Computer-aided diagnosis of pancreatic and lung cancer

When we talk about cancer diagnosis the most important thing is early diagnosis to prevent cancer cells from spreading. We may also consider the high cost of diagnostic tests. Our approach seeks to address both problems. It uses a software based on Bayesian networks that simulates the causeeffect relationships and gets the chance of suffering a pancreatic cancer or lung cancer. This software would support doctors and save a lot of time and resources

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine

It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. Although this latter disease has been thoroughly studied using different high-throughput technologies, its heterogeneous nature makes its understanding and proper treatment in patients a remaining challenge in clinical settings. Notably, given the outstanding role of host-microbiome interactions, the ecological interactions with microorganisms have become a new significant aspect in the systems that can contribute to the diagnosis and potential treatment of solid cancers. As a part of expanding precision medicine in the area of cancer research, efforts aimed at effective treatments for various kinds of cancer based on the knowledge of genetics, biology of the disease and host-microbiome interactions might improve the prediction of disease risk and implement potential microbiota-directed therapeutics. In this review, we present the state of the art of sequencing and metabolome technologies, computational methods and schemes in systems biology that have addressed recent breakthroughs of uncovering relationships or associations between microorganisms and cancer. Together, microbiome studies extend the horizon of new personalized treatments against cancer from the perspective of precision medicine through a synergistic strategy integrating clinical knowledge, high-throughput data, bioinformatics and systems biology

Molecular epidemiology study on genetically regulated gene expression in the colonic mucosa and its role in disease susceptibility

[spa] La expresión genética es un proceso celular clave, que además está relacionado con la susceptibilidad genética a enfermedades y rasgos complejos. La mayoría de genes se someten a splicing alternativo (AS). Las variantes genéticas que regulan la expresión genética y el AS se llaman ¿quantitative trait loci¿ (e/sQTLs). Técnicas estadísticas permiten predecir in silico la expresión genética en un tejido concreto a partir de datos genéticos. Esta aproximación se lleva a cabo en los estudios de asociación de transcriptoma completo (TWAS). Esta Tesis se compone de tres objetivos principales y presenta tres artículos. 1) Generar perfiles de expresión genética de la mucosa colónica de individuos sanos, así como sus diferencias a lo largo del colon y sus e/sQTLs asociados; 2) Desarrollar una aplicación web que permita explorar los datos de expresión genética en el colon; 3) Llevar a cabo un TWAS para proponer genes de susceptibilidad a enfermedad inflamatoria intestinal (EII). Como resumen de los resultados, 1) se generaron catálogos de e/sQTLs a partir de nuevos datos de expresión genética en colon de 445 individuos, y se encontraron más de 4,000 genes que varían sus niveles de expresión a lo largo del colon; 2) se desarrolló el "Colon Transcriptome Explorer", disponible públicamente en https://barcuvaseq.org/cotrex/; 3) se propusieron más de doscientos genes de susceptibilidad genética a EII. En conclusión, nuestros estudios proporcionan nuevos datos y evidencias sobre los genes involucrados en mecanismos de susceptibilidad a enfermedades relacionadas con el colon, y servirán de guía a otros investigadores para proponer nuevas hipótesis en este campo

Characterizing the Role of the Gut Microbiome in Colorectal Cancer.

The trillions of bacteria that inhabit the gastrointestinal tract, known collectively as the gut microbiome, are essential for both health and the normal functioning of the intestine. A growing literature now suggests that disruptive changes to this community are strongly associated with the development of colorectal cancer. However, it is unclear whether these disruptive changes directly contribute to disease or if they are just a consequence of colorectal cancer (CRC). Furthermore, the gut microbiome has not been explored as a potential non-invasive screen for CRC. Our hypothesis is that abnormalities in the gut microbiome can be utilized as a biomarker for detection of CRC at its earliest stages. Additionally, we postulate that these changes potentiate tumor development in the colon. To test these hypotheses, we first characterized the gut microbiome associated with human patients from three clinical groups representing three essential stages in CRC development: healthy, adenoma, and carcinoma. We demonstrated that a specific set of bacterial populations are associated with adenomas and carcinomas. The abundance of these bacterial populations was used to improve our ability to differentiate between healthy and diseased subjects and presents a viable screening tool for the earliest stages of CRC development. Next, we demonstrated using a mouse model of inflammation-driven colon cancer that there are dramatic, continual alterations in the gut microbiome during the development of tumors. By colonizing germ-free mice with the gut microbiome from tumor-bearing mice, we determined that these changes are directly responsible for increased tumor development. Using an antibiotic cocktail, we were able to demonstrate that manipulation of this microbial community can dramatically reduce tumor burden in mice. By varying the composition of this antibiotic cocktail we generated a broad spectrum of microbial communities with varying carcinogenic capacities. This method of manipulating the gut microbiome allowed us to identify potentially protective and carcinogenic bacterial populations for further mechanistic studies. Our results demonstrate that changes to the gut microbiome can serve as an effective non-invasive screen for the early detection of colorectal cancer and that interventions that target these changes may be an effective strategy for preventing the development of colorectal cancer.PhDMicrobiology & ImmunologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/107125/1/zackular_1.pd

