Advancing precision oncology through systematic germline and tumor genetic analysis: The oncogenetic point of view on findings from a prospective multicenter clinical trial of 666 patients.

INTRODUCTION: With the emergence of targeted therapies, there is a need to accurately identify more tumor biomarkers. The EXOMA trial was designed to offer tumor and germline exome sequencing (ES) to patients with solid malignant tumors and facing therapeutic failure. As hereditary cancer predispositions could be identified, with genetic counseling and health management implications, a genetic consultation was systematically established. This design needs to be discussed as genetic human resources are limited and indication of theranostic tests will increase. METHODS: Genetic counseling was conducted within 15 days following inclusion in the study for patients recruited between December 2015 and July 2019. In silico analyses from theranostic ES were limited to 317 genes involved in oncogenesis, from both tumor and blood DNA. RESULTS: Six hundred and sixty six patients had a genetic consultation before ES. In 65/666 patients, 66 germline pathogenic or likely pathogenic (P/LP) variants were identified in 16 actionable genes and seven non-actionable genes according to French guidelines. 24/65 patients had previously received genetic analysis for diagnostic purposes, and for 17 of them, a P/LP variant had already been identified. Among the 48/65 remaining cases for which the EXOMA protocol revealed a previously unknown P/LP variant, only 19 met the criteria for genetic testing for inherited cancer risk after familial survey. These criteria had not been identified by the oncologist in 10 cases. In 21/65 cases, the variant was considered incidental. DISCUSSION: In 7.4% of patients, an undiagnosed hereditary genetic predisposition was identified, whether or not related to the clinical presentation, and germline analysis impacted oncological management for only 6.3% of the cohort. This low percentage should be weighed against the burden of systematic genetic consultation and urgent circuits. Information or training tools to form oncologists to the prescription of germline genetic analyses should be explored, as well as information supports and patient preferences.

Custom multi­tumor next­generation sequencing panel for routine molecular diagnosis of solid tumors: Validation and results from three­year clinical use.

Molecular testing is extremely important in cancer care, starting as early as at diagnosis. In order to address the challenge of providing reliable results within the timeframe adapted to patient management and suitable to guide clinical decisions, a capture­based next­generation sequencing (NGS) panel focusing on ten genes known to harbor genetic variations which may be targeted by approved drugs in patients with cancer was designed and validated. Very favorable analytical performances were obtained for both solid and liquid biopsies. For solid biopsies, a low read depth (80X per nucleotide) led to the genotype detection accuracy of 100%. The read of raw data for liquid biopsies resulted in the 91.19% result concordance between paired solid and liquid samples. The present method met all the requirements for the ISO15189 certification. During our three­year experience of routinely using this panel, almost 2,300 samples from lung and colorectal cancers, melanomas and gastrointestinal stromal tumors have been analyzed. It was found that our panel detected slightly more gain­of­function variants than described in the literature. Surprisingly, loss­of­function variants were also detected in certain of the analyzed genes. Finally, liquid biopsy data revealed statistically different mutated allele frequencies between tumor types, but also between mutated genes and variants themselves. In conclusion, the use of our capture­based NGS panel is perfectly adapted to perform relevant molecular diagnosis in a time frame compatible with patient care.

Parallel evolution and differences in seroprevalence of SARS-CoV-2 antibody between patients with cancer and health care workers in a tertiary cancer centre during the first and second wave of COVID-19 pandemic: canSEROcov-II cross-sectional study.

