Personalized Prevention and Treatment of Gallbladder Cancer · 1 2015 Symposium Personalized...

2015 Symposium

Personalized Prevention and Treatment of Gallbladder Cancer

April, 24th

Heidelberg Center para América Latina, Santiago de Chile

Funded by Germany´s Excellence Initiative of Heidelberg University

Organisation team

Justo Lorenzo Bermejo (Chair) Statistical Genetics Group

Institute of Medical Biometry and Informatics University of Heidelberg, Germany

Katherine Marcelain

Program of Human Genetics, Institute of Biomedical Sciences Medical Faculty, University of Chile

Catterina Ferreccio

School of Medicine, Pontificia Universidad Católica de Chile Advanced Center for Chronic Diseases (ACCDiS), FONDAP, Santiago, Chile

Johanna Höhl

Heidelberg Center para América Latina, Santiago, Chile

1 2015 Symposium Personalized Prevention and Treatment of Gallbladder Cancer

Towards Personalized Prevention and Treatment of Gallbladder Cancer April 24th, 2015 ‐ Heidelberg Center para América Latina, Santiago de Chile, Chile

Objectives of the Symposium

To present recent advances towards personalized prevention and treatment of gallbladder cancer to the scientific and clinical community

To share and inventory international expertise in the field, and to incorporate interested scientists and clinicians

To establish priority areas of research (clusters) in order to enhance scientific interaction among cooperation partners

To define future collaborative strategies and concretize them into joint grant proposals

08:00‐09:30 Welcome Address

Opening Words (Manuel Kukuljan, Dean Faculty of Medicine, Universidad de Chile)

Building the Bridge Between Basic Research and Clinical Practice (Ricardo Armisén, Director of the Centro de Investigación y Tratamiento del Cancer, Faculty of Medicine, Universidad de Chile)

Session I: Towards Personalized Prevention: Genetics and Gallbladder Cancer in Chile

Ancestry Components and Gallbladder Cancer in Chile (Justo Lorenzo Bermejo, Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg)

Linkage and Family Studies on Disease Susceptibility (Christine Fischer, Institute of Human Genetics, Heidelberg Medical Faculty)

Coffee break (09:30‐10:00)

10:00‐11:30 Session II: Gallbladder Cancer Epidemiology

Epidemiology of Gallbladder Cancer in Chile: Infection and Aflatoxin (Catterina Ferreccio, Public Health Department, Pontificia Universidad Católica de Chile)

Identification of Genetic Biomarkers for Gallbladder Cancer Prevention and Treatment (Katherine Marcelain, Institute of Biomedical Sciences, Universidad de Chile)

Gallbladder Cancer and Inflammatory Markers in Shanghai & Chile / Chile BiLS Objectives & Study Design (Jill Koshiol, Division of Cancer Epidemiology and Genetics, NIH)

Epidemiological Research on Cancer Prevention at the German National Centre for Tumour Diseases (Dominique Scherer, Division of Preventive Oncology, Nationales Centrum für Tumorerkrankungen Heidelberg)

22015 Symposium Personalized Prevention and Treatment of Gallbladder Cancer

Towards Personalized Prevention and Treatment of Gallbladder Cancer April 24th, 2015 ‐ Heidelberg Center para América Latina, Santiago de Chile, Chile


12:00‐13:00 Session III: Biobanking

The Biobank of Universidad de Chile (Iván Gallegos, Director of the Biobank)

Standard Protocols to handle Gallbladder Cancer Specimens (Juan Carlos Roa, Department of Pathology, Pontificia Universidad Católica de Chile)

Lunch break (13:00‐14:00)

14:00‐15:30 Session IV: Towards Personalized Treatment of Gallbladder Cancer and the Microbiome

Clinical Trials on Gallbladder Cancer Treatment (Bettina Müller, Instituto Nacional del Cáncer and Clínica Alemana de Santiago)

Advanced Designs and Infrastructure for Clinical Trials (Meinhard Kieser, Institute of Medical Biometry and Informatics, University of Heidelberg)

Novel molecular approaches for detection and quantification of Enterobacteriaceae based on Illumina deep sequencing (NGS) and real‐time PCR (Ingrid Brettar, Helmholtz Centre for Infection Research, Germany)


16:00‐18:00 Session V: Delineating Joint Grant Applications

Collaborative Research supported by the German Research Foundation (DFG) (Gudrun Kausel, DFG representative in Chile)

