Molecular Oncology Flashcards
What is oncology?
Oncology is the study of tumors
A tumor or neoplasm can either be
Benign or malignant
What is the difference between a benign and malignant tumor?
A benign tumor is non-recurrent whereas a malignant tumor is invasive and recurs at multiple sites.
What is cancer?
Cancer is neoplasm that includes all malignant tumors whether solid of hematologic.
Define molecular oncology
This is the study of tumors at the molecular level, using techniques to allow direct detection of genetic alterations.
What are the three classifications of tumors?
Solid
Benign
Hematological
What are solid tumors?
Abnormal masses that usually contain no cysts or liquid, tumors designated by tissue of organ.
What are examples of solid tumors?
Carcinomas
Sarcomas
Teratocarcinomas
Carcinomas are tumors of the
Epithelial tissue.
Tumors of the epithelial tissue are called
Carcinomas.
What are sarcomas?
Tumors of the bone, cartilage, muscle, blood vessels, and fat tissue.
What is the name given to neoplasms occurring in the bone, cartilage, muscles, blood vessels, and even fat tissues?
Sarcomas
Neoplasms affecting multiple cell types are called
Teratocarcinomas.
A malignant tumor that starts in mucus-producing glands of the body is called
Adenocarcinoma
A benign glandular tumors is called
Adenoma
Hematological tumors arise from what?
WBCs
What is leukemia?
It is neoplastic disease of blood-forming tissue in which large amount of WBCs populate the bone marrow and peripheral blood.
What are lymphomas?
Neoplasms of lymphocytes that form discrete mass tissues.
What are tumors comprised of?
Genetically identical cells and a clonal nature.
What is cancer?
Uncontrolled cell division
What is the mechanism of cancer?
Alterations in cellular DNA accumulate over time in succeeding generations of daughter cells. These daughter cells with several mutations replace the cells previously comprising the tumor.
How is clonal expansion is normal cells?
They divide, arrest, differentiate, or expire in response to intracellular and extracellular signals controlling the cell division cycle.
How do normal cells know to divide and arrest division or expire?
Through intracellular and extracellular signals they receive that control their division.
How do cancerous cells come about?
From non-lethal mutations in DNA that disrupt the signaling process such that proliferation and survival are favored more than arrestation and expiration.
The transformation of a normal cell to a malignant cancer requires he acquisition of several capacities such as being
- Independent of external growth signals
- Insensitive to external anti-growth signals
- Able to avoid apoptosis (self-directed cell death)
- Capable of indefinite replication/proliferation
- Capable of sustained angiogenesis
- Capable of tissue invasion and metastasis
What is sustained angiogenesis?
Constant oxygen and energy giving or creating access to the vascular system.
Cancer-causing mutations occur in two many types of genes? Name them.
Two. Oncogenes and tumor suppressor genes.
What is the function of protocol-oncogenes?
Promote cell division and support cell survival.
What are examples of photo-oncogenes?
- Cell membrane receptors for growth factors, hormones
- Genes that inhibit apoptosis
What genes are typically in control of cell division and do not allow cell overgrowth?
Photo-oncogenes
Mutations occurring in photo-oncogenes cause them to become cancer promoting genes called
Oncogenes.
What are oncogenes
Mutated proto-oncogenes that promote cancer.
What is the function of tumor suppressor genes (TSG)?
Slow down or stop cell division.
Regulation of port-oncogenes.
TSF includes
Factors that control transcription and translation of genes required for cell division.
Proteins that repair DNA damage and promote apoptosis.
What are checkpoint proteins?
Proteins that suspend cell division when a problem is encountered during DNA synthesis or division.
What is the result seen from mutation in TSF?
Uncontrolled proliferation due to loss of negative regulation.
The most common single genetic change seen in cancer is loss or mutation of the transcription factor
p53
Loss or mutation in transcription factor p53 results in
Lack of regulation from TSG which normally halt cell cycling and induce cell apoptosis
Loss of what transcription factor leads to replication of damaged DNA and cells not undergoing apoptosis when necessary.
p53
Transcription factor p53 is encoded by what gene?
TP53
Gain of function mutation typically occurs in
Oncogenes
What is gain of function?
Amplification of translocation of DNA regions containing the oncogene or activating mutations, causing increased, faulty activity of the proteins.
