Malignancy after Augmentation Enterocystoplasty: A Nationwide Study of Natural History, Prognosis and Oncogene Panel Analysis.

PURPOSE: We report the natural history and prognosis of tumors after augmentation enterocystoplasty, with a molecular analysis using an oncogene panel to search for potential targeted therapies. MATERIALS AND METHODS: This multicenter, nationwide, retrospective study included 16 patients. A panel of 21 clinically relevant oncogenes was tested on archival tumor specimens using next-generation sequencing. Survival rate was the main clinical outcome and sequences were compared to the reference genome for the genetic outcome. RESULTS: Augmentation enterocystoplasties were performed mainly for congenital neurogenic bladder and bladder exstrophy at a median patient age of 17 years (range 4 months to 45 years). Most of the malignancies were diagnosed because of clinical manifestations, with a median latency period of 20 years. Adenocarcinomas were mainly found after gastrocystoplasty, whereas urothelial cell carcinomas were typically found after colocystoplasty. Of the 16 patients 13 were diagnosed at an advanced stage of the disease (positive lymph nodes in 7, distant metastases in 6). The overall 1-year survival rate was 56%. Only 3 patients remained disease-free at a median followup of 70 months. Of the 9 tumors with analyzable DNA 4 were wild-type and 5 harbored missense mutations (KIT-p.Pro573Ser, PDGFRA-p.Glu587Lys, KRAS-p.Gly12Asp, ERBB4p.Arg484Lys, CTNNB1-p.Ser37Phe and p.Ser47Asn). CONCLUSIONS: Malignancy after augmentation enterocystoplasty is diagnosed late with frequent metastases and a very low 1-year survival rate. More than half the tested samples harbored missense mutations in oncogenes accessible to targeted therapies. An international collaboration to enlarge the genetic panel analysis of these tumors may offer new therapeutic hope to patients.

Challenging BRAF/EGFR co-inhibition in NSCLC using sequential liquid biopsies.

OBJECTIVES: There is some controversy surrounding theBRAFV600E mutation in patients with lung adenocarcinomas. Although the BRAFV600E mutation is sensitive to BRAF inhibitors, the efficiency of these inhibitors on patients harboring an EGFRL858R/del19/EGFRT790M/BRAFV600E pattern remains unknown. MATERIALS AND METHODS: Here, we presented the case of a patient with initial response followed by progression on osimertinib. Resistance mutations (EGFRT790M, EGFRC797S, BRAFV600E, MET amp and HER2 amp) were assessed in the tissue or plasma DNA using NGS and digital droplet PCR at progression and during osimertinib treatment. RESULTS: Resistance to osimertinib coincided with the emergence of an additional tumor cell subpopulation carrying the knownBRAFV600E resistance mutation. The patient exhibited two tumor subclones (EGFRdel19/T790M and BRAFV600E) that displayed distinct responses to successive tyrosine kinase inhibitors. CONCLUSION: We report the first successful example of using sequential treatment with dabrafetinib/trametinib and osimertinib. Our finding provided that unique tumor biopsies deliver incomplete genetic information, and highlighted the complementary role of circulating tumor DNA to tissue biopsies and CT-scans to efficiently monitor response to osimertinib.

Extended-spectrum beta-lactamase-producing Escherichia coli in common vampire bats Desmodus rotundus and livestock in Peru.

Antibiotic resistance mediated by bacterial production of extended-spectrum beta-lactamase (ESBL) is a global threat to public health. ESBL resistance is most commonly hospital-acquired; however, infections acquired outside of hospital settings have raised concerns over the role of livestock and wildlife in the zoonotic spread of ESBL-producing bacteria. Only limited data are available on the circulation of ESBL-producing bacteria in animals. Here, we report ESBL-producing Escherichia coli in wild common vampire bats Desmodus rotundus and livestock near Lima, Peru. Molecular analyses revealed that most of this resistance resulted from the expression of blaCTX-M-15 genes carried by plasmids, which are disseminating worldwide in hospital settings and have also been observed in healthy children of Peru. Multilocus sequence typing showed a diverse pool of E. coli strains carrying this resistance that were not always host species-specific, suggesting sharing of strains between species or infection from a common source. This study shows widespread ESBL resistance in wild and domestic animals, supporting animal communities as a potential source of resistance. Future work is needed to elucidate the role of bats in the dissemination of antibiotic-resistant strains of public health importance and to understand the origin of the observed resistance.