Collaborative Research supported by the Comisión Nacional de Investigación Científica y Tecnológica (CONICYT) (Gonzalo Arenas Sepúlveda, Director of the International Relations Programme of CONICYT)

Group Work to outline Collaborative Grant Applications

Closing Remarks and Next Symposium


Ancestry Components and Gallbladder Cancer in Chile Justo Lorenzo Bermejo [1], Rosa González Silos [1], Barbara Peil [1], Felix Boekstegers [1], Katherine Marcelain [2], Macarena Fuentes [2,3], Francisco Rothhammer [2,3] [1] Institute of Medical Biometry and Informatics, University of Heidelberg, Germany, [2] Program of Human Genetics, Institute of Biomedical Sciences, Medical Faculty, University of Chile, [3] Instituto de Alta Investigación, Tarapacá University, Chile, and Centro de Investigaciones del Hombre en el Desierto, Arica, Chile Several publications have recently examined the genetic admixture in North and Latin America. We have conducted an aggregate-data study to investigate the relationship between ancestry components and mortality rates in Chile. Our study relied on genome-wide single nucleotide polymorphism data from 1376 Chileans, and on 9,641 deaths caused by gallbladder cancer between 2005 and 2011. The ADMIXTURE program was used for a supervised estimation of individual ancestry components. After fitting a linear regression model to estimate the expected regional ancestries adjusting for age, gender, educational level, socioeconomic status and salary, Poisson regression was used to quantify the association between regional mortality rates due to gallbladder cancer and the expected ancestry taking age, gender and calendar year into account. The average Native American, European and African ancestry components in our study amounted 48%, 49% and 3%, respectively. The Native American proportion was increased in the north (Arica y Parinacota and Tarapacá regions) and in the south (La Araucanía, Los Ríos, Los Lagos and Aisén regions) of Chile. The mortality due to gallbladder cancer was associated with Native American ancestry (1.2% increase in mortality per 1% increase in Native American ancestry, 95% confidence interval 0.1% to 2.4%, Pval=0.04). Details on study design, ancestry associations with related diseases, and the planned independent validation of results will be presented at the symposium.


Linkage Analysis in Gallbladder Cancer Families in Chile Christine Fischer [1], Katherine Marcelain [2], Pablo Felipe Báez Benavides [2], Catterina Ferreccio [3,4], Justo Lorenzo Bermejo [5] [1] Institute of Human Genetics, University of Heidelberg, Germany, [2] Program of Human Genetics, Institute of Biomedical Sciences, Medical Faculty, University of Chile, [3] School of Medicine, Pontificia Universidad Católica de Chile, [4] Advanced Center for Chronic Diseases (ACCDiS), FONDAP, Santiago, Chile, [5] Institute of Medical Biometry and Informatics, University of Heidelberg, Germany Linkage analysis can be used to detect candidate regions harbouring major disease genes by evaluation of recombination events between genomewide measured genetic marker loci and a hypothesized disease locus in families with clustering of cases. In the last years linkage analysis has successfully been combined with high thoughput sequencing technologies, for example Whole Exome Sequening (WES), to identify causative variants in candidate regions as recenlty demonstrated for familial melanoma. Ancestry components are irrelevant for linkage analysis in single families. The success of the method depends on the true mode of inheritance and the penetrance of major genes, and on the size and number of available families. So far linkage analysis has not been applied to gallbladder cancer families. We therefore started to collect families with aggregation of gallbladder cancer in Chile. We plan to type SNP-chips for available and reasonable family member in order to perform a linkage analysis. If suggestive candidate regions are found, a subset of affected and unaffected family members will undergo sequencing to finemap potentially causative genes. Typical problems, analysis strategies, and examples will be shown in more detail at the symposium.