BACKGROUND: Patients with cancer are a population at high risk of severe infection from SARS-CoV-2. Patients with cancer regularly attend specialised healthcare centres for management and treatment, where they are in contact with healthcare workers (HCWs). Numerous recommendations target both patients with cancer and HCWs to minimise the spread of SARS-CoV-2 during these interactions. OBJECTIVE: To investigate the parallel evolution of the COVID-19 epidemic in these 2 populations over time, we studied the seroprevalence of anti-SARS-CoV-2 antibodies after both the first and second waves of the pandemic, and in both cancer patients and HCWs from a single specialised anti-cancer centre. Factors associated with seropositivity were identified in both populations. METHODS: We conducted a cross-sectional study after the second wave of the COVID pandemic in France. All participants were invited to undergo serological testing for SARS-CoV-2 and complete a questionnaire collecting data about their working conditions (for HCWs) or medical management (for patients) during this period. Results after the second wave were compared to those of a previous study among 1011 patients with cancer and 663 HCWs performed in the same centre after the first wave, using the same evaluations. FINDINGS: We included 502 HCWs and 507 patients with cancer. Seroprevalence of anti-SARS-CoV-2 antibodies was higher after the second wave than after the first wave in both HCWs (15.1% versus 1.8%; p < 0.001), and patients (4.1% versus 1.7%; p = 0.038). By multivariate analysis, the factors found to be associated with seropositivity after the second wave for HCWs were: working in direct patient care (p = 0.050); having worked in a dedicated COVID-19 unit (p = 0.0036); contact with a person with COVID-19-positive in the workplace (p = 0.0118) or outside of the workplace (p = 0.0297). Among patients with cancer, only a contact with someone who tested positive for COVID-19 was found to be significantly associated with positive serology. The proportion of reported contacts with individuals with COVID-19-positive was significantly lower among patients with cancer than among HCWs (7.6% versus 40.7%, respectively; p < 0.0001) INTERPRETATION: Between the first and second waves of the epidemic in France, the seroprevalence of anti-SARS-CoV-2 antibodies increased to a lesser extent among patients with cancer than among their HCWs, possibly due to better self-protection, notably social distancing. The risk factors for infection identified among HCWs plead in favour of numerous intra-hospital contaminations, especially for HCWs in contact with high-risk patients. This underlines the compelling need to pursue efforts to implement strict hygiene and personal protection measures (including vaccination) to protect HCWs and patients with cancer.

A novel POLD1 pathogenic variant identified in two families with a cancer spectrum mimicking Lynch syndrome.

The POLD1 gene is involved in DNA proofreading to ensure accurate DNA replication. Some germline alterations in its exonuclease domain are associated with predisposition to cancers and colonic polyps. Only a few pathogenic variants have been clearly identified so far. Here we report a novel variant: c.1458G>T p.(Lys486Asn) that we classified as pathogenic, detected in two putatively unrelated families. The cancer spectrum was very similar to Lynch syndrome, implying an overlapped tissue susceptibility. The common presence of colonic polyps in carriers and the MMR proficient phenotype in tumors were distinctive features suggesting POLD1 implication. Some clinical characteristics observed in the carriers of this variant differed from those reported previously, suggesting a potential genotype/phenotype correlation, and very likely in relation to the functional importance of affected residues. Our findings provide further insight into understanding the role of POLD1 in cancer-related risk.

Does large NGS panel analysed using exome tumour sequencing improve the management of advanced non-small-cell lung cancers?

INTRODUCTION: Non-small-cell lung cancer (NSCLC) is one of the most common and deadly cancers. Several molecular drivers of oncogene addiction are now known to be strong predictive biomarkers for target therapies. Advances in large Next Generation Sequencing (LNGS) have improved the ability to detect potentially targetable mutations. However, the integration of LNGS into clinical management in an individualized manner remains challenging. METHODS: In this single-center observational study we included all patients with advanced NSCLC who underwent LNGS. Somatic and germline exome analysis was performed with a restriction on 323 cancer related genes. Variants were classified and Molecular Tumour Board (MTB) made therapeutic propositions. RESULTS: We performed LNGS analysis in 281 patients with advanced NSCLC between March 2015 and January 2018. Technical failure occurred in only 3% of cases. Three hundred and fifty-six targetable mutations were detected. At least one targetable mutation was found in 209 patients. For all these patients, the MTB was able to recommend treatment with a targeted agent based on the evaluation of the tumour's genetic profile and treatment history. Twenty-nine patients (13.9%) were subsequently treated with an MTB-recommended targeted therapy. We did not observe any improvement in terms of clinical benefit for these patients. CONCLUSIONS: In this case series, we show that including LNGS into routine clinical management was feasible but does not appear to provide clinical benefit in the management of patients with advanced NSCLC.