Loss of function typically occurs in
TSG
What is loss of function?
Inactivation of suppressor proteins either by deletion, translocation or other mutation.
How many mutations are required for onset of clinically observable tumors?
3 to 8
List the 4 types of mutations in cancer
Gene amplification
Gene deletion
Gene rearrangment
Point mutations
What is gene amplification?
Extra copies of a single gene are replicated or transcribed.
What is gene deletion?
This is loss of a sequence of nucleotides within an exon
What is gene rearrangement?
Normal or massive production of clonal populations in Ig-producing cells.
What is point mutation?
Replacement of a single nucleotide that can alter protein function.
What does the colorectal carcinoma model of cancer development suggest?
That tumors arise from mutational activation of protocol-oncogenes and mutational deactivation of TSG.
Which proto-oncogene on chromosome 12p at codon 12 acquires a point mutation of GGT to GAT to become an oncogene?
K-ras
K-ras is a proto-oncogene on what chromosome and what codon?
Chromosome 12p, codon 12.
What point mutation does photo-concogene K-ras acquire that making it an oncogene?
GGT to GAT
What genes are G-proteins that are important in intracellular signaling pathways of growth factors?
Ras genes
Is mutated Was permanently or impermanently active?
Permanent
What TSG on chromosome 5q21 acquires several frameshifts or nonsense mutations leading to its inactivation and production of shortened protein product?
APC
Alteration of at least how many genes is required for development of malignancy is colorectal cancer?
4 or 5
What two alterations are seen in colorectal cancer?
DCC TSG on chromosome 18q is deleted
P53 TSG on chromosome 17p is mutated.
Breast and ovarian cancers come from
Inherited germline mutations in BRCA1 (17q21) and BRCA2 (13q21) genes caused by point mutations or frameshift mutations.
Human epidermal growth factor receptor HER-2/neu mutation
How does HER-2/neu gene mutations result in breast cancer?
Via overproduction of receptor tyrosine kinase protein HER-2.
HER-2/neu breast cancers are detected by
Immunohistochemistry or FISH
What are the goals of using molecular techniques in cancer?
- Provide early diagnosis prior to clinical appearances so patient is monitored closely or have presymptomatic surgery
- Measure tumor aggressiveness so likelihood of recurrence is understood
- Assess residual disease after treatment
What can FISH detect?
Changes in increased copy numbers of oncogenes such as HER-2neu
What are conformers?
Secondary structures DNA forms through intramolecular bonds when denatured into single strands.
Shape of conformers is ermined by
The primary nucleotide sequence
What can change a conformer’s shape?
Polymorphism or mutation
SSCP can be resolved by
Gel or capillary electrophoresis
k-ras mutations can be detected by
SSCP or direct sequencing
P53 mutations can be detected by
SSCP
Direct sequencing
Immunohistochemistry
BRCA mutations can be detected using
Direct sequencing
Sequence specific PCR
Ig genes consists of
Many axons over long distances
What type of genes are said to consist of a supergene family?
Immunoglobulin genes
What must be appropriately brought together for transcription to take place in Ig genes?
Variable, joining and diverse regions
Ig gene transcription only occurs in
One of the homologous chromosomes
What are the steps in VDJ recombination (Ig gene recombination)
Germline configuration DJ recombination V and DJ recombination Transcription, slicing Translation, assembly
How many chains are seen in T cell receptors? Name them.
Two. ab and yd subunits.
What does T cell receptor rearrangement have in common with Ig genes
The variable domains of these subunits (ab and yd) go through VDJ gene rearrangement
What does it mean that normal populations of lymphocytes are polyclonal?
They are all very different.
Each lymphocyte undergoes VDJ rearrangement for Ig and TCRs independently. T or F?
True
When lymphoma and leukemia develop, the malignant cell population is monoclonal meaning
They are all derived from one gene rearrangement.
What is clonality?
It is the red flag (indication) of hematologic malignancy,
What are the targets for clonality detection?
Light and heavy chains of Its
Clonality is detected using
Hybridization techniques such as southern blot
PCR
Clonality comes as a result of
Cancer
Ig and TCR gene rearrangement are normal events used for
producing immune system diversity
What is exploited by molecular techniques in detecting B&T cell lymphomas/leukemias?
Lack of diversity (clonality) that is characteristic of cancer.