Epidemiology of Gallbladder Cancer in Chile: Infection and Aflatoxin Catterina Ferreccio [1], for the Gallbladder Cancer Chile Working Group (GBCChWG) [1] School of Medicine, Pontificia Universidad Católica de Chile & Advanced Center for Chronic Diseases (ACCDIS) Prior to 1976 typhoid fever (TF) was endemic in Chile, but from that year to 1986 it increased to hyper-endemic proportions, reaching the highest TF death rates ever reported; in 1990, TF dropped abruptly, presently rendering it to a rare disease status (TF mortality rates per 100,000 population were: 100, 10 and 0 in 1976-1986, 1990 and 2014 respectively). In 1980, the estimated prevalence of S. typhi chronic carriers was 6.9 per 1,000 inhabitants (Levine 1982, 1984); while during the same period, gallbladder surgery rates fell (Chianalle). This TF outbreak occurred during Pinochet’s economic “shock treatment” (Naomi Klein, 2007), associated with abrupt deterioration of living conditions and food and water safety in the country. Coincidental with this socioeconomic quasi-experiment, gallbladder cancer (GBC) reversed its historical downward trend and began a systematic increase, becoming the first cancer killer of women, with Chile having the highest rate of GBC worldwide. Simultaneously, the declining trend of stomach cancer deaths came to a halt. These changes in trend may be the result of population-wide exposure (before 1990) to enteric microorganisms causally associated with these cancers. By the late 80's, the population faced an obesity epidemic. Obesity is a known risk factor for gallstones and GBC - and for hepatocellular carcinoma (HCC)-, but not for stomach cancer. This may explain the upward trend of GBC, which continues despite the widespread use of cholecystectomies. In our recent case-control study we found higher levels of antibodies against the Vi antigen of S. typhi in GBC cases than in gallstones controls 2,2 (95%CI 0,4 – 12,1) and in population-based controls 2,9 (95%CI 0,6-15,7). GBC and exposure to aflatoxins. Contamination with aflatoxin has been identified in ají rojo (red chili peppers), food item that has been associated with GBC. Aflatoxin, in turn, is a well known liver carcinogen which had not been associated with GBC in humans. We recently confirmed the association of GBC with ají rojo; in addition, we found aflatoxin-albumin adducts in blood (AFB1-adducts) more frequently and with higher median levels in GBC (64%; 7.6 pg/mg) than in gallstone controls (18%; 3.5 pg/mg) and population-based controls (23%; 2,4 pg/mg); corresponding ORs (95% confidence intervals) for GBC were 5.8 (2.0-18.4) compared with gallstone controls and 13.2 (4.3-47.9) compared with population controls. Research questions: More sensitive molecular methods are needed to determine if S. typhi is viable in pre-cancerous or GBC lesions; if S. typhi interacts with other bacteria, diet, toxins, host genetics, female hormones or bile composition; if there is a niche for S. typhi outside the gallbladder or if S. typhi exists in a non-cultivable form. Regarding aflatoxins, prospective studies should confirm our findings, evaluate aflatoxin-related TP53 mutations in tumor tissue, and identify main sources of aflatoxin in Chile.


Identification of Genetic Biomarkers for Gallbladder Cancer Prevention and Treatment Katherine Marcelain [1,2], Pablo Felipe Báez Benavides [1,2], Ricardo Armisén [1,2], Ivan Gallegos [2,3], Olga Barajas [2,3], Bettina Muller [4], Fernando Gabbler [5], Catterina Ferreccio [6,7], Jill Koshiol [8], Justo Lorenzo Bermejo [9] [1] Institute of Biomedical Sciences, Medical Faculty, University of Chile, [2] Centro de Investigación y Tratamiento del Cáncer, [3] Hospital Clínico University of Chile, [4] Instituto Nacional del Cáncer, [5] Hospital San Borja Arriarán, [6] School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile, [7] Advanced Center for Chronic Diseases (ACCDiS), FONDAP, Santiago, Chile, [8] Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Maryland, USA, [9] Institute of Medical Biometry and Informatics, University of Heidelberg, Germany The familial aggregation of gallbladder cancer (GBC) and the increased incidence in the mapuche etnia point to inheritance as a major etiological component of GBC susceptibility, among other risk factors including the presence of gallstones (cholelitiasis) and obesity, which also have a remarkable genetic component. Gallstone diseases aggregate within families, and recent association studies have identified several susceptibility variants. In particular, individuals with a first-degree relative affected by GBC are five times more likely to develop gallbladder tumors than persons without affected relatives. Although this clearly points to an genetic component, only one genome-wide association study that included 41 Japanese patients has been published to date and, to our knowledgment, no study in families with GBC history has been performed yet. Because of the low worldwide prevalence of GBC, research on this disease has not been a priority in high-income countries, which has end up in poor development of early diagnosis strategies, unsuccessful treatments and high mortality rates. The ultimate objective of our research is the identification of novel genetic biomarkers for the personalized prevention and treatment of gallbladder cancer. To achieve this goal, we will: (1) identify genomic regions associated with GBC in families with several affected patients, (2) use genome-wide approaches to detect genetic and epigenetic factors conferring differential risk of GBC and cholelitiasis, (3) analyze the presence of mutations in cancer driver genes, as well as differential methylation in GBC tumor tissue and gallbladder tissue from patients with gallstones, and (4) characterize the presence of mutations in GBC tumors in genes suitable for currently available target therapies, in order to broad the therapeutic arsenal to effectively attack this tumor. The identification of genetic variants associated with an increased GBC risk should guide the development of personalized prevention strategies in Chile and the rest of the world. The detection of whole, pathway- and gene-specific methylation modifications will permit to understand the mechanisms of gallbladder carcinogenesis, pointing to potential targets for a personalized patient treatment.