TCR Clonality and Genomic Instability Signatures as Prognostic Biomarkers in High Grade Serous Ovarian Cancer.

PURPOSE: Immune infiltration is a prognostic factor in high-grade serous ovarian carcinoma (HGSC) but immunotherapy efficacy is disappointing. Genomic instability is now used to guide the therapeutic value of PARP inhibitors. We aimed to investigate exome-derived parameters to assess the tumor microenvironment according to genomic instability profile. METHODS: We used the HGSC TCGA (the cancer genome atlas) dataset with genomic characteristics, including homologous recombination deficiency (HRD), copy number variant (CNV) signatures, TCR (T cell receptor) clonality and abundance of tissue-infiltrating immune and stromal cell populations. We then investigated the relationship with survival data. RESULTS: In 578 HGSC patients, HRD status, CNV signature 7 and TCR clonality were associated with longer survival. The combination of high CNV signature 7 expression and HRD status or high CNV signature 3 expression and high TCR clonality was associated with a trend towards longer survival compared to each variable alone. Combining T cell infiltrate and TCR clonality improved the prognostic value compared to T cells infiltration alone. Prognostic value of TCR clonality was confirmed in an independent cohort. CONCLUSIONS: TCR clonality is an emerging prognostic biomarker that improves T cell infiltrate information. Analysis of TCR clonality combined with genomic instability could be an interesting prognostic biomarker.

TUMOSPEC: A Nation-Wide Study of Hereditary Breast and Ovarian Cancer Families with a Predicted Pathogenic Variant Identified through Multigene Panel Testing.

Assessment of age-dependent cancer risk for carriers of a predicted pathogenic variant (PPV) is often hampered by biases in data collection, with a frequent under-representation of cancer-free PPV carriers. TUMOSPEC was designed to estimate the cumulative risk of cancer for carriers of a PPV in a gene that is usually tested in a hereditary breast and ovarian cancer context. Index cases are enrolled consecutively among patients who undergo genetic testing as part of their care plan in France. First- and second-degree relatives and cousins of PPV carriers are invited to participate whether they are affected by cancer or not, and genotyped for the familial PPV. Clinical, family and epidemiological data are collected, and all data including sequencing data are centralized at the coordinating centre. The three-year feasibility study included 4431 prospective index cases, with 19.1% of them carrying a PPV. When invited by the coordinating centre, 65.3% of the relatives of index cases (5.7 relatives per family, on average) accepted the invitation to participate. The study logistics were well adapted to clinical and laboratory constraints, and collaboration between partners (clinicians, biologists, coordinating centre and participants) was smooth. Hence, TUMOSPEC is being pursued, with the aim of optimizing clinical management guidelines specific to each gene.

Seroprevalence of SARS-CoV-2 among the staff and patients of a French cancer centre after first lockdown: The canSEROcov study.

BACKGROUND: In view of the potential gravity of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection for patients with cancer, epidemiological data are vital to assess virus circulation among patients and staff of cancer centres. We performed a prospective study to investigate seroprevalence of SARS-CoV-2 antibodies among staff and patients with cancer at a large cancer centre, at the end of the period of first national lockdown in France and to determine factors associated with the risk of SARS-CoV-2 infection. METHODS: After the first lockdown, all medical and non-medical staff, as well as all patients attending the medical oncology department were invited to undergo serological testing for SARS-CoV-2 between 11 May and 30 June 2020. All participants were also invited to complete a questionnaire collecting data about their living and working conditions, and for patients, medical management during lockdown. FINDINGS: A total of 1,674 subjects (663 staff members, 1011 patients) were included. Seroprevalence was low in both staff (1.8%) and patients (1.7%), despite more features of high risk for severe forms among patients. None of the risk factors tested in our analysis (working or living conditions, comorbidities, management characteristics during lockdown) was found to be statistically associated with seroprevalence in either staff or patients. There was no significant difference in the proportion of symptomatic and asymptomatic subjects between staff and patients. Only fever, loss of smell, and loss of taste were significantly more frequent among seropositive patients, in both staff and patients. INTERPRETATION: We report very low seroprevalence of antibodies against SARS-CoV-2 in the staff (caregiving and non-caregiving) and patients of a large cancer care centre in which strict hygiene, personal protection, and social distancing measures were implemented.

