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MOLECULAR BIOLOGY > FINALS LEC: MOLECULAR DETECTION: ONCOLOGY > Flashcards

FINALS LEC: MOLECULAR DETECTION: ONCOLOGY Flashcards

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1
Q

Study of tumors/neoplasm  growth of tissue that exceeds and is not coordinated with normal tissue

A

ONCOLOGY

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2
Q

not recurrent

A

benign

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3
Q

invasive & tending to recur at multiple sites (cancer)

A

malignant

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4
Q

movement of tumor cells from the original (primary) site of the tumor to other locations

A

matastasis

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5
Q

suffix, to the tissue of origin

A

-Oma

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6
Q

study of cancer at the molecular level

A

Molecular oncology

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7
Q

An abnormal mass of tissue that usually does not contain cysts/liquid areas

A

SOLID TUMORS

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8
Q

tumor of epithelial origin

A

Carcinoma

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9
Q

tumor of bone, cartilage, muscle, blood vessels, or fat

A

sarcoma

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10
Q

multiple cell types

A

teratocarcinoma

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11
Q

Abbormal cells in the blood grow out of control

A

HEMATOLOGICAL MALIGNANCIES

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12
Q

large nos. of WBCs populate the bone marrow & peripheral blood

A

Leukemia

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13
Q

neoplasm of lymphocytes that form discrete tissue masses

A

Lymphoma

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14
Q

Plasma cell neoplasms: abnormal plasma cells/cells form tumors in the bones/soft tissues of the body

A

HEMATOLOGICAL MALIGNANCIES

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15
Q

is caused by nonlethal mutations in DNA affecting 2 types of genes that control the cell division cycle and cell survival

A

cancer

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16
Q

2 types of genes that control the cell division cycle and cell survival:

A

Oncogenes
Tumor-supressor genes

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17
Q

● Promote cell division ● Include cell membrane receptors, that are bound by growth factors, hormones, and other extracellular signals
● Support cell survival by inhibiting apoptosis
● >100 in the human genome

A

Oncogenes

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18
Q

● Factors that control transcription/translation of genes required for cell division
● Participate in repairing DNA damage & in promoting apoptosis
● Slow down/stop cell division by counteracting the movement of the cell from G1-to S (G1 checkpoint) or G2 to M phase (G2 checkpoint)
● >30 in the human genome

A

Tumor-supressor genes

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19
Q

IN CANCER CELLS

Gain-of-function mutations resulting from:
 Amplification/translocation of DNA regions containing the genes
 Activating mutations that cause aberrant activity of the proteins

A

Oncogenes

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20
Q

IN CANCER CELLS

Loss-of-function genes mutations  Inactivation of the gene products (deletion, translocation, mutation of the genes)

A

Tumor-supressor genes

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21
Q

Molecular diagnosis and treatment of cancer cells:

A

Detection of abnormalities in specific tumor suppressors or oncogenes

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22
Q

ANALYTICAL TARGETS OF MOLECULAR TESTING:

A

Tissue specific targets
Tumor-specific targets

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23
Q

● Molecular characteristics of the tissue from which a tumor arose
● Detection and monitoring the presence of tumor  abnormal amounts or locations of DNA, RNA, proteins or other molecules from these targets
● Examples: DNA/RNA from
1. Cytokeratin genes in gastric cancer 2. Carcinoembryonic antigen in breast cancer

A

Tissue specific targets

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24
Q

● Genetic structures resulting from mutations in oncogenes & tumorsuppressor genes that are associated with tumor development
● Solid tumors, leukemias, lymphomas ● Mutated cell free nucleic acid/circulating tumor cells can be detected in blood & other body fluids
● Examples: surface receptors, mutated proteins, tumor-associated antigen, metabolic markers

A

tumor-specific targets

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25
Q

 Tyrosine-kinase activity
 Normal activity: cell growth and division
 Overexpressed in 25%-30% of human breast cancers

A

Human epidermal growth factor receptor 2, HER/neu/erb-b2 1 (17q21.1)

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26
Q

Detection methods of Human epidermal growth factor receptor 2, HER/neu/erb-b2 1 (17q21.1)

A

IHC
SOUTHERN, NORTHERN, WESTERN BLOT
FISH
Chromogenic in situ hybridization (CISH)
Silver-enhanced in situ hybridization (SISH)

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27
Q

uses antibodies (fresh/frozen tissues)

A

IHC

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28
Q

gene amplification  increased RNA & proteins

A

Southern, northern, western blots

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29
Q

direct detection of increased copy nos. of the gene in DNA

A

FISH

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30
Q

standard bright-field microscope, genome & chromosome mutation detection

A

Chromogenic in situ hybridization (CISH)

31
Q

 Normal activity: cell signaling pathways that control cell division and survival
 Overexpressed in solid tumors

