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Molecular Diagnostics > Lecture 9: Oncology > Flashcards

Lecture 9: Oncology Flashcards

1
Q

What must B and T cells be able to recognize?

A

a wide variety of antigens (diversity)

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2
Q

What allows for even more diversity in B and T cells?

A

Somatic mutation

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3
Q

How are surface immunoglobulin and T-cell receptors structurally similar?

A

Heterodimer proteins, disulfide bonds, have variable (V) and constant (C) regions

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4
Q

How are surface immunoglobulin and T-cell receptors genetically similar?

A

Have large number of exons DNA recombination to functional receptor

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5
Q

Surface Immunoglobulin and T-cell receptors are involved in what process?

A

antigen recognition (by normal B & T-cells)

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6
Q

For DNA recombination in B and T cells what are the segments that can be transcribed and translated to millions of antigen receptors?

A

V, D, J, and C

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7
Q

What can increase the sensitivity of T cells to peptide antigen MHC complexes by ~100 fold?

A

CD4 and CD8

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8
Q

What are gene rearrangements?

A

normal events, can occur in lymphocytes

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9
Q

What are the classes of immunoglobulins?

A

IgG, IgD, IgA, IgM, and IgE respectively

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10
Q

What are the immunoglobulin light chain genes?

A

k, λ (kappa and lambda)

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11
Q

What are immunoglobulin light chain genes encodes by?

A

immunoglobulin kappa and lamnda

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12
Q

Does rearrangement in each cells occur independently? or dependently?

A

independently

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13
Q

What genes rearrange?

A

T-cell receptor genes (α, β, γ, δ) rearrange

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14
Q

What defines the classes of immunoglobulins?

A

Antibody genes immunoglobulin heavy chain genes IgH (γ, δ, α, μ, ε)

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15
Q

What is the variable domain of heavy chain made of?

A

three segments (V, D, & J)

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16
Q

What residues does VH genes encodes?

A

residues 1-94

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17
Q

What residues does JK encode?

A

residues 98-113

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18
Q

What residues does D gene encode?

A

residues 95-97

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19
Q

51 V x 27 D x 6 J =8262 ???

A

Heavy chain??? idk about this one

Sarahboo it’s 8262 different combinations silly

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20
Q

What do heavy and light Ig chains undergo?

A

random gene rearrangement

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21
Q

TCR rearrangement vs. Ig rearrangement

A

they are VERY similar

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22
Q

What are the 7 means of generating antibody diversity?

A
  1. Multiple germ-line gene segments
  2. Combinatorial V-(D)-J- joining
  3. Junctional flexibility
  4. P-region nucleotide addition (P-addition)
  5. N-region nucleotide addition (N-addition)
  6. Somatic hypermutation
  7. Combinatorial association of light and
    heavy chains
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23
Q

Population of cells with similar characteristics that are all derived from a single precursor cell

A

clonality

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24
Q

Normal lymphocyte populations are ____ with respect to Ig and TCR genes

A

polyclonal

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25
Q

Leukemia or lymphoma is ______ with regard to Ig or TCR rearranged genes

A

monoclonal

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26
Q

Neoplastic transformation of B and T lymphocytes occurs at different stages of B-cells and T-cell development at which the disordered lymphoid cells ______ in the normal differentiation scheme

A

arrested

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27
Q

B lymphocyte: Benign (Clonality of Lymphoid Proliferation Disorder)

A

Ig Light Chain, Heterogeneity

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28
Q

Plasma Cells: Benign (Clonality of Lymphoid Proliferation Disorder)

A

Heterogeneous Ig Electrophoresis

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29
Q

T Lymphocyte: Benign (Clonality of Lymphoid Proliferation Disorder)

A

Heterogeneous Variable Regions

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30
Q

B lymphocyte: Malignant (Clonality of Lymphoid Proliferation Disorder)

A

Ig Kappa or Lambda Only

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31
Q

Plasma Cells: Malignant (Clonality of Lymphoid Proliferation Disorder)

A

Monoclonal Ig Spike

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32
Q

T Lymphocyte: Malignant (Clonality of Lymphoid Proliferation Disorder)

A

Homogeneous Variable Regions

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33
Q

What is tumor cell clonality caused by?

A

gene rearrangement

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34
Q

Are rearrangements unique in each cell?

A

yes

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35
Q

What do rearrangements display?

A

allelic exlusion

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36
Q

Techniques for Clonality Determination

A

Morphology
Immunopathology
Cytogenetics
Molecular genetics

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37
Q

What is Morphology?