Further delineation of the NTHL1 associated syndrome: A report from the French Oncogenetic Consortium.

Biallelic pathogenic variants in the NTHL1 (Nth like DNA glycosylase 1) gene cause a recently identified autosomal recessive hereditary cancer syndrome predisposing to adenomatous polyposis and colorectal cancer. Half of biallelic carriers also display multiple colonic or extra-colonic primary tumors, mainly breast, endometrium, urothelium, and brain tumors. Published data designate NTHL1 as an important contributor to hereditary cancers but also underline the scarcity of available informations. Thanks to the French oncogenetic consortium (Groupe Génétique et Cancer), we collected NTHL1 variants from 7765 patients attending for hereditary colorectal cancer or polyposis (n = 3936) or other hereditary cancers (n = 3829). Here, we describe 10 patients with pathogenic biallelic NTHL1 germline variants, that is, the second largest NTHL1 series. All carriers were from the "colorectal cancer or polyposis" series. All nine biallelic carriers who underwent colonoscopy presented adenomatous polyps. For digestive cancers, average age at diagnosis was 56.2 and we reported colorectal, duodenal, caecal, and pancreatic cancers. Extra-digestive malignancies included sarcoma, basal cell carcinoma, breast cancer, urothelial carcinoma, and melanoma. Although tumor risks remain to be precisely defined, these novel data support NTHL1 inclusion in diagnostic panel testing. Colonic surveillance should be conducted based on MUTYH recommendations while extra-colonic surveillance has to be defined.

[CA 125 assay in the extension assessment of newly diagnosed breast cancers: why and how?] / Le CA 125 dans le bilan d'extension des cancers du sein nouvellement diagnostiqués : pourquoi et comment ?

CA 125 assay is sometimes combined in practice with the one of CA 15-3 and CEA in the extension assessment of breast cancers. The purpose of this work is to evaluate the contribution of the initial CA 125 as an indicator of distant metastases (DM) or of serous inflammation (SI). This retrospective study concerns a population of 620 patients with breast cancer without metastatic extension (n=325) or metastatic breast cancer (n=295) diagnosed at the Georges-François Leclerc center from 1998 to 2014. Seventy-four patients had SI. We showed that initial CA 125 level is linked to the TNM clinic status, the HER2 status, the nature and the number of metastatic locations, the inflammation of the tumor or serous. The ROC curves and logistic regression analyses show that CA 125 is an independent predictive criterion of DM presence (threshold of 55 kU/L): this is the only positive marker in 7% of patients with DM. At the threshold of 110 kU/L, the CA 125 is the only predictive biologic factor for SI. In conclusion, these data present the independent predictive value of CA 125 on the presence of DM or SI on condition of usinga specific threshold for each of these uses.

Clinical value of CA 15-3 for detection of distant metastases in newly diagnosed breast cancer.

The aim of the study is to investigate the clinical value of CA 15-3 for detection of distant metastases (DM) in newly diagnosed breast cancer. This retrospective study focuses on a population of 1,007 patients with locally advanced breast cancer (n=561) or metastatic breast cancer (n=446) diagnosed at the CGFL (Centre Georges Francois Leclerc) from March 1998 to October 2013. These patients underwent a measurement of CA 15-3 and an assessment of extension before any treatment. The cut-off value of CA 15-3 was determined and verified on two independents subpopulations determined in drawing lots. The ROC curve shows an AUC of 0.85 (p<0.0001). At the threshold of 50 kU/L, CA 15-3 before treatment has a predictive value on the existence of DM independently of the other prognostics factors. This predictive value has been found in every molecular subtype (AUC≥ 0.70; p≤ 0,085). The rate of false negative is of 38% and depends on the number and the type of the metastatic localization. Among the 28 patients without DM and a CA 15-3> 50 kU/L, 13 have developed DM and 11 died of cancer. In conclusion, these facts confirm the independently predictive value of CA 15-3 before treatment on the existence of DM and the complementarity of the marker with the assessment of extension by imagery.