Investigation of pre-XDR Beijing Mycobacterium tuberculosis transmission to a healthcare worker in France, 2016.

A case of occupational contamination of a healthcare worker by a pre-extensively drug-resistant (pre-XDR) Beijing strain of Mycobacterium tuberculosis at the University Hospital of Montpellier, France is reported. The index case was identified using genetic fingerprinting of isolates. This report underscores the risk of healthcare-associated contamination by pre-XDR tuberculosis (TB) in low-incidence countries and the importance of molecular tools for TB care. It also calls for increased vigilance in the management of multi-drug-resistant/XDR TB patients.

Rare EGFR exon 18 and exon 20 mutations in non-small-cell lung cancer on 10 117 patients: a multicentre observational study by the French ERMETIC-IFCT network.

BACKGROUND: There is scarce data available about epidermal growth factor receptor (EGFR) mutations other than common exon 19 deletions and exon 21 (L858R) mutations. PATIENTS AND METHODS: 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. RESULTS: 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). CONCLUSIONS: 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.

[Intrinsic radiosensitivity: predictive assays that will change daily practice]. / Radiosensibilité individuelle : les tests vont changer nos pratiques.

The impact of curative radiotherapy depends mainly on the total dose delivered homogenously in the targeted volume. Nevertheless, the dose delivered to the surrounding healthy tissues may reduce the therapeutic ratio of many radiation treatments. In a same population treated in one center with the same technique, it appears that individual radiosensitivity clearly exists, namely in terms of late side effects that are in principle non-reversible. This review details the different radiobiological approaches that have been developed to better understand the mechanisms of radiation-induced late effects. We also present the possibilities of clinical use of predictive assays in the close future.

[Identification of predictive biomarkers to radiotherapy outcome through proteomics approaches]. / Identification de marqueurs prédictifs de la réponse à la radiothérapie par approche protéomique.

The success of radiotherapy mainly depends on the total administered dose. This dose must be homogenously delivered onto the tumor and must preserve the surrounding healthy tissue. However, several patients are hypersensitive to ionizing radiations and may develop important radiation-induced early and late side effects. The prediction of these side effects remains currently impossible, involving to limit the given dose with the risk to decrease the therapeutic benefit for patients. Therefore, one of the major challenges in radiobiology is to accurately predict tumour radioresistance and to determine normal tissue radiosensitivity to tailor treatment. Several studies have been carried out and different predictive assays have been described in this field. However, none of them showed significant results for clinical use. For several years, many technological advances in proteomic fields have been performed in order to identify new biomarkers. After a brief description of the main characteristics of tumor radioresistance and normal tissue radiosensitivity, we will develop in this review the different approaches proposed so far to identify predictive tools of radiotherapy outcome. We will then analyze in detail how proteomic studies can improve the understanding of mechanisms associated with radiosensitivity of healthy tissue and radioresistance of tumor cells and how they could highlight new predictive biomarkers in radiobiology.

The contribution of proteomics to the identification of biomarkers for cutaneous malignant melanoma.

Despite significant advances in treatment of the melanoma during the past decade, the survival rate is little improved. A contributory factor to the poor outcome is the lack of appropriate sensitive and specific diagnostic, prognostic, and therapeutic response biomarkers. Many serum biomarkers have been evaluated in melanoma but their poor sensitivity and specificity remain serious limitations for their routine use in the clinical setting. Advances in proteomic instrumentation and methodology represent a very promising approach for improving the detection of new candidate markers or pattern of markers. However, the number of validated biomarkers is still limited and the reproducibility between studies remains unclear, impairing their use in clinical setting. In this review, we provide an updated overview of the biomarkers identified in melanoma through serum, cell lines, and tissue proteomic analysis. We also discuss on the emerging strategies used for the identification of new candidate melanoma biomarkers. Finally, we highlight the challenges remaining for clinical validation.

Proteomic analysis of differently archived breast cancer tissues.