Gallbladder Cancer Inflammatory Markers in Shanghai & Chile / Chile BiLS Objectives & Study Design Jill Koshiol [1], Felipe Castro [1], Troy J Kemp [2], Yu-Tang Gao [3], Juan Carlos Roa [4,5], Bingsheng Wang [6], Leticia Nogueira [1,7], Juan Carlos Araya [8,9], Ming-Chang Sheng [10], Asif Rashid [11], Ann W Hsing [12,13,14], Allan Hildesheim [1], Catterina Ferreccio [4,5], Ruth M Pfeiffer [15], Ligia Pinto [2] [1] Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, USA, [2] HPV Immunology Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, USA, [3] Department of Epidemiology, Shanghai Cancer Institute, China, [4] School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile, [5] Advanced Center for Chronic Diseases (ACCDiS), FONDAP, Santiago, Chile, [6] Department of General Surgery, Zhongshan Hospital, School of Medicine, Fudan University, China, [7] Texas Department of State Health Services, USA, [8] Hospital Dr Hernan Henríquez Aravena, Temuco, Chile, [9] Anatomic Pathology Department, Medicine Faculty, Universidad de La Frontera, Chile, [10] Department of Pathology, Shanghai Cancer Center, Fudan University, China, [11] Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA, [12] Cancer Prevention Institute of California, USA, [13] Stanford Cancer Institute, Palo Alto, California, USA, [14] Department of Health Research and Policy, Stanford School of Medicine, Palo Alto, California, USA, [15] Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, USA Most gallbladder cancer (GBC) cases arise in the context of gallstones, which cause inflammation, but few gallstone patients develop GBC. We hypothesized that inflammation/immune-related markers measured in bile and serum are elevated in GBC compared to gallstone patients. We measured 65 immune-related markers in serum and bile from 41 GBC and 127 gallstone patients from Shanghai, China, and verified serum-based results in 35 GBC and 31 gallstone patients from Chile. We calculated age- and sex-adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) for GBC versus gallstones. Comparing the highest versus lowest quantile, 15 markers (23%) were elevated in both serum and bile from GBC versus gallstone patients in the Shanghai study (p<0.05). The strongest OR was for interleukin-8 (IL-8) in serum (96.8, 95% CI: 11.9-790.2). Of these 15 markers, 6 were also significantly elevated in serum from Chile (CCL20, C-reactive protein, IL-8, CXCL10, resistin, serum amyloid A). Combining the serum data from Shanghai and Chile, the ORs for these 6 markers ranged from 7.2 (95% CI: 2.8-18.4) for CXCL10 to 58.2 (12.4-273.0) IL-8. We observed strong associations between immune-related markers and GBC versus gallstones, implicating inflammation above and beyond that generated by gallstones alone. These results suggest that inflammatory processes related to GBC are upregulated locally and reflected systemically. These mechanisms may be involved in gallbladder carcinogenesis. Future longitudinal studies are needed to identify the key players in cancer development, which may guide translational efforts to identify individuals at high risk of developing GBC. Details on will be presented at the symposium, along with preliminary GWAS data from the Chile pilot.