A

Monomorphous cell population

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38
Q

What is Immunopathology?

A

Monotypic Sig

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39
Q

What is Cytogenetics?

A

Recurrent chromosomal alteration (e.g., translocation)

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40
Q

What is Molecular genetics?

A

Clonal B- or T-cell gene rearrangements methods

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41
Q

What are all the clonal B- or T-cell gene rearrangements methods?

A

-Hybridization, blotting
-Standard PCR, RT-PCR, electrophoresis
-PCR with heteroduplex analysis, SSCP
-Real-time PCR with gene or patient-specific probes

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42
Q

What is an increasingly popular method to evaluate for the presence of B- or T cell clonality?

A

Polymerase Chain Reaction

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43
Q

What is the polymerase chain reaction analogous to?

A

Southern blot

44
Q

Polymerase Chain Reaction uses _______ V and J segment primers (recognize shared DNA sequences)

A

consensus

45
Q

Polymerase Chain Reaction may detect a _____ clonal population?

A

0.1%

46
Q

Involves evaluation of segments of DNA that code for variable regions of immunoglobulin and T-cell receptors (V and J segments)

A

Polymerase Chain Reaction

47
Q

What is an example of PCR?

A

Poly/Monoclonal Lymphocyte Populations by PCR

48
Q

Monoclonal populations are detected by _____ unique to the tumor cell population

A

Sharp bands

49
Q

What will normal (polyclonal) population yield? (PCR)

A

A polyclonal PCR product

50
Q

What will monoclonal populations will yield? (PCR)

A

a single PCR product

51
Q

What are the 3 classes of cancer?

A

Carcinomas, Sarcomas, and Hematopoietic and lymphoid malignant neoplasm such as leukemia and lymphoma

52
Q

What classes of cancer are solid tumors?

A

Carcinomas and Sarcomas

53
Q

Originate in epithelial tissue, such as the cells lining the intestine, bronchi, or mammary ducts

A

Carcinomas

54
Q

The tumor has arisen in mesenchymal tissue, such as bone muscle or connective tissue, or in nervous system tissue

A

Sarcomas

55
Q

Spread throughout the bone marrow, lymphatic system, peripheral blood

A

Hematopoietic and lymphoid malignant neoplasms, such as leukemia and lymphoma

56
Q

What class of cancer are circulating tumors?

A

lymphoid tumors

57
Q

Tumors arise from a ______ that has accumulated critical initiating mutations (genetic changes) and perhaps other epigenetic alterations.

A

single ancestral cell

58
Q

Is the number of mutations dependent on the tumor type?

A

no it is independent

59
Q

How many mutations needed for tumor formation?

A

multiple

60
Q

In some cases, mutations causing tumors are

A

present in all cells (genetic predisposition)

61
Q

What are the multistage process of carcinogenesis?

A

normal cell to initiated cell to preneoplastic lesion to malignant tumor

62
Q

What is the clonal basis of cancer development?

A

-Defects in cellular differentiation
-Defects in growth control
-Resistance to cytotoxicity
-Activation of Protooncogenes
-Inactivation of of Tumor Suppressor Genes

63
Q

Molecular Detection- Differential PCR for Her2/neu Amplification. What is the process used?

A

Co-amplify by PCR and analyze by gel electrophoresis

64
Q

Hereditary Cancer Characters

A
  • Multiple affected relatives
  • Early age of cancer onset (clinical disease)
  • Bilaterally affected organs (such as in breast cancer)
  • Multiple primary cancers in the same individual
  • Known associated cancers occurring in the same family (such as breast and
    ovarian cancers)
  • Autosomal dominant of inheritance
65
Q

Mutations in what genes are inherited in an autosomal dominant pattern? What does that mean?

A

BRCA1 & BRCA2
one copy of altered gene in each cell is sufficient to increase a person’s chance of developing cancer

66
Q

What chromosome arm is breast cancer susceptibility gene: BRCA1 localized to?

A

arm 17q

67
Q

How many different mutations have been identified in BRCA1 gene?

A

120

68
Q

The BRCA1 gene is mutated in what percentage of hereditary breast cancers?

A

45%

69
Q

The BRCA1 gene is mutated in what percentage of patients with breast/ovarian cancer?

A

90%

70
Q

What are the features of the BRCA1 gene?

A

23 exons, large exon 11 (100kb) that contains 60% of coding sequence

71
Q

What is the BRCA1 protein expression and phosphorylation dependent on?

