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Molecular Diagnostics > Molecular Identification of Somatic Mutations in Cancers > Flashcards

Molecular Identification of Somatic Mutations in Cancers Flashcards

1
Q

Stochastic

A

Randomly occurred

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2
Q

Genetic Drift

A

Variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce.

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3
Q

Punctuation (tumor growth)

A

A catastrophic event that induces a radical change in phenotype, typically followed by strong selection for that phenotype.

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4
Q

Chromothripsis

A

A mutational process of clustered chromosomal rearrangements occurs in a single event in localized and confined genomic regions in one or a few chromosomes,

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5
Q

Chromoplexy

A

Multiple chromosomes are involved in chains of translocations.

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6
Q

Kataegesis

A

Localized hypermutation resulting in many single-base-pair changes in a small region.

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7
Q

Linear Evolution

A

The process where successively fitter mutants arise and sweep to fixation, replacing less fit lineages.

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8
Q

Branched Evolution

A

Multiple subclones, each with different selective growth advantages and effectively a distinct phenotype, co-occur within the tumor.

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9
Q

Neutral Evolution

A

New mutations confer no fitness advantage, and

lineage size is determined by time of emergence. The absence of selection.

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10
Q

Fitness

A

In tumors, it is intuitively understood as the net growth rate of lineages relative to other lineages.

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11
Q

Mechanistic

A

In purely physical terms.

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12
Q

Proliferation

A

The ability of cells to evade the homeostatic regulation of physiologically normal tissues.

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13
Q

Negative Selection

A

Also known as purifying selection. When subclones that have reduced fitness are more likely to be lost or remain at low frequencies within the population. This type of selection is particularly important in the context
of how the immune system interacts with cancer cells and is critical for predicting the efficacy of
immunotherapy.

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14
Q

Neoantigens

A

Mutations that cause cell surface markers that can be recognized by the immune system.

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15
Q

Subclone

A

A subpopulation of cells that descended from another clone but then diverged by accumulating another driver mutation.

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16
Q

Genome Doubling

A

A common feature of cancer evolution (∼30% of cases) and is thought to be a driver of copy number instability.

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17
Q

Passenger Mutations

A

Mutations that do not provide a selective growth advantage, and thus do not promote cancer development.

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18
Q

Structural Variants

A

Large genomic alterations, encompassing at least 50 bp.

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19
Q

Copy Number Alterations

A

Somatic changes to chromosome structure that result in gain or loss in copies of sections of DNA, and are prevalent in many types of cancer.

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20
Q

Hypermutation

A

Mutation that is abnormally frequent.

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21
Q

Somatic

A

Originating in the body.

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22
Q

Germline

A

The cells that form the egg, sperm and the fertilized egg.

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23
Q

Synonymous Mutation

A

A change in the DNA sequence that codes for amino acids in a protein sequence, but does not change the encoded amino acid.

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24
Q

Nonsynonymous Mutation

A

A change in the DNA sequence that codes for amino acids in a protein sequence and does change the encoded amino acid.

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25
Q

Progeny

A

A descendant.

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26
Q

Squamous

A

Spindle cell differentiation.

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27
Q

Spindle Cell

A

Cell that is longer than wide, seen in some sarcomas.

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28
Q

Sarcoma

A

A rare type of cancer that grows in connective tissue like bones, nerves, muscles, tendons, cartilage and blood vessels of the arms and legs.

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29
Q

Phylogenetic

A

Relating to the evolutionary development and diversification of a species or group of organisms, or of a particular feature of an organism.

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30
Q

Neoplasm

A

A new and abnormal growth of tissue in some part of the body, especially as a characteristic of cancer.

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31
Q

Oncogenic

A

Causing development of a tumor

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32
Q

CRISPR Genome Editing

A

A genetic engineering technique in molecular biology by which the genomes of living organisms may be modified. It is based on a simplified version of the bacterial CRISPR - Cas9 antiviral defense system.