Epidemiological Research on Cancer Prevention at the German National Centre for Tumour Diseases Dominique Scherer [1] [1] Division of Preventive Oncology, National Center for Tumor Diseases, Heidelberg, Germany Our mission is to reduce the burden of cancer by fostering cancer prevention in its three areas: (a) primary prevention (identification of risk factors and mechanisms), (b) secondary prevention (early detection) and (c) tertiary prevention (improving clinical outcomes of cancer patients). To fulfill these goals the main research areas have been defined as molecular epidemiology, cancer survivorship and pharmacogenetics, energy balance and cancer. Interdisciplinary and international collaborations with clinical partners (particularly at the German National Center for Tumour Diseases), basic scientists and other researchers are central to achieving our goals. We conduct several large-scale epidemiologic studies on biomarkers (genetic, genomic, epigenetic, proteomic, metabolomic) in key pathways linked to colorectal cancer risk, with the goal to identify biomarkers that can be used to improve primary, secondary and tertiary prevention strategies. We use an integrative approach in combining different informative datasets, including omics, clinical and epidemiological data, for a comprehensive characterization of the tumor and will finally translate the scientific discoveries into individual and population health. A main focus is the collaboration on the international level within large-scale well-renown consortia. Specific research topics are pharmacogenetics (interaction between use of NSAIDs, non-steroidal anti-inflammatory drugs, and genetic variants in cancer prevention), investigation of genetic and genomic biomarker for improved long-term prognosis and quality of life of colorectal cancer patients and investigation of the obesity-colorectal cancer link.


The Biobank of Universidad de Chile Iván Gallegos [1], Sebastian Indo [1,3], Valeria Salinas [4], Karla Ramos [1], Katherine Marcelain [1,2], Ricardo Armisen [1,2], Alicia Colombo [1,2] [1] Centro de Investigación y Tratamiento del Cáncer, Medical Faculty, University of Chile, [2] Institute of Biomedical Sciences, Medical Faculty, University of Chile, [3] Department of Medical Technology, Medical Faculty, University of Chile, [4] Biomedical Neuroscience Institute, Medical Faculty, University of Chile Effective biomedical research is supported by BioBanks, biorepositories which store human biological specimens and related data. The establishment of a BioBank at the Universidad of Chile is motivated by the need of a systematic collection of biological specimens and health information on participants in oncology research studies (colorectal, gallbladder and thyroid cancer). High, standardized quality of biological samples and associated patient clinical information are key elements for biomedical research essential for the discovery and identification of biomarkers, diagnostic tools and treatment strategies, often referred to as personalized medicine. Our BioBank was born as a Tumor BioBank but has been transformed into a diseases-specific BioBank, which during its first years has focused on increasing the number of stored samples and establishing standard operative procedures (SOPs) for tissue sampling, storage and collection of clinical data taking advantage of BioBank stage 1.0. Currently, we are improving our expertise in standardization of storage procedures, bio-specimen quality control, and informatic systems to track over time data concerning enrollment and participant consent (BioBank stage 2.0). Our final purpose after future updates (Biobank stage 3.0) is to support research in personalized medicine with the highest standards of operation and adequate funding, training and certification.


Standard Protocols to handle Gallbladder Cancer Specimens Juan Carlos Roa [1], Volkan Adsay [2] [1] Department of Pathology, Pontificia Universidad Católica de Chile, and ACCDIS- CITO, Santiago, Chile, [2] Department of Pathology, Emory University, Atlanta, Georgia, USA Historically, pathologic under-sampling of gallbladder specimens has led to under-diagnosis and under-staging. For those patients in whom there is no clinical or imaging suspicion for GBC and no apparent abnormality on gross examination, there is no consensus on a uniform pathologic examination protocol. In many countries no microscopic examination is recommended or performed in these situations. Considering that most gallbladder cancers (GBC) are clinically unapparent on gross evaluation, this would mean several thousand cholecystectomies in which GBC may be undiagnosed every year. To address this issue, a specific, step-wise pathology sampling protocol has been proposed. Particularly in areas of high GBC prevalence, for normal appearing gallbladders on gross examination, a minimum of 3 random areas and the cystic duct margin should be submitted for microscopic assessment. A finding of dysplasia or neoplasia on initial random sampling prompts a complete sampling of the gallbladder. In contrast to some reports, this practice is supported by data that indicates that a significant number of patients initially found to have dysplasia will harbor an invasive malignancy. Consensus Statements: Particularly in high incidence areas, routine gallbladder specimens should be pathologically assessed with a minimum examination to include microscopic evaluation of three sections and the cystic duct margin. During the initial analysis, a finding of high grade dysplasia, hyalinizing cholecystitis, and/or neoplastic polyps should prompt complete sampling of the entire gallbladder specimen to accurately stage any associated invasive malignancy. Gallbladder specimens with proven cancer should be extensively sampled, with determination of prognostic factors including microscopic depth of tumor invasion, tumor involvement of cystic duct margin, Rokitansky Aschoff sinuses, and serosal vs. hepatic surface involvement. Provided medical fitness for surgery, data support the resection of all gallbladder polyps greater than 1.0 cm in diameter and those with imaging evidence of vascular stalks.


