast cancers based on expression profiling have been proposed as alternatives. ...However, their reliability and clinical utility have been repeatedly questioned, notably because most of them were derived from relatively small initial patient populations. We analyzed the transcriptomes of 537 breast tumors using three unsupervised classification methods. A core subset of 355 tumors was assigned to six clusters by all three methods. These six subgroups overlapped with previously defined molecular classes of breast cancer, but also showed important differences, notably the absence of an ERBB2 subgroup and the division of the large luminal ER+ group into four subgroups, two of them being highly proliferative. Of the six subgroups, four were ER+/PR+/AR+, one was ER-/PR-/AR+ and one was triple negative (AR-/ER-/PR-). ERBB2-amplified tumors were split between the ER-/PR-/AR+ subgroup and the highly proliferative ER+ LumC subgroup. Importantly, each of these six molecular subgroups showed specific copy-number alterations. Gene expression changes were correlated to specific signaling pathways. Each of these six subgroups showed very significant differences in tumor grade, metastatic sites, relapse-free survival or response to chemotherapy. All these findings were validated on large external datasets including more than 3000 tumors. Our data thus indicate that these six molecular subgroups represent well-defined clinico-biological entities of breast cancer. Their identification should facilitate the detection of novel prognostic factors or therapeutical targets in breast cancer.
There is scarce data available about epidermal growth factor receptor (EGFR) mutations other than common exon 19 deletions and exon 21 (L858R) mutations.
EGFR exon 18 and/or exon 20 mutations were ...collected from 10 117 non-small-cell lung cancer (NSCLC) samples analysed at 15 French National Cancer Institute (INCa)-platforms of the ERMETIC-IFCT network.
Between 2008 and 2011, 1047 (10%) samples were EGFR-mutated, 102 (10%) with rare mutations: 41 (4%) in exon 18, 49 (5%) in exon 20, and 12 (1%) with other EGFR mutations. Exon 20 mutations were related to never-smoker status, when compared with exon 18 mutations (P < 0.001). Median overall survival (OS) of metastatic disease was 21 months 95% confidence interval (CI) 12–24, worse in smokers than in non-smoker patients with exon 20 mutations (12 versus 21 months; hazard ratio HR for death 0.27, 95% CI 0.08–0.87, P = 0.03). Under EGFR-tyrosine kinase inhibitors (TKIs), median OS was 14 months (95% CI 6–21); disease control rate was better for complex mutations (6 of 7, 86%) than for single mutations (16 of 40, 40%) (P = 0.03).
Rare EGFR-mutated NSCLCs are heterogeneous, with resistance of distal exon 20 insertions and better sensitivity of exon 18 or complex mutations to EGFR-TKIs, probably requiring individual assessment.
Background: Cancer treatment has been significantly promoted by molecular profiling of patients, providing a personalized mutational landscape, allowing for tailored therapy. The SHIVA trial was a ...randomized proof-of-concept phase II clinical trial, aimed at testing the hypothesis of treating patients based on these profiles with molecularly targeted agents (MTA) in a histology agnostic manner. The trial results showed no statistically significant difference in PFS between the MTA and control arm. The addition of functional information on identified mutations and their response to MTA's may improve treatment outcomes. Materials and Methods: The molecular profile of 13 patients assigned to the RTK/MAPK MTA arm in the trial was established along with their SHIVA treatment regimens. This data served as the basis for analysis of the potentially actionable genes. We utilized the NovellusDx Functional Annotation for Cancer Treatment (FACT), a functional mutational analysis platform, to reveal activated signaling pathways (known mutations, as well as VUS's) and measure the activity of these mutations in the presence of the MTA's administered in the trial. Results: Using FACT we uncovered the functional significance of 5 VUS's and 5 previously annotated mutations in 8 of the 13 patients in the RTK/MAPK group, as well as combinations of mutations within this group. This analysis provided evidence as to the oncogenic activity of the VUS's as well as the oncogenic activity of combination of mutations identified in the patients. Furthermore, the response of these patients' mutations to the MTA's used was measured in-vitro, blinded to the actual clinical results. We found that VUS in FLT3. PDGFRA and 2 of the 3 KIT alterations were not activating mutations as measured by analysis of their respective downstream signaling pathways. Conversely, the third KIT VUS was found to be activating and responsive to Imatinib inhibition. These results suggest different therapeutic options than the ones administered, which need to be further investigated. Conclusions: Today. NGS guided treatment is the foundation of precision medicine. This proof of concept analysis offers a new and innovative method for characterization of patient molecular profiles and their in-vitro response to MTA's. The abundance of mutations classified as VUS and multiple mutations in different genes reveals the complexity in assigning the optimal MTA and the necessity of a functional assay. The prognostic predictions of FACT of the patients subdivided the RTK/MAPK group into potentially responsive and patients with no molecular basis for a benefit in MTA treatment. The use of this novel functional approach provides the additional layer of evidence that can materialize the promise of precision medicine.
The transition of ductal carcinoma in situ (DCIS) to invasive breast carcinoma requires tumor cells to cross the basement membrane (BM). However, mechanisms underlying BM transmigration are poorly ...understood. Here, we report that expression of membrane-type 1 (MT1)-matrix metalloproteinase (MMP), a key component of the BM invasion program, increases during breast cancer progression at the in situ to invasive breast carcinoma transition. In the intraductal xenograft model, MT1-MMP is required for BM transmigration of MCF10DCIS.com breast adenocarcinoma cells and is overexpressed in cell clusters overlying focal BM disruptions and at the invasive tumor front. Mirrored upregulation of p63 and MT1-MMP is observed at the edge of MCF10DCIS.com xenograft tumors and p63 is required for induction of MT1-MMP-dependent invasive program in response to microenvironmental signals. Immunohistochemistry and analysis of public database reveal that p63 and MT1-MMP are upregulated in human basal-like breast tumors suggesting that p63/MT1-MMP axis contributes to progression of basal-like breast cancers with elevated p63 and MT1-MMP levels.
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