A

the cell cycle

72
Q

What is BRCA1 protein?

A

large nuclear phosphoprotein

73
Q

The BRCA1 Protein is probably a ____ and involved in ___

A

DNA- binding transcription factor; DNA repair ***

74
Q

What arm is breast cancer susceptibility gene BRCA2 localized to?

A

arm 13q

75
Q

What percentage of early onset hereditary breast cancer does BRCA2 gene account for?

A

40-45%

76
Q

Do mutations in BRCA2 gene contribute significantly to risk for development of ovarian cancer?

A

NO

77
Q

How big is the BRCA2 gene?

A

70 kb in size, 27 exons

78
Q

BRCA2 is required to prevent breakdown of the stalled ______

A

replication forks***

79
Q

BRCA2 gene and protein disruption of function leads to?

A

chromosomal rearrangements

80
Q

Mutation in the BRCA2 gene and protein may cause ______ and predisposition to cancer.

A

genomic instability***

81
Q

Prevalence of BRCA gene mutation is more common in what community?

A

Ashkenazi Jewish Community (185del AG; 5382ins C; 6174 del T)

82
Q

How to know if there is a mutation of BRCA1 185delAG present by SSP-PCR?

A

The 180bp product indicates the present of mutation

83
Q

What is the 3rd most common non-skin cancer diagnosed in men and women in the U.S and second highest cause of cancer deaths?

A

Colorectal Cancer

84
Q

Is colorectal cancer?

A

highly curable when it is detected early enough

85
Q

Molecular CRC Testing

A
  • MSI, MMR IHC ***
    – MSI-H Sporadic (15%)
    – MSI-H Lynch (2-3%)
  • KRAS ***
  • BRAF ***
  • PIK3CA
  • PTEN
  • APC, SMAD4, BMPRIA,STK11
  • Septin 9
86
Q

Detection Methods for CRC

A

Tumor screening assay (90% sensitivity)

87
Q

Detect affected patients with tumor MSI by…

A

– PCR (paraffin works well)
– MMR Immunohistochemistry: MLH-1, MSH-2, MSH-6,
PMS2
– Blood germ line mutation analysis
– Detect affected family members

88
Q

Tumor screening assays for CRC has ___% sensitivity

A

90%

89
Q

KRAS mutation in ___-____% CRC’s

A

30-40%

90
Q

~__% of colorectal cancers have BRAF mutations?

A

10%

91
Q

What does KRAS and BRAF Detection highly predict?

A

lack of response to anti-EGFR Rx

92
Q

What plays a key role in determining proper and most cost-effective Rx in stage III-IV CRC?

A

Laboratory

93
Q

What downstream marker may be useful in KRAS wild type tumors?

A

BRAD, PIK3CA, PTEN

94
Q

What are molecular test for KRas?

A

-Sequencing, Sequenom, allele
-Specific PCR, and melt curve analysis

95
Q

What predicts anti-EGFR non-response in KRAS WT?

A

KRAS and BRAF detection

96
Q

What is the BRAF mutation (BRAF V600E)?

A

-T to A transversion
-Valine to glutamate at codon 600 (BRAF V600E)

97
Q

What percentage of Hereditary Non-Polyposis Colorectal Carcinoma (HNPCC) have MSI?

A

85-90%

98
Q

What is inferred by testing for MSI?

A

mutations in genes of the MMR system (loss of function)

99
Q

What does MSI analysis determine?

A

gene function

100
Q

What is direct sequencing used to detect?

A

actual gene mutation

101
Q

What are the two major types of lung cancer?

A

Small Cell Lung Cancer (SCLC)
Non-Small Cell Lung Cancer (NSCLC)

102
Q

What percentage of lung cancers are NSCLC?

A

85-90%

103
Q

What is it called when lung cancer has characteristics of both types? Is it common?

A

mixed small cell/large cell cancer; NOT common

104
Q

What is the leading cause of lung cancer?

A

Smoking

105
Q

What percentage of lung cancer deaths are linked to smoking?

A

80% (many others are caused by exposure to secondhand smoke)

106
Q

American Cancer Society Guideline 2018: Tests for Newly Diagnosed NSCLC Patients

A

-Low-dose CT scans for lung cancer screening
-Biomarker Detection

107
Q

What is the minimum necessary for biomarker detection of NSCLC patients?

A

PD-L1 IHC, EGFR, ALK, ROS1, BRAF

Molecular Diagnostics (12 decks)

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