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33
Q

Gliobastoma

A

A cancerous tumor which develops in the brain.

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34
Q

Deep Sequencing

A

Measures the sizes of the lineages within a population.

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35
Q

High Fidelity Sequencing

A

High accuracy and long read sequencing

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36
Q

Multiregion Sequencing

A

Reveals the transcriptional landscape of the immune microenvironment.

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37
Q

Adenomas

A

Benign tumors starting in the epithelial tissue of a gland or gland-like structure.

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38
Q

Epithelial Tissue

A

The thin layer of tissue covering organs, glands, and other structures.

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39
Q

Carcinoma

A

A type of cancer that starts in cells that make up the skin or the tissue lining organs, such as the liver or kidneys.

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40
Q

Intratumor Heterogeneity

A

Integration of inputs from genetic, phenotypic, and microenvironmental heterogeneity, in turn increasing the odds of both pre-existence of tolerant and resistant subpopulations, and the ability to evolve new adaptations.

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41
Q

Whole-exome Sequencing

A

Next-generation sequencing (NGS) method that involves sequencing the protein-coding regions of the genome.

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42
Q

Cell Renal Carcinoma

A

A disease in which malignant (cancer) cells form in tubules of the kidney.

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43
Q

Heterogeinety

A

The state of being diverse in character.

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44
Q

Lymphoma

A

A cancer of the lymphatic system of the body involving immune cells.

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45
Q

Lymphatic System

A

An organ system that is part of the immune system, and complementary to the circulatory system. It is made up of a large network of lymphatic vessels, lymph nodes, lymphatic or lymphoid organs, and lymphoid tissues. The vessels carry a clear fluid called lymph back towards the heart, for re-circulation.

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46
Q

Lymphatic Vessel

A

A thin tube that carries lymph (lymphatic fluid) and white blood cells through the lymphatic system.

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47
Q

Lymph Node

A

Small structures that work as filters for harmful substances. They contain immune cells that can help fight infection by attacking and destroying germs that are carried in through the lymph fluid.

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48
Q

Lymphatic Organs

A

Lymphoid organs. Bone marrow, thymus, spleen, lymph nodes, tonsils, and mucous membranes.

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49
Q

Lymphoid Tissues

A

Cells and organs that make up the lymphatic system, such as white blood cells (leukocytes), bone marrow, and the thymus, spleen, and lymph nodes. Lymphoid tissue has several different structural organizations related to its particular function in the immune response.

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50
Q

Lymph

A

A colorless fluid containing white blood cells, which bathes the tissues and drains through the lymphatic system into the bloodstream.

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51
Q

Thymus

A

An organ that is part of the lymphatic system, in which T lymphocytes grow and multiply. The thymus is in the chest behind the breastbone.

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52
Q

Spleen

A

An organ that is located in the upper-left part of the abdomen, not far from the stomach, that produces lymphocytes, which are important elements in the immune system. The spleen is the largest lymphatic organ in the body.

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53
Q

Tonsils

A

Part of the body’s immune system. Because of their location at the throat and palate, they can stop germs entering the body through the mouth or the nose. The tonsils also contain a lot of white blood cells, which are responsible for killing germs.

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54
Q

Leukocytes

A

White blood cells. The cells of the immune system that are involved in protecting the body against both infectious disease and foreign invaders. They are produced and derived from multipotent cells in the bone marrow known as hematopoietic stem cells. They are found throughout the body, including the blood and lymphatic system.

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55
Q

Lymphocyte

A

A type of white blood cell in the immune system, includes natural killer cells, T cells, and B cells. They are the main type of cell found in lymph, which prompted the name “lymphocyte”.

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56
Q

T Cells

A

Lymphocyte immune cells that protect the body from pathogens and cancer cells.

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57
Q

Hamatopoietic Stem Cells

A

The stem cells that give rise to other blood cells.

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58
Q

Killer Cells

A

A white blood cell which destroys infected or cancerous cells.