Papillomavirus E5: the smallest oncoprotein with many functions

Papillomaviruses (PVs) are established agents of human and animal cancers. They infect cutaneous and mucous epithelia. High Risk (HR) Human PVs (HPVs) are consistently associated with cancer of the uterine cervix, but are also involved in the etiopathogenesis of other cancer types. The early oncoproteins of PVs: E5, E6 and E7 are known to contribute to tumour progression. While the oncogenic activities of E6 and E7 are well characterised, the role of E5 is still rather nebulous. The widespread causal association of PVs with cancer makes their study worthwhile not only in humans but also in animal model systems. The Bovine PV (BPV) system has been the most useful animal model in understanding the oncogenic potential of PVs due to the pivotal role of its E5 oncoprotein in cell transformation. This review will highlight the differences between HPV-16 E5 (16E5) and E5 from other PVs, primarily from BPV. It will discuss the targeting of E5 as a possible therapeutic agent

Colorectal Cancer

The projections for future growth in the number of new patients with colorectal cancer in most parts of the world remain unfavorable. When we consider the substantial morbidity and mortality that accompanies the disease, the acute need for improvements and better solutions in patient care becomes evident. This volume, organized in five sections, represents a synopsis of the significant efforts from scientists, clinicians and investigators towards finding improvements in different patient care aspects including nutrition, diagnostic approaches, treatment strategies with the addition of some novel therapeutic approaches, and prevention. For scientists involved in investigations that explore fundamental cellular events in colorectal cancer, this volume provides a framework for translational integration of cell biological and clinical information. Clinicians as well as other healthcare professionals involved in patient management for colorectal cancer will find this volume useful

Quantifying the pro- and antimutagenic roles of DNA damage and repair

Genome integrity is essential to the survival of any living organism. The genome is constantly challenged by a multitude of endogenous and exogenous mutagenic factors such as environmental exposures or replication errors. Therefore, evolution has supplied cells with a number of repair mechanisms to protect their genetic information; however, excessive exposures or defects in the repair machinery can lead to the accumulation of deleterious mutations which may cause a range of diseases including cancer. Different mutational processes often leave behind characteristic patterns of mutations, so-called mutational signatures. Mutational signature analysis of tumours has gained a lot of attention recently, because it may reveal carcinogenic exposures and also therapeutic vulnerabilities. So far, over 50 mutational signatures have been identified using pattern recognition in large cancer cohorts, reflecting the action of a range of known mutagenic processes, such as UV light, tobacco smoke or mismatch repair deficiency, but for many mutational signatures an underlying generative process is still unknown. The search for the causes behind a given mutational signature is further complicated by the fact that every alteration in the DNA results from failed or incorrect repair of a DNA lesion, hence there are two factors which jointly shape the mutational spectrum of any mutagenic process. In this thesis, I quantify the variability of mutational signatures in model organisms and in human cancer and explore the diversity of DNA damage-repair interactions. Using data from a large mutagenesis screen in C. elegans, including over 50 DNA repair deficient genetic backgrounds, 12 genotoxins and nearly 200 combinations thereof, I characterise the mutational spectra and genomic features of a range of DNA repair deficiencies, and describe the mutational signatures of genotoxins across multiple genetic backgrounds. Importantly, the mutagenic contributions of genetic and mutagenic factors can vary dev pending on the DNA repair components available: over 35% of genotoxin-knockout combinations demonstrated a measurable effect on the mutation rate compared to expected values, and about 10% also presented a new mutational spectrum. Analysis of mutational signatures in cancer exomes demonstrates the relevance of C. elegans results to cancer investigation. Mismatch repair deficiency patterns extracted from C. elegans are comparable to those in gastrointestinal tumours, and help to dissect convoluted mutational processes. The antagonism between DNA damage and repair drives variability in cancer genomes as well: the observed interaction effects were low in magnitude, but evolutionary considerations suggest that cancer risk may be substantially elevated even by small increases in mutagenicity. In summary, this thesis presents the first comprehensive analysis of mutagenic DNA damage-repair interactions using experimental and cancer data. The results show that mutations result from the opposing pro- and anti-mutagenic forces of DNA damage and repair, which shape mutational signatures in highly variable ways. This variation has to be acknowledged and integrated into mutational signature analysis to ensure reliable interpretation and applicability in clinical oncology. Lastly, the cross-species comparison shows that the fundamental laws of mutagenesis are acting similarly across eukaryotic organisms reminding that many mutational processes fuelling tumorigenesis are not exclusive to cancer, but also drive variation and the evolution of species.My PhD studies were funded by the EMBL International PhD Programme