Currently, the most common practice of human breast tissue preservation is formalin fixation which ensures good quality for histopathological analyses but damages DNA, RNA, and proteins, impairing their usefulness for molecular analysis and biomarker investigations. We investigated the potential value of a non-toxic fixative for sparing proteins preserved in paraffin-embedded breast biopsies. Specimens were fixed in formalin-free fixative prior to paraffin embedding, and then processed for quality and quantity of protein conservation. Similar protein patterns were observed in formalin-free fixative and frozen tissues using mono- and bi-dimensional electrophoresis, as well as western blotting. Protein patterns assessed by mass spectrometric analysis were found to be identical for frozen and formalin-free-fixed tissues. Immunohistochemistry using various antibodies showed comparable results for both tissue storage methods. In conclusion, we believe that formalin-free fixative represents an easy-to-use alternative to formalin for archived tissue and for biomarker investigations, since it simultaneously protects both the histomorphology and the integrity of macromolecules.

Autoantibody signatures: progress and perspectives for early cancer detection.

Becoming invasive is a crucial step in cancer development, and the early spread of tumour cells is usually undetected by current imaging technologies. In patients with cancer and no signs of overt metastases, sensitive methods have been developed to identify circulating autoantibodies and their antigen counterparts in several cancers. These technologies are often based on proteomic approaches, and recent advances in protein and antibody microarrays have greatly facilitated the discovery of new antibody biomarkers in sera from cancer patients. Interestingly, in a clinical application setting, combinations of multiple autoantibody reactivities into panel assays have recently been proposed as relevant screening tests and validated in several independent trials. In addition, autoantibody signatures seem to be particularly relevant for early detection of cancer in high-risk cancer patients. In this review, we highlight the concept that immunogenic epitopes associated with the humoural response and key pathogenic pathways elicit serum autoantibodies that can be considered as relevant cancer biomarkers. We outline the proteomic strategies employed to identify and validate their use in clinical practice for cancer screening and diagnosis. We particularly emphasize the clinical utility of autoantibody signatures in several cancers. Finally, we discuss the challenges remaining for clinical validation.

[Interest of blood markers in predicting radiation-induced toxicity]. / Intérêt des marqueurs sanguins dans la prédiction de la toxicité radio-induite.

The oncologic outcome and the total dose are highly correlated with the treatment by ionizing radiation. The dose increase (total or per fraction) may provoke late-side effects that are potentially irreversible. The radiation-induced CD8 lymphocyte apoptotic value and the molecular modifications within the lymphocyte are capable of predicting the level of risk of developing late-side effects after curative intent radiotherapy. In this review, we present the different blood assays in this setting and discuss the current possibilities of researches, namely those involving the proteomic process.

Pemphigus vulgaris antigen mRNA quantification for the staging of sentinel lymph nodes in head and neck cancer.

BACKGROUND: Molecular diagnosis has been proposed to enhance the intra-operative diagnosis of sentinel lymph node (SLN) invasion in head and neck squamous cell carcinoma (HNSCC). Although cytokeratin (CK) mRNA quantification with real-time reverse transcriptase-PCR (QRT-PCR) has produced encouraging results, the more discriminating markers remain to be identified. METHODS: Pemphigus vulgaris antigen (PVA), squamous cell carcinoma antigen (SCCA), and CK17 mRNA were quantified using QRT-PCR, and the results were compared with an extensive histopathological examination of the entire SLNs on 78 SLNs harvested from 22 patients with HNSCC. RESULTS: SCCA and CK17 quantification showed significantly higher mRNA values for macrometastases (MAs) than for either negative or isolated tumour cell (ITC) SLNs (P<0.01). Pemphigus vulgaris antigen allowed the discrimination of all MAs and micrometastases from both negative and ITC SLNs (P<0.001). For the neck staging of patients, considering metastatic vs non-metastatic status, receiver-operating characteristic curve analysis found areas under the curve of 93.8, 97.9, and 100% for CK17, SCCA, and PVA, respectively. With PVA, a cutoff value of 562 copies per 100 ng of cDNA permitted the correct distinction between patients with positive as opposed to negative neck nodes in all cases. CONCLUSION: PVA seems to be a highly promising marker for accurate intra-operative SLN staging in HNSCC by QRT-PCR.

Serum protein signature may improve detection of ductal carcinoma in situ of the breast.

