The population incidence of cancer

In this thesis stochastic techniques are used in attempts to understand cancer risk, its relationship to patient age and genotype, as well as its distribution in human populations. The starting point for the thesis is the general observation that cancer incidence grows in approximate proportion to an integer power of age. Quasi-mechanistic mathematical models of cancer incidence have suggested that the integer power in a given case is related to the number of crucial cellular events that must occur for a malignant tumour to evolve from a healthy tissue. This idea and its limitations are explored. Further applications of cancer incidence models are then evaluated and developed. Specifically, a critical examination is presented of the notion that increases in risk associated with a particular predisposing germline gene mutation, can provide information about the disease-associated activity of that gene. Finally, there is a discussion of heterogeneity in liability to cancer. Methods for quantifying this heterogeneity and its effect on incidence patterns are investigated

Spatial structure increases the waiting time for cancer

Cancer results from a sequence of genetic and epigenetic changes which lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells, and thus, to a selective advantage of pre-cancerous cells. The notion of cancer progression as an evolutionary process has been experiencing increasing interest in recent years. Many efforts have been made to better understand and predict the progression to cancer using mathematical models; these mostly consider the evolution of a well-mixed cell population, even though pre-cancerous cells often evolve in highly structured epithelial tissues. We propose a novel model of cancer progression that considers a spatially structured cell population where clones expand via adaptive waves. This model is used to asses two different paradigms of asexual evolution that have been suggested to delineate the process of cancer progression. The standard scenario of periodic selection assumes that driver mutations are accumulated strictly sequentially over time. However, when the mutation supply is sufficiently high, clones may arise simultaneously on distinct genetic backgrounds, and clonal adaptation waves interfere with each other. We find that in the presence of clonal interference, spatial structure increases the waiting time for cancer, leads to a patchwork structure of non-uniformly sized clones, decreases the survival probability of virtually neutral (passenger) mutations, and that genetic distance begins to increase over a characteristic length scale, determined here. These characteristic features of clonal interference may help to predict the onset of cancers with pronounced spatial structure and to interpret spatially-sampled genetic data obtained from biopsies. Our estimates suggest that clonal interference likely occurs in the progressing colon cancer, and possibly other cancers where spatial structure matters.Comment: 21 page

Mathematical modeling of Lynch syndrome carcinogenesis

Cancer is one of the leading causes of disease-related death worldwide. In recent years, large amounts of data on cancer genetics and molecular characteristics have become available and accumulated with increasing speed. However, the current understanding of cancer as a disease is still limited by the lack of suitable models that allow interpreting these data in proper ways. Thus, the highly interdisciplinary research field of mathematical oncology has evolved to use mathematics, modeling, and simulations to study cancer with the overall goal to improve clinical patient care. This dissertation aims at developing mathematical models and tools for different spatial scales of cancer development at the example of colorectal cancer in Lynch syndrome, the most common inherited colorectal cancer predisposition syndrome. We derive model-driven approaches for carcinogenesis at the DNA, cell, and crypt level, as well as data-driven methods for cancer-immune interactions at the DNA level and for the evaluation of diagnostic procedures at the Lynch syndrome population level. The developed models present an important step toward an improved understanding of hereditary cancer as a disease aiming at rapid implementation into clinical management guidelines and into the development of novel, innovative approaches for prevention and treatment