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59
Q

B Cells

A

A type of white blood cell that makes antibodies, part of the immune system, and develop from stem cells in the bone marrow.

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60
Q

Truncal

A

Of or affecting the trunk of the body, or of a nerve.

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61
Q

Ubiquitous

A

Found everywhere.

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62
Q

Single-cell Sequencing

A

Examines the sequence information from individual cells with optimized next-generation sequencing (NGS) technologies, providing a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment. In cancer, sequencing the DNA of individual cells can give information about mutations carried by small populations of cells.

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63
Q

Elucidate

A

To make something clear.

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64
Q

Transcriptome

A

The sum total of all the messenger RNA molecules expressed from the genes of an organism.

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65
Q

Epigenome

A

A record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism’s offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.

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66
Q

Immune Cell Repertoire

A

Encompasses the different sub-types an organism’s immune system makes of immunoglobulins or T-cell receptors. These help recognize pathogens. The sub-types, all differing slightly from each other, can amount to tens of thousands, or millions in a given organism. Such a wide variety increases the odds of having a sub-type that recognizes one of the many pathogens an organism may encounter. Too few sub-types and the pathogen can avoid the immune system, unchallenged, leading to disease.

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67
Q

Immunoglobulins

A

Any of a class of proteins present in the serum and cells of the immune system, which function as antibodies.

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68
Q

Morphological

A

Relating to the form or structure of things.

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69
Q

Multi-omics

A

A biological analysis approach in which the data sets are multiple “omes”, such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome.

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70
Q

Splice-site Mutations

A

RNA sequence changes that alter or abolish correct mRNA splicing during the process of precursor mRNA maturation. Splice site mutations can result in the complete skipping of one or more exons, retention of introns, creation of a pseudo-exon, or activation of a cryptic splice site within an exon or an intron.

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71
Q

Pseudo-exons

A

Intronic sequences that are flanked by apparent consensus splice sites but that are not observed in spliced mRNAs.

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72
Q

Cryptic Splice Site

A

A mRNA sequence that has the potential for interacting with the spliceosome. Mutations, including splice site mutations, in the underlying DNA or errors during transcription can activate a cryptic splice site in part of the transcript that usually is not spliced.

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73
Q

Isoforms

A

Any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence

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74
Q

Myeloid

A

Having to do with or resembling the bone marrow. May also refer to certain types of hematopoietic (blood-forming) cells found in the bone marrow.

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75
Q

Polyposis

A

A condition characterized by the presence of numerous internal polyps, especially a hereditary disease (familial adenomatous polyposis) which affects the colon and in which the polyps may become malignant.

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76
Q

Tumorigenesis

A

The production or formation of a tumor or tumors.

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77
Q

Growth Arrest

A

Any damage to the growth plate. This damage can be caused by fractures, infection, benign bone tumors, developmental conditions (e.g., Blount disease ), metabolic conditions or a lack of blood supply to the growth plate.

78
Q

Angiogenesis

A

The development of new blood vessels.

79
Q

Missense Mutations

A

A point mutation in which a single nucleotide change results in a codon that codes for a different amino acid.

80
Q

Nonsense Mutations

A

A point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product.

81
Q

UTRs

A

Untranslated regions.

82
Q

Polynucleotide Tracts

A

A repeat of three or more of single or double nucleotides.

83
Q

Kataegis

A

A pattern of localized hypermutations identified in some cancer genomes, in which a large number of highly patterned basepair mutations occur in a small region of DNA. The mutational clusters are usually several hundred basepairs long, alternating between a long range of C→T substitutional pattern and a long range of G→A substitutional pattern. This suggests that kataegis is carried out on only one of the two template strands of DNA during replication. Compared to other cancer-related mutations, such as chromothripsis, kataegis is more commonly seen; it is not an accumulative process but likely happens during one cycle of replication.

