Tumor pathogenesis

Genetic and epigenetic alterations in cancer

Oncogenes Tumor Suppressor Genes Invasion and Metastasis

Jimin Shao

shaojimin@zju.edu.cn

Carcinogensis is multistep process, involving the multiple genetic and /or epigenetic changes, leading to the activation of oncogenes and the inactivation of tumor suppressors in cells.

Genetic and epigenetic alterations in cancer

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resection chemotherapyradiotherapy biotherapyprediction

Molecular changes during tumorigenesis and cancer development

1. The Genetic Basis of Cancer

Cancer associated genetic mutations are most often found in: proto-oncogenes and tumor suppressor genes.

These genes normally regulate the natural processes of cell fate to keep tissues and organs healthy.

Introduction to Special Issue: Cancer Genomics:Zahn LM, Travis J. Cancer genomics. A medical renaissance? Introduction. Science. 2013;339(6127):1539

Michael R. Stratton. Exploring the Genomes of Cancer Cells: Progress and Promise. Science 331, 1553 (2011).

(1) Exploring the Genomes of Cancer Cells

(2) Large-Scale Genomic Initiatives

Several coordinated efforts to exploit whole genome sequencing to identify the genetic mutations in different cancer types and subtypes.

The data generated by these initiatives are reshaping our definition of cancer: cancer is a group of diseases defined not only by the anatomical site from which they originate, but also by the genetic alterations that are driving their formation.

This new knowledge is rapidly advancing precision medicine.

The Cancer Genome Atlas (TCGA):

NCI and the National Human Genome Research Institute (NHGRI) launched TCGA (cancergenome.nih.gov) in 2006.

charting the genomic changes in more than 20 types or subtypes of cancer.

For each form of cancer being studied, tumor and normal tissues from hundreds of patients are analyzed.

TCGA database: Data generated through TCGA are freely available and widely used by the cancer research community.

International Cancer Genome Consortium (ICGC)

Launched in 2008, the ICGC (icgc.org) comprises research groups around the world, including some from TCGA.

To harmonize the many large-scale genomic projects underway by generating, using, and making freely available common standards of data collection and analysis.

To identify the genetic changes in 50 different types or subtypes of cancer, and it currently has 53 project teams studying more than 25,000 tumor genomes. For each form of cancer being studied, tumor and normal tissues from approximately 500 patients are analyzed.

Data generated by ICGC project teams are freely available and widely used by the cancer research community.

St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project (PCGP)

in 2010 to sequence the genomes of both normal and cancer cells from more than 600 children with cancer.

The PCGP (pediatriccancergenomeproject.org) is the largest investment to date aimed at understanding the genetic origins of childhood cancers.

(3) Cancer Genome Landscapes

Comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). These studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains 2~8 of these “driver gene” mutations; the remaining mutations are passengers. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. Drive genes: increasing the selective growth advantage of tumor cells.Mut-driver genes contain a sufficient number or type of driver gene mutations. Epi-driver genes are expressed aberrantly in tumors through changes in DNA methylation or chromatin modification that persist as the tumor cell divides

[Vogelstein B, et al. Cancer Genome Landscapes. Science, 2013, 339:1546]

Number of somatic mutations in representative human cancers, detected by genomewide sequencing studies. Numbers in parentheses indicate the median number of nonsynonymous mutations per tumor in a variety of tumor types .

How Many Genes Are Mutated in a Typical Cancer?

Other Types of Genetic Alterations in Tumors

Most solid tumors display widespread changes in chromosome number (aneuploidy), deletions, inversions, translocations, and other genetic abnormalities

Protein-coding genes account for only ~1.5% of the total genome, and the number of alterations in noncoding regions is proportionately higher than the number affecting coding regions. The vast majority of the alterations in noncoding regions are presumably passengers.

All of the known driver genes can be classified into 12 signaling pathways. These pathways can be organized into three core cellular processes.

What causes cancer: A sequential series of alterations in well-defined genes that alter the function of a limited number of pathways.A common and limited set of driver genes and pathways is responsible for most common forms of cancer. These genes and pathways offer distinct potential for early diagnosis: the genes themselves, the proteins encoded by these genes, and the end products of their pathways are, in principle, detectable in many ways:Analyses of relevant body fluids: urine for genitourinary cancers, sputum for lung cancers, and stool for gastrointestinal cancers. Molecular imaging: the presence, location and extent of cancer.

Cancer genome sequencing has an impact on the clinical care of cancer patients.

The recognition that certain tumors contain activating mutations in driver genes encoding protein kinases has led to the development of small-molecule inhibitor drugs targeting those kinases.

Two representative pathways (RAS and PI3K):

Red: proteins encoded by the driver genes.

Yellow balls: sites of phosphorylation.

Examples of therapeutic agents.

2. Beyond Genetics: The role of Epigenetics Each cell in an individual contains the same 25,000 genes.

Special chemical marks on DNA and histones together determine genome accessibility, and thus gene usage, in a given cell type.