Knowledge Management Approaches for predicting Biomarker and Assessing its Impact on Clinical Trials

The recent success of companion diagnostics along with the increasing regulatory pressure for better identification of the target population has created an unprecedented incentive for the drug discovery companies to invest into novel strategies for stratified biomarker discovery. Catching with this trend, trials with stratified biomarker in drug development have quadrupled in the last decade but represent a small part of all Interventional trials reflecting multiple co-developmental challenges of therapeutic compounds and companion diagnostics. To overcome the challenge, varied knowledge management and system biology approaches are adopted in the clinics to analyze/interpret an ever increasing collection of OMICS data. By semi-automatic screening of more than 150,000 trials, we filtered trials with stratified biomarker to analyse their therapeutic focus, major drivers and elucidated the impact of stratified biomarker programs on trial duration and completion. The analysis clearly shows that cancer is the major focus for trials with stratified biomarker. But targeted therapies in cancer require more accurate stratification of patient population. This can be augmented by a fresh approach of selecting a new class of biomolecules i.e. miRNA as candidate stratification biomarker. miRNA plays an important role in tumorgenesis in regulating expression of oncogenes and tumor suppressors; thus affecting cell proliferation, differentiation, apoptosis, invasion, angiogenesis. miRNAs are potential biomarkers in different cancer. However, the relationship between response of cancer patients towards targeted therapy and resulting modifications of the miRNA transcriptome in pathway regulation is poorly understood. With ever-increasing pathways and miRNA-mRNA interaction databases, freely available mRNA and miRNA expression data in multiple cancer therapy have created an unprecedented opportunity to decipher the role of miRNAs in early prediction of therapeutic efficacy in diseases. We present a novel SMARTmiR algorithm to predict the role of miRNA as therapeutic biomarker for an anti-EGFR monoclonal antibody i.e. cetuximab treatment in colorectal cancer. The application of an optimised and fully automated version of the algorithm has the potential to be used as clinical decision support tool. Moreover this research will also provide a comprehensive and valuable knowledge map demonstrating functional bimolecular interactions in colorectal cancer to scientific community. This research also detected seven miRNA i.e. hsa-miR-145, has-miR-27a, has- miR-155, hsa-miR-182, hsa-miR-15a, hsa-miR-96 and hsa-miR-106a as top stratified biomarker candidate for cetuximab therapy in CRC which were not reported previously. Finally a prospective plan on future scenario of biomarker research in cancer drug development has been drawn focusing to reduce the risk of most expensive phase III drug failures

