Download Tumor suppressor genes(TSGs)

Tumor pathogenesis
Genetic and epigenetic alterations in
cancer
 Oncogenes
 Tumor Suppressor Genes
 Invasion and Metastasis

Jimin Shao
[email protected]
Genetic and epigenetic alterations in cancer
 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.
 Molecular changes during tumorigenesis and cancer development
prediction
resection
radiotherapy
chemotherapy
biotherapy
3
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
(1) Exploring the Genomes of Cancer Cells
Michael R. Stratton. Exploring the Genomes of Cancer Cells: Progress and Promise. Science 331, 1553 (2011).
(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
[Vogelstein B, et al. Cancer Genome Landscapes. Science, 2013, 339:1546]
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
How Many Genes Are Mutated in a Typical Cancer?
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 .
 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 welldefined 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 smallmolecule 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 RNAs
The 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 signals
Cancer cells are generally resistant to growth-preventing signals from their
neighbours.
 Tissue invasion and metastasis
Cancer cells can break away from their site or organ of origin to invade
surrounding tissue and spread (metastasis) to distant body parts.
 Limitless reproductive potential
Non-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 angiogenesis
Cancer 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;
 Tumor Microenvironment
(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 tumor
microenvironments 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 the
extracellular 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)
 Signaling Interactions in the Tumor Microenvironment during Malignant Progression
(Upper) The assembly and collective
contributions of the assorted cell types
constituting the tumor microenvironment are
orchestrated and maintained by
reciprocal 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)
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）
Fuctions of proto-oncogenes
Proto-oncogenes have been identified at all levels of the
various signal transduction cascades that control
cell growth, proliferation, and differentiation:
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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:


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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.
Classification of proto-oncogenes
 Growth factors, e.g. V-sis, PDGF-b, int-2
 Receptor Tyrosine Kinases, e.g. Her-2/neu/ erbb2,
 Membrane Associated Non-Receptor Tyrosine Kinases,
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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
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

Translocation
Amplification
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
Caretaker
Gatekeeper
Mechanism for the inactivation of TSGs
1.
2.
3.
4.
Mutation: point mutation or frameshift mutation, p53
Deletion: LOH or homozygous deletion, Rb
Viral oncoprotein inactivation: p53, Rb
Promoter hypermethylation, histone modification
changes: p16
Rb
function
Rb regulates G1/S transition
Rb inactivation by
viral oncoprotein
RB: Cell Cycle Controller
P53
Function as gatekeeper
Inactivation of p53 in cancer
•LOH on 17p13 in a number of tumors
Bax
•Point mutation on exon 5-8 “hot-spot”
(Dominant negative mutation)
•MDM2 negative regulation
• viral-oncogene products inactivation