Lecture 18: Cancer-Critical Genes

Cancer-Critical genes Search for cancer-critical genes Cancer cells are genetically unstable, they contain many mutations, most of which are not cancerrelated Cancer-critical genes are those which are repeatedly altered in human cancers The total number of cancer critical genes are about 300, which is 1% of the genes in human genome They include signal proteins, receptors, transcriptional regulators, DNA repair enzymes, CAMs, metabolic enzymes, etc. Many mutations in tumor cells are merely passengers The height of the peaks represents the frequency of mutation in large sample of colorectal cancers The most common mutations are the drivers of cancer, while the rare ones are passengers, which are unrelated to cancer progression and occur due to genetic instability Many cancers have an extraordinarily disrupted genome Intrachromosomal rearrangements are more common On average, 17% of genome is duplicated and 16% of the genome is deleted in cancer genomes In addition to that, there are epigenetic changes Only a few mutations provide selective advantage to pass the barriers Two distinct categories of cancer critical genes: oncogenes and tumor suppressor genes Mutations in proto-oncogenes —> proto-oncogenes turn into oncogenes —> gain of function —> cancer Mutation in tumor suppressor gene —> loss of function —> cancer Oncogenes act in a dominant and tumor suppressor genes act in a recessive manner Oncogenes have more missense mutations, while tumor suppressor genes have more truncations A method to identify oncogenes DNA is extracted from tumor cells It’s broken into fragments Each fragment is introduced into mouse-derived cell line, which already has some cancer mutations If a fragment contains an oncogene, small colonies of transformed (abnormally proliferating) cells will appear Sequence the fragment and identify oncogene Oncogene Ras was the first one to be identified (mutated in 30% of tumors) Tumor suppressor genes can also be identified by inserting them in cells and looking for cancer cells. • A. True • B. False Transformed cells lose contact inhibition in cell culture: hey grow on top of each other Example of an oncogene that results from a deletion in a coding sequence: deletion in EGF receptor can make it active in the absence of a signal Deletion of the extracellular part makes the receptor consistently active, resulting in uncontrollable proliferation Common in brain tumor, glioblastoma Myc proto-oncogene turns into an oncogene by application Proto-oncogenes Myc and Ras are the members of another pathway which stimulates cell division Ras - GTPase, helps to transmit the signal to enter the cell cycle. Mutation which leads to cancer makes it transmit the signal without any signal Myc - gene regulatory proteins which promotes cell division. Overproduction causes cancer. In cancer, Myc can be amplified or fused with a stronger promoter due to a chromosomal translocation In order to progress through the cell cycle, both mitogens and growth factors are necessary Mitogens usually bind to RTK receptors to promote cell cycle progression However, growth factors that signal the presence of necessary nutrients are also necessary Pathways that respond to the presence of glucose in blood can also be altered to promote cancer This explains why people with obesity and type 2 diabetes have cancer risk increased about 2-3 fold Abnormal activation of a pathway that responds to growth factors can lead to cancer Cells responds to growth factors, such as insulin, through the RTK/PI3 kinase/Akt/mTOR pathway Activation of this pathway results in increased glucose uptake and its utilization in production of lipids to build membrane components. It also leads to increased protein synthesis Abnormal activation can explain the increased rate of glycolysis in cancer cells A mutation can be in growth factor receptor, or in other components, such as a dephosphorylates the PIP3 products of PI3 kinase, PTEN PTENis a tumor suppressor protein Onset of tumors occurs earlier in mice carrying two oncogenes to mice carrying only one Cancer occurs randomly in some cells of the knockout mice, while other cells remain norma. This tells us that more mutations are necessary to cause cancer In the cellular regulatory pathways that control growth and proliferation, the products of oncogenes are stimulatory components and the products of tumor suppressor genes are inhibitory components. • A. True • B. False How to identify a tumor suppressor? More difficult than to identify an oncogene: you have to find something, which is missing in cancer cells A lot might be missing because a lot of non-cancer-related mutations are produced as a side effect It’s easier for some rare cancers that have small number of mutations Example of such cancer: retinoblastoma. The tumor suppressor gene, which was discovered - Rb (from retinoblastoma) Sometimes it’s obvious that a fragment of chromosome was lost. Then