GENOMIC AND TRANSCRIPTOMIC LANDSCAPE OF COLORECTAL PREMALIGNANCY

Colorectal cancer (CRC) is the third most commonly diagnosed cancer among men and women in the United States, with 3 to 5 percent of the cases diagnosed in the background of a hereditary form of the disease. Biologically, CRC is divided into two groups: microsatellite instable (MSI) and chromosomally unstable (CIN). Genomic and transcriptomic characterization of CRC has emerged from large-scale studies in recent years due to the advancement of next-generation sequencing technologies. These studies have identified key genes and pathways altered in CRC and provided insights to the discovery of therapeutic targets. Despite the wealth of knowledge acquired in the carcinoma stage, there have been insufficient efforts to systematically characterize premalignant lesions at the molecular level, which could lead to a better understanding of neoplastic initiation, risk prediction, and the development of targeted chemoprevention strategies. The challenge in characterizing premalignancy has always been the limited availability of sample material. This challenge is tackled by getting more samples, integrating public datasets, deploying better technology that use less amount of nucleic acids and in-silico tools to extract multi-layer information from the same experiment. My genomic study consisted of whole exome sequencing (WES) and high-depth targeted sequencing on 80 premalignant lesions bulk tissue and crypts to assess clonality and mutational heterogeneity. WES results showed the presence of multiple clone in premalignancy based on clustering somatic mutation allele frequency. In addition, I determined that multiple clones originate from independent crypts harboring distinct APC and KRAS alterations. In my second study, I performed immune expression profiling and assessment of mutation and neoantigen rate of 28 premalignant lesions with DNA mismatch repair (MMR) deficient and proficient background using RNAseq. My results showed an activated immune profile despite low mutational and neoantigen rate, which challenges the canonical view in MMR-deficient carcinoma stage that immune activation is largely due to high mutation and neoantigen rate. In the last study, I performed transcriptomic sub-classifications of 398 premalignant lesions that associate them with different carcinomas subtypes, and clinical and histopathological features. My results revealed two major findings: prominent immune activation and WNT and MYC activation in premalignancy. In summary, my large-scale genomic and transcriptomic analyses of colorectal adenomas have identified key molecular characteristics in early colorectal tumorigenesis and provide a foundation for discovering novel preventive strategies

The paradox of cancer genes in non-malignant conditions: implications for precision medicine.

Next-generation sequencing has enabled patient selection for targeted drugs, some of which have shown remarkable efficacy in cancers that have the cognate molecular signatures. Intriguingly, rapidly emerging data indicate that altered genes representing oncogenic drivers can also be found in sporadic non-malignant conditions, some of which have negligible and/or low potential for transformation to cancer. For instance, activating KRAS mutations are discerned in endometriosis and in brain arteriovenous malformations, inactivating TP53 tumor suppressor mutations in rheumatoid arthritis synovium, and AKT, MAPK, and AMPK pathway gene alterations in the brains of Alzheimer's disease patients. Furthermore, these types of alterations may also characterize hereditary conditions that result in diverse disabilities and that are associated with a range of lifetime susceptibility to the development of cancer, varying from near universal to no elevated risk. Very recently, the repurposing of targeted cancer drugs for non-malignant conditions that are associated with these genomic alterations has yielded therapeutic successes. For instance, the phenotypic manifestations of CLOVES syndrome, which is characterized by tissue overgrowth and complex vascular anomalies that result from the activation of PIK3CA mutations, can be ameliorated by the PIK3CA inhibitor alpelisib, which was developed and approved for breast cancer. In this review, we discuss the profound implications of finding molecular alterations in non-malignant conditions that are indistinguishable from those driving cancers, with respect to our understanding of the genomic basis of medicine, the potential confounding effects in early cancer detection that relies on sensitive blood tests for oncogenic mutations, and the possibility of reverse repurposing drugs that are used in oncology in order to ameliorate non-malignant illnesses and/or to prevent the emergence of cancer

Causal models in epidemiology: past inheritance and genetic future

The eruption of genetic research presents a tremendous opportunity to epidemiologists to improve our ability to identify causes of ill health. Epidemiologists have enthusiastically embraced the new tools of genomics and proteomics to investigate gene-environment interactions. We argue that neither the full import nor limitations of such studies can be appreciated without clarifying underlying theoretical models of interaction, etiologic fraction, and the fundamental concept of causality. We therefore explore different models of causality in the epidemiology of disease arising out of genes, environments, and the interplay between environments and genes. We begin from Rothman's "pie" model of necessary and sufficient causes, and then discuss newer approaches, which provide additional insights into multifactorial causal processes. These include directed acyclic graphs and structural equation models. Caution is urged in the application of two essential and closely related concepts found in many studies: interaction (effect modification) and the etiologic or attributable fraction. We review these concepts and present four important limitations. 1. Interaction is a fundamental characteristic of any causal process involving a series of probabilistic steps, and not a second-order phenomenon identified after first accounting for "main effects". 2. Standard methods of assessing interaction do not adequately consider the life course, and the temporal dynamics through which an individual's sufficient cause is completed. Different individuals may be at different stages of development along the path to disease, but this is not usually measurable. Thus, for example, acquired susceptibility in children can be an important source of variation. 3. A distinction must be made between individual-based and population-level models. Most epidemiologic discussions of causality fail to make this distinction. 4. At the population level, there is additional uncertainty in quantifying interaction and assigning etiologic fractions to different necessary causes because of ignorance about the components of the sufficient cause