Clinical value of CEA for detection of distant metastases in newly diagnosed breast cancer: comparison with CA 15-3.

The aim of the study is to investigate the clinical value of CEA (carcinoembryonic antigen) for detection of distant metastases (DM) in newly diagnosed breast cancer. This retrospective study focuses on a population of 929 patients with locally advanced breast cancer (n=521) or metastatic breast cancer (n=408) diagnosed at the CGFL (Centre Georges Francois Leclerc) from 1998 to 2014. These patients underwent a measurement of CA 15-3, a measurement of CEA and an assessment of extension before any treatment. The initial concentrations of CEA are correlated with conventional prognostic factors. The cut-off value of CEA was determined and verified on two independents subpopulations determined in drawing lots. The ROC curve shows an AUC of 0.82 (p<0.0001). At the threshold of 6.7 µg/L, CEA before treatment has a predictive value on the existence of DM independently of the CA 15-3 and other prognostic factors. The combination of CEA and CA 15-3 increases significantly the predictive value of CA 15-3 on the whole population (sensitivity increased by 9%) and on tumors expressing hormonal receptors. Concerning the only CEA the rate of false negative is of 52% and depends on the number and the type of the metastatic localization. Among the 28 patients without DM and a CEA > 6.7 µg/L, 15 have developed DM and 2 a new cancer. Thirteen will die of cancer. In conclusion, these facts confirm the independently predictive value of CEA before treatment on the existence of DM and its complementarity with CA 15-3 during the assessment of extension by imagery.

Identification and validation of a factor of commutability between platelet counts performed on EDTA and citrate.

The anticoagulant mostly employed for platelet count is EDTA. The Francophone Group of Cellular Hematology recommends checking of blood smear stained with May-Grünwald Giemsa any thrombocytopenia less than 100 G/L without medical history or whether an alarm is generated by the cell counter. The pseudo-thrombocytopenia (PTP) with EDTA is the best known artifact in platelet count. A sample of blood on citrated tube is necessary to get rid of the interference. The objective of this study was to compare the platelet counts obtained on EDTA (numEDTA) and citrate (numCTAD) tubes and to define, then validate a factor of conversion between both methods. The prevalence of PTP EDTA is 0.26%. The PTP was transient in 80% of the patients. The numEDTA and numCTAD+10% (numCTAD increased by 10% to take dilution into account) are correlated but are not equivalent. The numCTAD+10% underestimate numEDTA significantly. The systematic bias is removed if we increase by 17% numCTAD. The factor of correction is stable over a period of 3 hours.

[Validation steps for the detection of L858R mutation in EGFR gene by real time quantitative PCR]. / Validation de méthode de la recherche de la mutation L858R par PCR en temps réel utilisant les sondes fluorescentes Taqman® dans les cancers bronchiques non à petites cellules.

Since January 16(th) 2010, the French legislation requires that the medical laboratories must be accredited according to ISO 15189 standards. This concerned all the biological medical technics, including molecular biology technics. In this work, we described the validation steps by real time quantitative PCR of L858R mutation in EGFR gene, frequently detected in non-small lung cancers (NSCLC). Epidermal growth factor - tyrosine kinase inhibitors (EGFR-TKIs) are authorized in Europe for the treatment of metastatic NSCLC after failure of, at least one, prior chemotherapy. Thus, in view of accreditation of this analysis, we have used the recommendation of the COFRAC (Comité français d'accréditation) and INCa (Institut national du cancer). Several parameters have been tested, such as the primers, the limit of detection, and the sensitivity and specificity of the method. In addition, a risk study has been evaluated. Although long and fastidious, the method of validation is required to perform analysis in optimal conditions to guaranty optimal results for the patients.

[CEA and early detection of relapse in breast cancer subtypes: Comparison with CA 15-3]. / ACE et diagnostic précoce de récidive dans les différents sous-types moléculaires de cancer du sein : comparaison au CA 15-3.