Ductal carcinoma in situ (DCIS) of the breast is part of a spectrum of preinvasive lesions that originate within normal breast tissue and progress to invasive breast cancer. The detection of DCIS is important for the reduction of mortality from breast cancer, but the diagnosis of preinvasive breast tumors is hampered by the lack of an adequate detection method. To identify the changes in protein expression during the initial stage of tumorigenesis and to identify the presence of new DCIS markers, we analysed serum from 60 patients with breast cancer and 60 normal controls using mass spectrometry. A 23-protein index was generated that correctly distinguishes the DCIS and control groups with sensitivities and specificities in excess of 80% in two independent cohorts. Two candidate peptides were purified and identified as platelet factor 4 (PF-4) and complement C3a(desArg) anaphylatoxin (C3a(desArg)) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In an independent serum set of 165 patients, PF-4 and C3a(desArg) were significantly upregulated in DCIS compared with non-cancerous controls, as validated using western blot and enzyme-linked immunosorbent assay. We conclude that our serum protein-based test, used in conjunction with image-based screening practices, could improve the sensitivity and specificity of breast cancer detection.

Humoral response to cancer as a tool for biomarker discovery.

There is an important need to find relevant biomarkers that show high sensitivity and specificity for early diagnosis and prognosis of cancer. An immune response to cancer is elicited in humans, as demonstrated in part by the identification of autoantibodies against a number of tumor-associated antigens in sera from patients with different types of cancer. Identification of tumor-associated antigens and their cognate autoantibodies is a promising strategy for the discovery of relevant biomarkers. During the past few years, proteomic approaches, including SEREX, SERPA and, more recently, protein microarrays, have been the dominant strategies used to identify tumor-associated antigens and their cognate autoantibodies. In this review, we aim to describe advantages, drawbacks, and recent improvements of these approaches for the study of humoral responses.

Proteomic analysis of RCL2 paraffin-embedded tissues.

Histopathological diagnosis in most of the world's hospitals is based upon formalin-fixed and paraffin-embedded (FFPE) tissues. Although this standard fixation and embedding procedure keeps the tissue in excellent form for morphological and immunohistological analysis, FFPE is inappropriate for nucleic acids and protein studies. We investigated the potential value of RCL2, a new non-toxic fixative, for sparing proteins preserved in paraffin-embedded tissues. Normal colonic mucosa tissue was fixed in RCL2 prior to paraffin embedding (RCL2P), and then processed for quality and quantity of protein conservation, as compared to frozen and FFPE tissues using complementary proteomic analysis approaches. Using 4 different protein extraction protocols, RCL2P tissue consistently showed the highest protein yield. Similar protein patterns were observed with RCL2P and frozen tissues using mono and bi-dimensional electrophoresis. Moreover, membrane, cytoplasmic and nuclear proteins, as well as phosphorylated proteins, were successfully detected using western-blot. Furthermore, protein patterns observed by mass spectrometry analysis after laser-captured microdissection were found to be identical for frozen and RCL2-fixed tissues. At last, immunohistochemistry using various antibodies showed comparable results between both tissue storage methods. We concluded that RCL2 has great potential for performing both morphological and molecular analyses on the same archival paraffin-embedded tissue sample, and can be a new method for investigating protein biomarkers.

Comprehensive proteomic analysis of the human milk proteome: contribution of protein fractionation.

In-depth analysis of the milk proteome by mass spectrometry is challenged by the presence of few high-abundance proteins that interfere with the detection of lower-abundance proteins. Here, we evaluated the proteomic analysis of milk samples following a strong anion exchange fractionation procedure using denaturating conditions ensuring the disruption of protein-protein interactions. Crude whey or skim milk and their different resulting fractions were analyzed by protein chip array mass spectrometry. Using protein chip array mass spectrometry, several high-abundance proteins were localized in distinct fractions increasing the total number of unique peptides and proteins detected. This total number increased by about 20-30% by combining different chromatographic surface arrays used for capture. Reproducible results were obtained in human skim milk and whey; however this approach was not successful with milk fat globule membrane and required refinement. Hence, milk profiling by anion exchange fractionation combined to protein chip array mass spectrometry represents a promising tool to detect unknown low-abundance milk proteins that may ultimately prove useful as biomarkers of diseases transmitted by breastfeeding.