지루각화증의 유전학적 발생과 진행과정 기작의 이해

학위논문 (박사)-- 서울대학교 대학원 : 의과대학 의과학과, 2019. 2. 최무림.어떤 종류의 DNA 변화는 양성종양과 악성종양에서 공유되며, 같은 유전자 변화에도 불구하고 세포, 조직, 임상적인 경과가 다르다. 그렇기에 양성종양의 유전체학을 연구하는 방법으로 악성종양 치료의 새로운 접근법을 제시할 수 있을 것이다. 그러나 현재 양성 종양의 유전체는 많이 연구되지 않았다. 지루각화증은 피부의 양성종양이다. FGFR3 및 PIK3CA 변이가 지루각화증을 일으키는 것이 발견되었으나, 전장 유전체 분석은 아직 이루어진 바 없다. 본 연구는 49 명의 환자에게서 얻은 51 개의 지루각화증과 정상 침 샘플들을 분석하였다. 8 개의 조직에서 전장 엑솜 시퀀싱을 통해 Somatic mutation, copy number variation, loss of heterozygous 분석을 진행하였고, 나머지 43 개 샘플에서는 생어 시퀀싱과 SNP array 를 이용하여 전장 엑솜 시퀀싱에서 발견된 변이들의 분포를 연구하였다. 그 결과 FGFR3, PIK3CA, ZNF750 유전자들의 변이가 지루각화증의 major driver 임을 발견하였으며, 그 외에도 NOTCH1, chr3q29 microdeletion, MSH2-MSH6, TERT1 promoter, RB1 등도 driver 로 작동할 수 있음을 발견했다. FGFR3 과 ZNF750 의 loss of function 조합은 지루각화증의 acanthotic subtype 과 연관되었고, 단 두유전자의 변이만으로 지루각화증이 발생하는 것으로 보인다. FGFR3 과 PIK3CA activation 변이는 hyperkeratotic subtype 과 연관되어 있었다. Minor allele frequency 분석과 Laser microdissection 실험을 통해 FGFR3, ZNF750, PIK3CA 변이가 특정 순서를 따라 발생함을 보였다. Base change 분율 분석을 통해 자외선 노출 정도와 나이가 각각 지루각화증의 유전체학적인 risk factor 임을 보였다. 본 연구를 통해 지루각화증의 유전체학적 배경과 발생과정, 조직학적 분화의 유전적 원인을 제시할 수 있었다.Same genetic modifications are shared by both benign and malignant tumors. Understanding this different cellular, histologic and clinical outcome could reveal new strategy in cancer treatment. However, genetic landscape of benign hyperplasia is largely understudied. Seborrheic keratosis (SK) is a benign skin hyperplasia with no known related malignancy. FGFR3 and PIK3CA are known drivers of SK, but no whole-genome level study has been done, and reason for its senescence is not fully revealed. In this study, 51 SK samples from 49 patients were studied in the whole-genome level. Somatic mutation, copy number alteration (CNA), and loss of heterozygosity (LOH) events were found from 8 pilot samples using whole exome sequencing (WES), and recurrent driver mutation were confirmed with Sanger sequencing and SNP arrays in 43 follow-up samples. FGFR3, ZNF750, and PIK3CA were identified as key drivers of SK. Other potential drivers include NOTCH1, chr3q29 microdeletion, MSH2-MSH6, TERT1 promoter, and RB1. FGFR3 with ZNF750 LoF only occurs in the acanthotic subtype and is sufficient to induce SK without any more genetic change. FGFR3 with PIK3CA induces hyperkeratotic subtype of SK. The order of genetic events and clonal evolution pathway was determined by minor allele frequency analysis and laser microdissection. SK somatic mutation profile revealed the UV effect. Thus, SK shares many genetic pathways with other malignant events, and its genomic landscape provides various level of complexity in its development.Abstract ......................................................................................................... i Table of Contents ................................................................................... iii List of Tables and Figure ...................................................................... v Introduction ................................................................................................ 1 1. Cancer genomics using NGS ........................................................... 1 2. Malignancies of skin ....................................................................... 3 3. Clinical features of SK .................................................................... 5 4. Genetic features of SK (review of previous studies on SK) ........... 6 5. Rationale - why study genomics of SK? ......................................... 8 Materials and Methods ......................................................................... 13 Chapter 1: Genetics of acanthotic SK ............................................ 18 Result ........................................................................................................... 19 1. WES of SK reveals causal gene: FGFR3, and ZNF750 & other candidates .......................................................................................... 19 2. FGFR3 and ZNF750 in extended sample data sets ....................... 31 3. CNV and LOH confirmed by SNP array ...................................... 40 4. Clonal evolution of ZNF750 revealed by laser microdissection. .. 51 Discussion ................................................................................................... 56 Chapter 2: Genetics of hyperkeratotic SK ..................................... 60 Result ............................................................................................................ 61 1. WES of SK reveals causal gene: FGFR3 and PIK3CA & other candidates ........................................................................................... 61 2. FGFR3 and PIK3CA of hyperkeratotic SK in extended data set .. 68 3. CNV confirmed by SNP array ....................................................... 70 4. Clonal evolution of FGFR3 and PIK3CA revealed by WES and laser microdissection ............................................................................................................ 75 5. Histologic subtypes of SK is determined by genetic profile .......... 80 6. Exposure to UV and increasing age as risk factors of SK ............. 81 7. Recurrent mutations in both histology ........................................... 85 Discussion ................................................................................................... 89 Conclusion .................................................................................................. 92 References .................................................................................................. 96 Abstract in Korean ................................................................................ 107Docto