A

Epidermal growth factor receptor, EFGR (7p12)

32
Q

Detection methods of Epidermal growth factor receptor, EFGR (7p12)

A

IHC
qPCR
SSP-PCR, SSCP, direct sequencing, NGS

33
Q

to assess gene copy no. through increased gene expression

A

qPCR

34
Q

mutations

A

SSP-PCR, SSCP, direct sequencing, NGS

35
Q

 Small GTP-binding proteins that receive signals from the cell surface proteins & activate the initial steps of the mitogen-activated protein kinase (MAPK) pathway cascade
 Gain-of-function mutations in ras protooncogenes
 cancers
 Mutations in these genes are the most common oncogene mutations in human cancers (codons 12, 13, 22, & 61 in exons 2 & 3 of the KRAS gene)
 Detection methods of mutation: direct sequencing, pyrosequencing

A

Kirsten rat sarcoma viral oncogene homolog, K-ras (12p12); neuroblastoma ras, Nras (1p13); & Harvey rat sarcoma viral oncogene homolog, H-ras (11p15)

36
Q

 Ewing sarcoma: group of tumors arising from primitive neuroectodermal tissue (PNET)
 Diagnosis and prognosis: a. cytogenetic methods b. molecular methods: RT-PCR, with amplification control (GAPDH or 18S RNA) on tissue/liquid biopsies

A

Ewing sarcoma, EWS (22q12)

37
Q

group of tumors arising from primitive neuroectodermal tissue (PNET)

A

Ewing sarcoma

38
Q

 Detection methods:
a. FISH
b. RT-PCR
c. Semi-nested PCR
d. Agarose gel electrophoresis & EtBr staining (PCR product detection)

A

Synovial sarcoma translocation, chromosome 18 – Synovial sarcoma breakpoint 1 & 2, SYT-SSX1, SYT-SSX2 t(X;18) (p11.2;q11.2)

39
Q

rare type of cancer of the muscle, fat, fibrous tissue, blood vessels, or other supporting tissue of the body

A

Synovial sarcoma

40
Q

 Detection methods: FISH, RT-PCR, qPCR, RNA sequencing

A

Paired box-fokhead in Rhabdomyosarcoma, PAX3-FKHR, PAX7-FKHR, t(1;13), t(2;13)

41
Q

most common soft tissue sarcoma of childhood (10% of all solid tumors in children)  alveolar RMS, embryonal (RMS-E), & primitive (RMS-P)

A

Rhabdomyosarcoma (RMS)

42
Q

 Mutations in this gene is found in all types of cancers and also aids in the diagnosis of LiFraumeni syndrome
 Detection methods: IHC, microarrays/panel sequencing, SSCP, direct sequencing

A

Tumor protein 53, TP53 (17p13)

43
Q

gene product of TP53, DNA-binding protein that controls expression of other genes and participates also in the arrest of cell division in the event of DNA damage

A

p53

44
Q

 Carriers (autosomal recessive mutations)  develops leukemia (B-cell lymphocytic leukemia, T-cell prolymphocytic leukemia), lymphoma (mantle cell lymphoma), or other types of cancers
 Detection methods: direct DNA sequencing, SSCP, functional test for the repair of dsbreaks induced by irradiation, test for other family members

A

Ataxia telangiectasia mutated gene, ATM (11q22)

45
Q

DNA repair and/or control of the cell cycle

A

ATM protein

46
Q

neurological disorder that affects the part of the brain that controls motor movement & speech; predisposition to cancer

A

Ataxia telangiectasia (AT)

47
Q

 Gene products are involved in DNA dsbreak repair by homologous recombination
 Screening tests for mutation: SSCP, protein truncation testes, chromosome breakage tests, etc.
 Clinical application method: direct sequencing
 Other detection methods: SSP-PCR, allelespecific oligomer hybridization

A

Breast cancer 1 gene, BRCA1 (17q21), & breast cancer 2 gene, BRCA2 (13q12)

48
Q

mutation in BRCA1 (60%-80% lifetime risk of breast/ovarian cancer)

A

Women

49
Q

mutation in BRCA2 (increased risk of breast/colon/prostate cancer)

A

Men

50
Q

Functions as a tumor-suppressor gene, promoting cell differentiation

A

von Hippel-Lindau gene, VHL (3p26)

51
Q

 genetic condition involving abnormal growth of blood vessels in organs (eyes, kidneys, adrenal glands, etc.)
 predisposition for renal cell carcinoma & other cancers
 deletions, point mutations, splice-site mutations
 Somatic mutations: renal cell carcinoma & tumors of the adrenal glands
 Detection method: direct sequencing