What does malignancy translocation involve?
Relocation of proto-oncogene from one chromosome to another.
Translocation causes
Cell growth regulators or cell cycle regulators to be either rover expressed or non-functional.
Chromosomal mutation in Burkitt’s lymphoma
t(8;14) t(2;8) t(8;22)
Chromosomal mutation in Mantle cell lymphoma
t(11;14)
CM in Follicular lymphoma
t(14;18) t(8;14)
CM in acute myeloid leukemia
t(8;21) t(6;9)
CM in acute lymphoid leukemia
t(9;22) t(12;21) t(8;14)
CM in chronic myeloid leukemia
t(9;22) t(11;22)
CM in chronic lymphoid leukemia
t(14;19) 14q+ +12
What is Hodgkin’s lymphoma?
B cell malignancy that causes lymph node swelling and fatigue.
What is the classic characteristic seen in Hodgkin’s disease?
Clonal B cells called Reed Sternberg cells
Which lymphoma has the best prognosis?
Hodgkin’s lymphoma
All other lymphomas (non-Hodgkin’s) involve malignancies of
B and T cells
What is lymphoblastic lymphoma?
Predominantly of T cell origin that is sometimes hard to distinguish from leukemia, -30% of childhood NHL
What is small non-cleaved cell lymphoma?
Burkitt’s and non-burkett’s, B cell origin, 40-50% of childhood NHL
What is large cell lymphoma?
Heterogenous group B and T lineage, 20-25% of childhood NHL
Childhood NHL are divided into
Lymphoblastic (30%)
Small non-cleaved cell lymphomas (40-50%)
Large cell lymphoma (20-25%)
What is Burkitt’s lymphoma?
t(8;14) chromosomal mutation in which there’s breakage of chromosome 8 with segments juxtaposed unto chromosome 14 near Ig heavy chain gene locus.
What gene is normally on chromosome 8?
c-myc
What is the function of c-myc?
Codes for a transcription factor that regulates gene expression related to cell division.
How does translocation cause BL?
Translocation moves c-myc from normal promoter region resulting in over expression of c-myc and subsequent B cell malignancy.
What is mantle cell lymphoma?
t(11;14) chromosomal mutation in which there is translocation of cyclin D1 (BCL-1 or PRAD-1) gene on chromosome 11 to 14.
t(11;14) CM causes
over expression of cyclin D1 which allows passage from G1 to S phase of cell cycle.
What is follicular lymphoma?
t(14;18) chromosomal mutation in which there is translocation of BCL-2 gene on chromosome 14 to 18
What is the function of BCL-2?
Preventing apoptosis of long-lived B cells
When translocated, BCL-2
Allows survival of cells that should normally die
What are leukemias?
Malignancies of B and T cells in the bone marrow that spread to peripheral blood.
What are the 4 major types of leukemias?
Acute myeloid leukemia (AML)
Acute lymphatic leukemia (ALL)
Chronic myeloid leukemia (CML)
Chronic lymphatic leukemia (CLL)
What is CML?
t(9;22) chromosomal mutation in which there is translocation of part of the c-abl gene on chromosome 9 to the BCR gene on chromosome 22.
Translocation of part of the c-abl gene of chromosome 9 to back gene on chromosome 22 results in
Chimeric/fusion gene with head of RBC gene on tail of c-abl gene
BCR and c-abl genes are both
Tyrosine kinase enzymes that phosphorylate other proteins.
What is the effect of improper kinase activity?
Normal growth signal transduction is altered.
Philadelphia chromosome is associated with what leukemia?
Chronic myeloid leukemia
What is Philadelphia chromosome?
Shortened chromosome 22 due to translocation.
What are myelomas?
Malignancy of plasma cells or mature B cells (Ab secreting cells)
Malignancy of antibody-secreting cells is called
Myeloma
How is clonality detected?
PCR
Southern blot
How are translocations detected?
FISH RT PCR (quantity number or percentage of cells with translocation)
For leukemias such as AML and CML, it is important to assay for
Minimal residual disease
What is minimal residual disease?
Small number of malignant lymphocytes that may remain during treatment.
What is minimal residual disease assay used for?
Monitor effectiveness of treatment or if patient is coming out of remission.
MRD is typically assayed using what method?
Reverse transcriptase RT PCR