This retrospective study evaluates the interest of CEA measurement for early detection of breast cancer recurrences. Among 804 patients with invasive breast cancer, we selected 97 patients without recurrence (WR) for 5 years or more, 32 with a local recurrence (LR) and 131 with at least one distant metastasis (DM). Elevated CEA and CA 15-3 levels (>3.1 µg/L and >26 kU/L respectively) were found in 6 % and 22 % of patients with RL respectively and in 49 % and 69 % of patients with DM. Both CEA and CA 15-3 retained a significant value in predicting DM by univariate and multivariate analysis. Higher sensitivity of CEA and CA 15-3 were found in tumors with positive hormonal receptor status. CEA and CA 15-3 levels at DM were raised respectively in 23 and 65 % of the triple negative group, 58 and 75 % of the luminal, 56 and 78 % of the luminal-HER2 and 50 and 30 % of HER2-enriched group (P=0.0094 and 0.0252 respectively). The combination of CEA and CA 15-3 increased CA 15-3 sensitivity in especially luminal and HER2-enriched groups. In conclusion, elevated CA 15-3 and CEA levels at initial diagnosis of recurrence were found to be associated with hormonal receptor status and breast cancer subtypes. The combination of CEA and CA 15-3 appeared useful especially luminal and HER2-enriched groups.

Restoring Anticancer Immune Response by Targeting Tumor-Derived Exosomes With a HSP70 Peptide Aptamer.

BACKGROUND: Exosomes, via heat shock protein 70 (HSP70) expressed in their membrane, are able to interact with the toll-like receptor 2 (TLR2) on myeloid-derived suppressive cells (MDSCs), thereby activating them. METHODS: We analyzed exosomes from mouse (C57Bl/6) and breast, lung, and ovarian cancer patient samples and cultured cancer cells with different approaches, including nanoparticle tracking analysis, biolayer interferometry, FACS, and electron microscopy. Data were analyzed with the Student's t and Mann-Whitney tests. All statistical tests were two-sided. RESULTS: We showed that the A8 peptide aptamer binds to the extracellular domain of membrane HSP70 and used the aptamer to capture HSP70 exosomes from cancer patient samples. The number of HSP70 exosomes was higher in cancer patients than in healthy donors (mean, ng/mL ± SD = 3.5 ± 1.7 vs 0.17 ± 0.11, respectively, P = .004). Accordingly, all cancer cell lines examined abundantly released HSP70 exosomes, whereas "normal" cells did not. HSP70 had higher affinity for A8 than for TLR2; thus, A8 blocked HSP70/TLR2 association and the ability of tumor-derived exosomes to activate MDSCs. Treatment of tumor-bearing C57Bl/6 mice with A8 induced a decrease in the number of MDSCs in the spleen and inhibited tumor progression (n = 6 mice per group). Chemotherapeutic agents such as cisplatin or 5FU increase the amount of HSP70 exosomes, favoring the activation of MDSCs and hampering the development of an antitumor immune response. In contrast, this MDSC activation was not observed if cisplatin or 5FU was combined with A8. As a result, the antitumor effect of the drugs was strongly potentiated. CONCLUSIONS: A8 might be useful for quantifying tumor-derived exosomes and for cancer therapy through MDSC inhibition.

[Clinical value of CA 15-3 for early detection of relapse in locally advanced breast cancer]. / Intérêt clinique du CA 15-3 dans la détection précoce des récidives de cancer du sein localement avancé.

This retrospective study evaluates the interest of CA 15-3 measurement for early detection of breast cancer recurrences. Among 804 patients with invasive breast cancer we selected 117 patients without recurrence (WR) for 5 years or more, 33 with a local recurrence (LR) and 149 with at least one distant metastasis (DM). The sensitivity of CA 15-3 depends on the type of recurrence ([LR] or [DM]), the localization of unique DM, the presence and the number of metastatic sites, on hormonal receptor status and tumor subtypes. The number of metastatic sites and hormonal receptor status are independent predictive criteria of an elevation of CA 15-3. The analysis of ROC curve in order to separate patients with DM and patients WR shows an AUC of 0.87 (p<0.0001). The optimal discriminative threshold is 26 kU/L. In conclusion, these data confirm that CA 15-3 increase depends on the kind of evolution and on initial tumor's hormonal status.