Clinical Trials on Gallbladder Cancer Treatment Bettina Müller [1,2] [1] Instituto Nacional del Cáncer, Santiago, Chile, [2] Clínica Alemana de Santiago, Chile Gallbladder cancer is now considered a distinct clinical entity, allowing a separate analysis from that of other malignancies of the biliary tree. Symptoms related to a malignant tumor of the gallbladder including jaundice and abdominal pain or a palpable abdominal mass occur in a late stage of the disease. The majority of patients with operable gallbladder cancer are diagnosed by cholecystectomy performed for presumed benign disease, mostly cholelithiasis, a clinical entity known as incidental gallbladder cancer. Given the poor prognosis if tumor invasion beyond the muscular layer and/or nodal metastasis is found, adjuvant treatments have been implemented, but few data are available to guide treatment decisions in this setting. The results of 2 ongoing phase 3 trials in this setting are eagerly awaited. Neoadjuvant therapies are an attractive strategy but have not been explored in phase 2 or 3 trials, and only case series have been published. For advanced disease, a multidisciplinary treatment approach including biliary drainage procedures and palliative support is needed in the management of this aggressive disease. Palliative chemotherapy with a combination of gemcitabine and cisplatin or oxaliplatin is the standard treatment based on the findings of two phase 3 trials that showed improved overall survival compared to single agent chemotherapy and best supportive care. Efforts are underway to optimize this treatment by the use of different combination chemotherapy schemes. One ongoing phase 3 trial is exploring second line treatment versus best supportive care. Several phase 2 studies have been reported investigating the role of targeted agents against EGFR, VEGF, HER2 and MEK. Unfortunately, none of the open trials encountered focus on gallbladder cancer nor include high prevalence areas. International collaboration to enhance our knowledge of gallbladder cancer should be encouraged.


Advanced Designs and Infrastructure for Clinical Trials Meinhard Kieser [1] [1] Institute of Medical Biometry and Informatics, University of Heidelberg, Germany Choice of appropriate study designs and application of appropriate tools during conduct play a key role for the success of clinical trials. Based on the example of a recently published clinical trial, where the Institute of Medical Biometry and Informatics of the University of Heidelberg (IMBI) was responsible for biostatistics and data management, common difficulties during the planning stage of clinical trials are illustrated. It is shown, how implementation of advanced trial designs may resolve these problems. Furthermore, the importance of an experienced and well-equipped data management team as well as its tasks and actions are stressed. Finally, the infrastructure for performing clinical trials available at the IMBI is sketched. Reference: Diener, M.K., Knebel, P., Kieser, M., et al. (2014): Effectiveness of triclosan-coated PDS Plus versus uncoated PDS II sutures for prevention of surgical site infection after abdominal wall closure: the randomised controlled PROUD trial. The Lancet 384:142-152.