[A novel fixed paraffin-embedded tissue processing for proteomic analysis]. / Etude d'un nouveau fixateur pour l'analyse du protéome tissulaire.

Human tissues are an important biological material for the discovery of biomarkers and identification of novel therapeutic targets. Formalin fixed and paraffin embedded (FFPE) tissue represents the most abundant supply of archival material for clinical and molecular analyses. Although FFPE preserves the cellular and architectural morphologic details in tissue sections, formalin facilitates the formation of protein-protein crosslinks rendering FFPE tissues refractory to many protein studies. The aim of this study was to assess the feasibility of proteomic investigations of a new non-toxic fixative using a comprehensive panel of proteomic methods. Tissues were processed for quality and quantity of protein conservation, as compared to frozen and FFPE tissues using complementary proteomic analysis approaches. Similar protein patterns were observed between our tissue fixative protocol and frozen tissues using mono and bidimensional electrophoresis and protein identification by mass spectrometry was not affected. Several proteins were successfully detected using western blot and immunohistochemistry showed comparable results between both tissue storage methods. We demonstrate that our new fixative protocol represents an easy-to-use alternative to FFPE compatible with both current diagnostic pathology practice and tissue proteomic investigations.

Proteomics-based identification of HSP60 as a tumor-associated antigen in early stage breast cancer and ductal carcinoma in situ.

The detection of autoantibodies in cancer patients has been shown to constitute an excellent tool for early diagnosis. Because breast cancer still lacks early diagnostic markers, we investigated novel tumor-associated antigens and related autoantibodies in sera from patients with early stage breast cancer compared to autoimmune disease, other cancers, and healthy volunteers, using a proteomics-based approach. Among the 26 protein antigens specifically recognized by early stage breast cancer sera, we focused on Heat Shock Protein 60 (HSP60). Using ELISA, we investigated the frequency of autoantibodies directed against this protein in the sera of 240 individuals, comprising patients with either ductal carcinoma in situ (DCIS) ( n = 49) or early stage breast cancer ( n = 58), other cancers ( n = 20), autoimmune disease ( n = 20), and healthy subjects ( n = 93). Autoantibodies directed against HSP60 were present in 16/49 (31%) early stage breast cancer and 18/58 (32.6%) DCIS patients, compared to 4/93 (4.3%) healthy subjects. In particular, autoantibodies were present in 11/23 patients (47.8%) with high-grade DCIS, compared to 5/26 (19.2%) with low-grade DCIS. HSP60 mRNA levels were significantly higher in primary breast cancer compared to healthy breast tissues. Using immunohistochemistry, we found that HSP60 expression gradually increases from normal through DCIS to invasive tissues. Our results indicate that HSP60 autoantibodies may be of interest in terms of clinical utility for the early diagnosis of breast cancer and more particularly in DCIS. Moreover, HSP60 overexpression during the first steps of breast carcinogenesis may be functionally correlated to tumor growth and/or progression.

Detection of prion after decontamination procedures: comparative study of standard Western blot, filter retention and scrapie-cell assay.

Prion diseases such as Creutzfeldt-Jakob disease represent a unique infection control problem because the infectious agent exhibits an unusual resistance to conventional chemical and physical decontamination methods. We investigated the reliability and sensitivity of a filter retention assay and standard Western blot to detect the scrapie form of cellular prion protein (PrPSc), the most commonly used surrogate prion disease marker, on tissue infected samples, treated with five commercially available decontamination solutions currently used in hospitals. Major discrepancies were observed between the two immunoblot methods. By using Western blot, we observed that three decontamination solutions have a strong ability to reduce PrPSc levels, whereas in the filter assay, none have this effect and two even enhanced the detection of PrPSc. We used an original and rapid ex vivo approach called the scrapie-cell assay to analyse the persistence of infectivity on scrapie-treated tissues. We observed that tissues remained infectious after treatment with the decontaminant in concordance with in vivo data. This study suggests that conventional PrPSc detection methods are not adapted for the rapid study of a large number of prion decontaminants tested on infectious tissues, and that the scrapie-cell assay could be proposed as a relevant alternative method.