HPV and potential prognostic markers in primary vaginal carcinoma

The overall aim of this PhD thesis is to evaluate HPV status and immunohistochemical expression of different biomarkers, including tumor suppressor p16, proliferation marker Ki67, molecular markers in the LRIG family, WRAP53ß, and dyskerin as well as immune markers CD4+ and CD8+ TILs, and their correlation to clinical manifestations and survival as part of a search for potential prognostic factors in women diagnosed with primary vaginal cancer. Paper I evaluates the presence of HPV in vaginal cancer tumor samples, as well as immunohistochemical expression of p16 and Ki-67. This study includes 68 short-term and long-term survivors diagnosed with vaginal cancer. The results, which have been correlated with both clinical parameters and survival, show presence of HPV in 43% of patients, with HPV16 found in 63% of the HPV-positive cases. HPV-positivity did not correlate with improved survival but did correlate with low histopathological grade. High expression of p16 was found in 54% of cases and correlated with low histopathological grade (p=0.004), HPV-positivity (p=0.032) and long-term survival (p=0.047). High expression of Ki-67, found in only 34% of patients, correlated negatively with histopathological grade (p<0.001) and tumor size (p=0.047). The results suggest that evaluation of p16 and Ki67 may be of value in tumor grading, while expression of p16 may also serve as a possible marker for HPV-positivity. In this study, high p16 expression, in contrast with positive HPV status and presence of Ki-67, was associated with improved survival in the univariate analysis, whereas multivariate analysis indicated that only histopathological grade and tumor size remain as independent prognostic factors. Paper II focuses on the LRIG (leucine-rich repeats and immunoglobulin-like domains) proteins – LRIG1, LRIG2 and LRIG3. Expression of these three proteins is often altered in cancer and has significance for cancer progression. The LRIG1 protein acts as a tumor suppressor, while the function of the remaining two is still unclear. We evaluated immunohistochemical expression of LRIG1, LRIG2, and LRIG3 in tumor samples from a cohort of 70 patients, diagnosed with vaginal cancer between 1975 and 2002, in order to find out whether such expression relates to clinical manifestations and survival. Our results show high (>50% of the cells) expression of LRIG1 and LRIG2 in 72% of tumors, but conversely, little or no expression of LRIG3. The latter two markers did not correlate with any clinical manifestations or survival, while high expression of LRIG1 correlated with HPV positivity and with improved cancer-specific survival (HR 0.35: 95% CI 0.68- 0.73) in vaginal cancer patients. Paper III addresses the molecular factors dyskerin and WRAP53ß in vaginal cancer. These two proteins play a role in the telomerase holoenzyme complex and are upregulated in different cancers. Expression of dyskerin and WRAP53ß was assessed by immunohistochemistry in 68 tumor samples drawn from the same study population as in study II. Most of the tumor samples demonstrated low to moderate expression of dyskerin. This protein is associated with shorter survival time and worse cancer-specific survival (HR 3.701: CI 95% (1.094-12.517). WRAP53ß was also expressed in most cells from the tumor samples, albeit without any association to clinical manifestations or prognosis. Paper IV is concerned with immune response as it relates to presence of CD4+ (Tumor Infiltrating Lymphocyte) TILs and CD8+ TILs in vaginal cancer tumor samples and also addresses the potential association between TILs, p16 expression and HPV status with clinical manifestations and survival. Once again, immunohistochemistry staining was used to evaluate CD4+ and CD8+ TIL infiltration along with p16expression in 69 tumor samples from the same study cohort used for the two previous studies. The results howed higher density CD4+ and CD8+ TIL infiltration in both HPV-positive and p16-positive tumors. High infiltration of CD4+ and CD8+ TILs in tumor samples implies better prognosis. Tumors demonstrating p16 overexpression in addition to high CD8+ TIL infiltration were associated with statistically significant (p=0.033) improvement in prognosis. In contrast, absence of p16 in HPV-negative tumors correlates with a substantially worse prognosis (p= 0.010). In summary, the studies in this thesis, which is concerned with exploring potential prognostic markers in vaginal cancer, identify p16 as a prognostic marker of interest, especially when considered in light of HPV status. Moreover, LRIG1 and dyskerin may be novel prognostic markers of potential interest, while LRIG2, LRIG3, and WRAP53ß appear to fall short in this regard. Furthermore, CD8+ TILs may also be of interest as a prognostic factor, especially when considered together with HPV status and p16 expression. Although this thesis implicates p16 expression together with HPV status as clinically relevant prognostic factors in vaginal cancer, future studies, using larger study cohorts, will be needed to validate these results for improved diagnostics and treatment strategies for women diagnosed with vaginal cancer.