researchers look if another allele has any mutations There are new powerful techniques to identify the difference between normal and cancer cells total mRNA: Representative difference analysis Studies of rare hereditary cancer syndromes first identified tumor suppressor genes Rob was first identified in a rare form of the eye cancer, retinoblastoma Both copies of Rb should be lost to cause cancer In hereditary retinoblastoma, cancers happen in both eyes (spontaneous loss of the second copy of Rb) In nonhereditary retinoblastoma, cancers occur in just one eye; happens very rarely (both copies of Rb spontaneously lost in the same cell) Both genetic and epigenetic mechanisms can inactivate tumor suppressor genes Tumor suppressor genes may be silenced by genetic or epigenetic changes on both chromosomes Frequency of epigenetic silencing of five tumor suppressor genes in four different cancers BRAC1 and hMLH1 affect genomic stability Epigenetic inactivation by packaging in heterochromatin or CG methylation of the promoter regions is a common mechanism of tumor suppressor silencing Phosphorylation of Rb protein by cyclin/CDK relieves inhibition of E2F and allows it to activate transcription of S-phase genes Mutations in the p53 pathway enable cancer cells to survive and proliferate despite stress and DNA damage p53 functions in cancer prevention Plays a role in apoptosis, genomic stability, and inhibition of angiogenesis Activates DNA repair proteins when DNA has sustained damage Arrests cell cycle at the G1/S checkpoint (holds the cell cycle until the DNA repair proteins did the damage) Initiates apoptosis if DNA damage proves to be irreparable People who inherit only one functional copy of the TP53 gene will most likely develop tumors in early adulthood Loss of p53 most often results in an aneuploidy phenotype Increased amount of p53 can cause premature aging Cell cycle arrest by p53 in response to DNA damage Named after is protein product molecular weight p53 stimulates apoptosis or halts cell division if DNA is damaged or something is wrong with a cell cycle Low level under normal conditions: MDM2 (ubiquitin ligase) targets if to degradation. It also promotes its translocation from the nucleus to the cytosol High level when something is wrong Activates transcription of several genes and micro-RNAs p53 is mostly activated by phosphorylation of its activation domain It results in a conformational change that leads to its activation It also increases the stability of p53 Activation of p53 Protein kinases that phosphorylate and thus activate p53 can be divided into two groups: MAPK family, which responds to several types of stress, such as membrane damage, oxidative stress, osmotic shock, heat shock, etc. Protein kinases that respond to several forms of DNA damage (ATR, ATM, CHK1, CHK2, etc.) Oncogenes also stimulate p53 activation p53 expression can be stimulated in response to UV light Structure of p53 Transcription-activation domain, which activates transcription factors Two domains important for apoptotic activity DNA-binding domain Oligomerization domain: p53 forms tetramers before binding to DNA Some other domains responsible for nuclear localization Mutations in which domain of p53 require both alleles to be mutated in order to cause cancer (receive loss-of function mutations)? • A. Oligomerization domain • B. DNA binding domain • C. Both types are recessive Cancer -causing mutations in p53 are of two types Mutations in the DNA binding domain are recessive loss-of-function mutations (both copies of p53 need to be lost to cause cancer) Mutations in oligomerization domain prevent the formation of tetramers necessary for transcription activation. They have a dominant negative effect on the function of p53 Colon cancer originates from small polyps that can become malignant Polyps are initially benign and can be removed during colonoscopy, a routine examination for colon cancer performed each 10 years after age 50 This usually prevents the colon cancer. However, if colon cancer becomes metastatic, the 5 years survival rate is about 5% Addition of mutations in colorectal cancer is associated with the cancer progression The APC (Adenomatous polyposis coli) gene is the most commonly mutated gene in all colorectal cancers APC is a part of beta-catenin destruction complex. Mutations in APC gene can promote accumulation of beta catenin resulting in upregulation of genes causing increased cell division APC is a tumor suppressor gene K-Ras is a member of Ras superfamily. K-Ras upregulates the glucose transporter, thereby contributing to the switch to glycolysis metabolic pathways Smad4 is a transcription factor that is activated by TGFbeta signaling molecule. TGFbeta inhibits cell growth. When Smad4 is mutated, cells start to proliferate uncontrollably Some colorectal cancers have defects in DNA mismatch Repair To get cancer, both alleles of ____ should always get mutated • A. RB • B. TP53 • C. Both TP53 and Rb