Epigenetic defects in conjunction with permanent changes in the genetic material of the cell promote cancerous behaviors.

Some epigenetic abnormalities are reversible.

Epigenetic Therapies (The FDA approved):

DNA methylation inhibitors: azacitidine (Vidaza) and decitabine (Dacogen) for

the treatment of myelodysplastic syndrome (MDS,骨髓增生异常综合征 ).

Histone deacetylase inhibitors: romidepsin (Istodax) and vorinostat (Zolinza) for the treatment of certain lymphomas.

In July 2014, the FDA approved belinostat (Beleodaq), which targets multiple types of histone deacetylases, for the treatment of patients with peripheral T-cell lymphoma who had become resistant to or had relapsed on prior therapies.

There are at least four different DNA modifications and 16 classes of histone modifications

Noncoding RNAsThe entire genome is transcribed; however, only 2% of this is subsequently translated.

The ‘‘noncoding’’ RNAs (ncRNAs) can be roughly categorized into small (under 200 nucleotides) and large ncRNAs.

The small ncRNAs include small nucleolar RNAs (snoRNAs), PIWI-interacting

RNAs (piRNAs), small interfering RNAs (siRNAs), and microRNAs (miRNAs).

Many of these families show a high degree of sequence conservation across species and are involved in transcriptional and posttranscriptional gene silencing through specific base pairing with their targets.

The long ncRNAs (lncRNAs) demonstrate poor cross-species sequence conservation, and their mechanism of action in transcriptional regulation is more varied.

These lncRNAs appear to have a critical function at chromatin, where they may act as molecular chaperones or scaffolds for various chromatin regulators, and their function may be subverted in cancer.

3. Hallmarks of cancer

. (Hanahan D, Weinberg RA. Hallmarks of Cancer: The Next Generation. Cell 2011, 144:646)

Self-sufficiency in growth signals

Cancer cells do not need stimulation from external signals (in the form of growth factors) to multiply.

Insensitivity to anti-growth signalsCancer cells are generally resistant to growth-preventing signals from their neighbours.

Tissue invasion and metastasisCancer cells can break away from their site or organ of origin to invade surrounding tissue and spread (metastasis) to distant body parts.

Limitless reproductive potentialNon-cancer cells die after a certain number of divisions. Cancer cells escape this limit and are apparently capable of indefinite growth and division (immortality).

Sustained angiogenesisCancer cells appear to be able to kick start this process, ensuring that such cells receive a continual supply of oxygen and other nutrients.

Evading apoptosis

Apoptosis is a form of programmed cell death, the mechanism by which cells are programmed to die after a certain number of divisions or in the event they become damaged. Cancer cells characteristically are able to bypass this mechanism.

Deregulated metabolism

Most cancer cells use abnormal metabolic pathways to generate energy, a fact appreciated since the early twentieth century with the postulation of the Warburg hypothesis, but only now gaining renewed research interest.

Evading the immune system

Cancer cells appear to be invisible to the body’s immune system.

Unstable DNA

Cancer cells generally have severe chromosomal abnormalities, which worsen as the disease progresses.

Inflammation

Recent discoveries have highlighted the role of local chronic inflammation in inducing many types of cancer.

Intracellular Signaling Networks Regulate the Operations of the Cancer Cell.

An integrated circuit operates within normal cells and is reprogrammed to regulate hallmark capabilities within cancer cells.

Separate subcircuits (in differently colored fields) orchestrate the various capabilities.

There is considerable crosstalk between subcircuits.

Each of these subcircuits is connected with signals originating from other cells in the tumor microenvironment.

4. Outside Influences

Cancer is much more complex than an isolated mass of proliferating cancer cells;

Interactions between cancer cells and tumor microenvironment, as well as interactions with the person as a whole, profoundly affect cancer development;

(Upper) An assemblage of distinct cell types constitutes most solid tumors. Both the parenchyma and stroma of tumors contain distinct cell types and subtypes that collectively enable tumor growth and progression. Notably, the immune inflammatory cells present in tumors can include both tumor-promoting as well as tumor-killing subclasses.(Lower) The distinctive microenvironments of tumors. The multiple stromal cell types create a succession of tumormicroenvironments that change as tumors invade normal tissue and thereafter seed and colonize distant tissues.The abundance, histologic organization, and phenotypic characteristics of the stromal cell types, as well as of theextracellular matrix (hatched background), evolve during progression, thereby enabling primary, invasive, and then metastatic growth. The surrounding normal cells of the primary and metastatic sites, shown only schematically, likely also affect the character of the various neoplastic microenvironments. (Not shown are the premalignant stages in tumorigenesis, which also have distinctive microenvironments that are created by the abundance and characteristics of the assembled cells.) (Hanahan D, Weinberg RA. Hallmarks of Cancer: The Next Generation. Cell 2011, 144:646)