Peto\u27s Paradox and the Evolution of Cancer Suppression

In order to successfully build and maintain a multicellular body, somatic cells must be constrained from proliferating uncontrollably and destroying the organism. If all mammalian cells were equally susceptible to oncogenic mutations and had identical tumor suppressor mechanisms, one would expect that the risk of cancer would be proportional to the body size and lifespan of a species. This is because a greater number of cells and cell divisions over a lifetime would increase the chance of accumulating mutations that result in malignant transformation. Peto’s paradox is the clash between the theory that cancer incidence should increase with body size and lifespan, and the observation that it does not. In this thesis, I present the first comprehensive survey of empirical evidence across mammals in support of Peto’s paradox in addition to computational models that explore the numerous hypotheses that may help resolve the paradox. I provide a detailed examination of tumor suppression in African elephants (Loxodonta africana) and show that the genome contains redundant copies of the tumor suppressor gene TP53. I give evidence that these redundant copies are actively transcribed and also observe an increased apoptotic response after exposure to ionizing radiation, which may be linked to the expression of these genes. Few genomes of large, long-lived organisms are currently available, which motivated my work to provide the sequence and de novo assembly of the humpback whale (Megaptera novaeangliae) genome. In this genome, I discovered a set of tumor suppressor genes that have evolved at an accelerated rate along the whale lineage, which is suggestive of adaptation. Additionally, I find one gene that has undergone convergent evolution between the African elephant and the humpback whale. The overarching goal of my research is to gain a better understanding of how evolution has suppressed cancer in large, long-lived organisms in the hopes of ultimately developing improved cancer prevention in humans

A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer.

Mammary tumors in dogs hold great potential as naturally occurring breast cancer models in translational oncology, as they share the same environmental risk factors, key histological features, hormone receptor expression patterns, prognostic factors, and genetic characteristics as their human counterparts. We aimed to develop in vitro tools that allow functional analysis of canine mammary tumors (CMT), as we have a poor understanding of the underlying biology that drives the growth of these heterogeneous tumors. We established the long-term culture of 24 organoid lines from 16 dogs, including organoids derived from normal mammary epithelium or benign lesions. CMT organoids recapitulated key morphological and immunohistological features of the primary tissue from which they were derived, including hormone receptor status. Furthermore, genetic characteristics (driver gene mutations, DNA copy number variations, and single-nucleotide variants) were conserved within tumor-organoid pairs. We show how CMT organoids are a suitable model for in vitro drug assays and can be used to investigate whether specific mutations predict therapy outcomes. Specifically, certain CMT subtypes, such as PIK3CA mutated, estrogen receptor-positive simple carcinomas, can be valuable in setting up a preclinical model highly relevant to human breast cancer research. In addition, we could genetically modify the CMT organoids and use them to perform pooled CRISPR/Cas9 screening, where library representation was accurately maintained. In summary, we present a robust 3D in vitro preclinical model that can be used in translational research, where organoids from normal, benign as well as malignant mammary tissues can be propagated from the same animal to study tumorigenesis