A

Von Hippel-Lindau syndrome

52
Q

 Myc family proteins: increase the expression of several genes
a. c-myc oncogene (8q24.21): amplified in breast & ovarian cancer, lymphomas, & leukemias
b. l-myc (1p34.2): amplified in oral cancer c. n-myc (2p24): amplified in neuroblastoma & retinoblastoma
 Detection methods: IHC, FISH, sequencing, array analysis, transcription of n-myc through qPCR

A

V-myc myelocytomatosis viral-related oncogene, neuroblastoma-derived, MYCN or n -myc (2p24)

53
Q

coding for a membrane receptor tyrosine kinase  rearranged in a variety of human cancers (1%-3% lung adenocarcinomas)

A

ROS1 oncogene

54
Q

its gene product participates in sending signals to the nucleus

A

RET proto-oncogene

55
Q

 ALK: receptor tyrosine kinase
 Chromosomal rearrangements (most common), mutations, or amplifications tumors (lymphomas, neuroblastoma, & nonsmall cell lung cancer)
 Detection methods: FISH & sequencing

A

Anaplastic lymphoma receptor tyrosine kinase (ALK) proto-oncogene, 2p23.1

56
Q

receptor tyrosine kinase

A

ALK

57
Q

 Kit protein:
transmembrane receptor with tyrosine kinase activity
 Gene mutation: gastrointestinal stromal tumors (GISTs), mast cell disease, & AML
 Detection methods: a. IHC: increased KIT protein
b. Sequencing: missense mutations

A

V-Kit Hardy-Zuckerman 4 feline sarcoma oncogene homolog, KIT, c-KIT (4q12)

58
Q

transmembrane receptor with tyrosine kinase activity

A

Kit protein

59
Q

gastrointestinal stromal tumors (GISTs), mast cell disease, & AML

A

Gene mutation

60
Q

 Contraction & expansion of nucleotide repeat sequences in DNA
MICROSATELLITE INSTABILITY (MSI)
 Cause: dysfunction of 1 or more components of mismatch repair (MMR) systems
 Lynch syndrome or hereditary nonpolyposis colorectal cancer (HNPCC)
 Inherited cancer predisposition syndrome, 3%-5% of colon cancers & 3% endometrial cancers
 Increased risk of developing other cancers  MMR mutations in MSH2 & MLH1 genes  Detection methods: direct sequencing, IHC, MSI analysis, PCR, gel/capillary gel electrophoresis (more bands/peaks in the tumor tissue than the normal)
 National Cancer Institute: recommended the screening of BAT25 & BAT26; & D5S346, D2S123, & D17S250 for MSI determination

A

MICROSATELLITE INSTABILITY (MSI)

61
Q

 Inherited cancer predisposition syndrome, 3%-5% of colon cancers & 3% endometrial cancers
 Increased risk of developing other cancers
 MMR mutations in MSH2 & MLH1 genes

A

Lynch syndrome or hereditary nonpolyposis colorectal cancer (HNPCC)

62
Q

 Deletion/inactivation of a functional allele, leaving a mutated allele

 Detection methods: PCR & capillary electrophoresis (amplification of heterozygous STR/VNTR loci closely linked to the disease gene)

A

LOSS OF HETEROZYGOSITY (LOH)

63
Q

A laboratory test done on a sample of blood (plasma/serum), urine, or other body fluid to look for cells & nucleic acids released by the tumors into a person’s body fluids

A

LIQUID BIOPSY

64
Q

LIQUID BIOPSY 2 approaches:

A
  1. Cell-free or circulating free nucleic acids
  2. Circulating tumor cells (CTC)
65
Q
  1. Cell-free or circulating free nucleic acids
    Targeted:
A

directed at specific mutations (sequencing/PCR methods)

66
Q
  1. Cell-free or circulating free nucleic acids
    Untargeted:
A

whole exomes or gene panels (sequencing & CGH)

67
Q

most frequent source material

A

Plasma DNA

68
Q

Mechanism of tumor metastases from 1 tissue site to another (2 to >50 cells)

A

Circulating tumor cells (CTC)

69
Q
  1. Circulating tumor cells (CTC)
    Isolation methods:
A

antibody capture, negative depletion of leukocytes

70
Q
  1. Circulating tumor cells (CTC)
    DNA:
A

allele-specific PCR or other sensitive methods

71
Q

Series of intrachromosomal recombination events mediated by recombinase enzymes that recognize specific sequences flanking the gene segments

A

GENE REARRANGEMENTS

72
Q

Normal intrachromosomal breaking & specific sequences flanking joining of DNA in the genes coding for immunoglobulins and T-cell receptors

A

V(D)J RECOMBINATION

73
Q

 Gene encoding the immunoglobulin heavy chain is located on chromosome 14
 As B lymphocytes mature, selected gene segments are joined together so that the rearranged gene contains only 1 of each V (variable), D (diversity) & J (joining) gene segments

A

Immunoglobulin heavy-chain gene rearrangement in B cells

MOLECULAR BIOLOGY (9 decks)

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