Novel molecular approaches for detection and quantification of Enterobacteriaceae based on Illumina deep sequencing (NGS) and real-time PCR Ingrid Brettar [1], Manfred G Höfle [1] [1] Helmholtz Centre for Infection Research, Department of Vaccinology & Applied Microbiology, Research Group Microbial Diagnostics, Braunschweig, Germany Chronic Salmonella typhi infections have been shown to be often associated with gallbladder cancer. However, it is often difficult to detect S. typhi in gallbladder specimen by culture based methods, and even molecular approaches have restricted success. This may be due to several reasons, such as i) lack of sensitivity of the detection method, and/or ii) secondary effects of the S. typhi infection leading to adverse effects such as a change of the biliary microbial community. As shown by Wu et al. (2013), the biliary tract microbial community of gallstone patients is strongly impacted by a dysbiosis of the gut, and contains a major fraction of the gut microbiome. A chronic S. typhi infection may on the one hand impact the gallbladder directly. On the other hand, S. typhi may impact the overall gut microbiome and thus influence the gallbladder microbiome leading to adverse effects. To support the search for the impact of S. typhi with respect to gallbladder cancer, we suggest a three step molecular approach for analyses of gallbladder specimen (tissue, stones, bile) comprising i) a sensitive detection of S. typhi, ii) a comprehensive targeted screening for human pathogenic Enterobacteriaceae and iii) analyses of the complete microbiome. S. typhi specific primers are available and suitable for detection and quantification of S. typhi by real-time PCR. Enterobacterial primers comprising the branch of highly relevant human pathogens were designed and are currently tested and optimised in an ongoing EU-project. A set of optimised bacterial primers for generation of the biliary microbiome were shown to give an excellent overview about the bacterial community thereby avoiding amplification of human DNA. Enterobacterial and Bacterial primers will be used in a combined protocol for Illumina-based Next Generation Sequencing (NGS) and real-time PCR. Current work indicates that these detection methods may allow a comprehensive insight into the community of Bacteria, Enterobacteriaceae and Salmonella present in the biliary specimen at the needed high sensitivity and resolution. The possibilities of these molecular diagnostic approaches will be explained, and the research needs discussed with the project partners.


Collaborative research supported by German Research Foundation DFG Gudrun Kausel [1] [1] Academic Representative DFG in Chile, Institute of Biochemistry and Microbiology, Faculty of Science, Universidad Austral de Chile, Valdivia, Chile Latin America`s scientific potential is constantly growing and the region is becoming increasingly significant for science. Among German researchers interest in cooperation with research partners in this region is increasing considerably where Chile ranks second after Brazil in funding statistics. International cooperation is possible in all DFG programs (http://dfg.de/en/research_funding/programmes/index.jsp) including individual grants, coordinated programs such as Priority Programs, Research Training Groups, Collaborative Research Centers, DFG Research Centers, Research Units, Graduate Schools, Excellence Clusters. Further programs address infrastructure, career development and prizes. All these funding instruments are designed for German researchers, this means a scientist holding a PhD and developing his scientific work in Germany. Therefore the applicant not necessarily has German nationality but is employed at a German university –the DFG mainly supports basic research in all fields at universities. External scientist may be invited via Mercator fellow program. In addition particular programs for initiation of contacts and international cooperation are available. Since decades DFG and CONICYT organize joint calls for initiation projects mainly funding mobility. In 2010 in a joint call German-Chilean research projects were funded covering all items including consumables necessary to develop the collaborative scientific work. At present preparation of German-Chilean applications to institutionally presented proposals in a coordinated program, International Research Training Group, reflect the demand for more long-standing thorough funding schemes to support readily connected research groups in a defined area. During the recent visit of DFG president to Chile, together with president of CONICYT, both expressed their compromise to strengthen collaboration. Therefore we look forward to more flexible funding instruments for joint investigation projects.


Symposium Participants

Johanna Acevedo [email protected]

Monica Ahumada [email protected]

Gonzalo Arenas [email protected]

Ricardo Armisén [email protected]

Pablo Felipe Báez Benavides [email protected]

Federico Batiz [email protected]

Olga Barajas [email protected]

Enrique Bellolio [email protected]

Maria Bertran [email protected]

Ingrid Brettar ingrid.brettar@helmholtz‐hzi.de

Alicia Colombo [email protected]

Paz Cook [email protected]

Catterina Ferreccio [email protected]

Christine Fischer [email protected]‐heidelberg.de

Claudia Foerster [email protected]

Fernando Gabler Neale [email protected]

Ivan Gallegos [email protected], [email protected]

Katy Heise [email protected]

Johanna Hoehl [email protected]

Gudrun Kausel [email protected]

Meinhard Kieser [email protected]‐heidelberg.de

Jill Koshiol [email protected]

Mercedes López [email protected]

Justo Lorenzo Bermejo [email protected]‐heidelberg.de

Katherine Marcelain [email protected]

Bettina Müller [email protected]

Igor Nova [email protected]

Juan Carlos Roa [email protected]

Dominique Scherer dominique.scherer@nct‐heidelberg.de

Vanessa Van De Wyngard [email protected]

Miguel Angel Villaseca Hernández [email protected]

Karla Ramos [email protected]


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