Tumor Microenvironment

(Upper) The assembly and collective contributions of the assorted cell types constituting the tumor microenvironment are orchestrated and maintained byreciprocal heterotypic signaling interactions, of which only a few are illustrated.(Lower) The intracellular signaling depicted in the upper panel within the tumor microenvironment is not static but instead changes during tumor progression as a result of reciprocal signaling interactions between cancer cells of the parenchyma and stromal cells that convey the increasingly aggressive phenotypes that underlie growth, invasion, and metastatic dissemination. Importantly, the predisposition to spawn metastatic lesions can begin early, being influenced by the differentiation program of the normal cell-of-origin or by initiating oncogenic lesions. Certain organ sites (sometimes referred to as ‘‘fertile soil’’ or ‘‘metastatic niches’’) can be especially permissive for metastatic seeding and colonization by certain types of cancer cells, as a consequence of local properties that are either intrinsic to the normal tissue or induced at a distance by systemic actions of primary tumors. Cancer stem cells may be variably involved in some or all of the different stages of primary tumorigenesis and metastasis.(Hanahan D, Weinberg RA. Hallmarks of Cancer: The Next Generation. Cell 2011, 144:646)

Signaling Interactions in the Tumor Microenvironment during Malignant Progression

Oncogene

An oncogene is a gene that when mutated or expressed at abnormally-high levels contributes to converting a normal cell into a cancer cell.

Cellular oncogene (c-onc)：

--- proto-oncogene （ proto-onc）： normal physiologic version

--- Oncogene ： altered in cancer

Viral oncogene （ v-onc）

Proto-oncogenes have been identified at all levels of the various signal transduction cascades that control

cell growth, proliferation, and differentiation: extracellular proteins function as growth factors, membrane proteins as cell surface receptors cellular proteins that relay signals proteins in nucleus, which activate the transcription and

promote the cell cycle

This signaling process involves a series of steps that: begin from the extracellular environment to cell membrane; involve a host of intermediaries in the cytoplasm; end in the nucleus with the activation of transcription factors

that help to move the cell through its growth cycle.

Fuctions of proto-oncogenes

Growth factors, e.g. V-sis, PDGF-int-2 Receptor Tyrosine Kinases, e.g. Her-2/neu/ erbb2, Membrane Associated Non-Receptor Tyrosine Kinases,

e.g. src, Lck G-Protein Coupled Receptors e.g. Mas Membrane Associated G-Proteins , e.g. Ras Serine/Threonine Kinases e.g. Raf Nuclear DNA-Binding/Transcription Factors, e.g. myc, fos Others

Apoptosis regulators, e.g. Bcl-2,Regulators of cell cycle, e.g. Cyclin D1, CDK4

Classification of proto-oncogenes

Mechanisms of Oncogene Activation

1. Gene amplification, e.g. myc, CCND1

2. Point mutation, e.g. ras,

3. Chromosomal rearrangement or translocation the transcriptional activation of proto-onc. the creation of fusion genes, e.g. abl-bcr

4. Viral insertion activation, e.g. c-Myc

Amplification

Translocation

Ras

Locates on chromosome 11, codes for a protein with GTPase activity

relays signals by acting as a switch: When receptors on the cell surface are stimulated, Ras is switched on and transduces signals that tell the cell to grow. If the cell-surface receptor is not stimulated, Ras is not activated and so the pathway that results in cell growth is not initiated.

mutated in about 30% of human cancers so that it is permanently switched on, telling the cell to grow regardless of whether receptors on the cell surface are activated or not.

非活化型： α、 β、 γ 三聚体结合GDP

活化型： α 亚基结合GTP，与 βγ 亚基分离

Ras relays signals from the cell surface receptors to the nucleus

Ras relays signals by acting as a switch

Prospect

A breakthrough for our understanding of the molecular and genetic basis of cancer

Provided important knowledge concerning the regulation of normal cell proliferation, differentiation, and programed cell death.

The identification of oncogene abnormalities has provided tools for the molecular diagnosis and monitoring of cancer.

Oncogenes represent potential targets for new types of cancer therapies.

Tumor suppressor genes

Definition: genes that sustain loss-of function mutations in the development of cancer

Tumor suppressor genes: functional categories and tumor associations

Gate-keeper

Caretaker

Mechanism for the inactivation of TSGs

1. Mutation: point mutation or frameshift mutation, p53

2. Deletion: LOH or homozygous deletion, Rb

3. Viral oncoprotein inactivation: p53, Rb

4. Promoter hypermethylation, histone modification changes: p16

Rb

function

Rb regulates G1/S transition

Rb inactivation by

viral oncoprotein

RB: Cell Cycle Controller

P53Function as gatekeeper

Bax

Inactivation of p53 in cancer •LOH on 17p13 in a number of tumors

•Point mutation on exon 5-8 “hot-spot” (Dominant negative mutation)

•MDM2 negative regulation

• viral-oncogene products inactivation