84
Q

Gene Expression Signatures

A

A single or combined group of genes in a cell with a uniquely characteristic pattern of gene expression that occurs as a result of an altered or unaltered biological process or pathogenic medical condition.

85
Q

Kinase

A

An enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule.

86
Q

Metazoan

A

Multicellular, mitochondrial eukaryotes. Today Metazoa encompasses all animals with differentiated tissues, including nerves and muscles.

87
Q

Rhabdoid Tumors

A

An aggressive pediatric soft tissue sarcoma that arises in the kidney, the liver, the peripheral nerves and all miscellaneous soft-parts throughout the body. RT involving the central nervous system (CNS) is called atypical teratoid rhabdoid tumor. RT usually occurs in infancy or childhood.

88
Q

Chromoanasynthesis

A

Characterized by the presence of chromosomal duplications and triplications locally clustered on one single chromosome, or a few chromosomes, associated with various other types of structural rearrangements.

89
Q

Whole-Genome Sequencing

A

The process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism’s genome at a single time. This entails sequencing all of an organism’s chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.

90
Q

Chromatin Immunoprecipitation Sequencing

A

A type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites, and possibly defining cistromes. ChIP also aims to determine the specific location in the genome that various histone modifications are associated with, indicating the target of the histone modifiers.

91
Q

Luciferase Assay

A

Used to investigate a variety of cellular processes using bioluminescent light output as a sensitive measure of biological activity.

92
Q

Luciferase

A

A generic term for the class of oxidative enzymes that produce bioluminescence and is usually distinguished from a photoprotein.

93
Q

Hypermethylation

A

An increase in the epigenetic methylation of cytosine and adenosine residues in DNA.

94
Q

Epigenome

A

A record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism’s offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.

95
Q

Trimethylation

A

The addition of three methyl groups, especially to an amine of a chromatin.

96
Q

Amine

A

An organic compound derived from ammonia by replacement of one or more hydrogen atoms by organic groups.

97
Q

Transcriptional Repressors

A

Proteins that bind to promoters in a way that impedes subsequent binding of RNA polymerase. Although this repression mechanism is found at several promoters, there is a growing list of repressors that inhibit transcription initiation in other ways.

98
Q

Adenocarcinoma

A

Cancers that start in glandular tissues that make mucus or fluid, such as the lung, breast, prostate, or colon. Adenocarcinomas are considered a specific type (subtype) of carcinomas.

99
Q

DNA Methyltransferase

A

A family of enzymes that catalyzes the transfer of a methyl group to DNA. DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine as the methyl donor.

100
Q

Retrotransposition

A

Gene duplication is often mediated by this, whereby a gene is duplicated at a new location thanks to the action of genetic elements called retrotransposons.

101
Q

Retrotransposons

A

Also called Class I transposable elements or transposons via RNA intermediates. A type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the process reverse transcription using an RNA transposition intermediate.

102
Q

Microsatellite Instability

A

The condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR). The presence of MSI represents phenotypic evidence that MMR is not functioning normally.

103
Q

Genome Instability

A

Also, genetic instability or genomic instability. Refers to a high frequency of mutations within the genome of a cellular lineage. These mutations can include changes in nucleic acid sequences, chromosomal rearrangements or aneuploidy. Occurs in bacteria. In multicellular organisms, genome instability is central to carcinogenesis, and in humans it is also a factor in some neurodegenerative diseases such as amyotrophic lateral sclerosis or the neuromuscular disease myotonic dystrophy.

104
Q

Macroadenomas

A

A tumor that typically develops in the pituitary gland, a pea-sized organ behind the eyes. They are almost always noncancerous.

105
Q

Hepatellocellular Carcinoma

A

The most common form of liver cancer often seen in people with chronic liver diseases like cirrhosis.

106
Q

Somatic Mosaicism

A

The genetic heterogeneity resulting from somatic mutations.

107
Q

Copy Number Variants

A

A section of the genome that has a different number of repeats or copies than the reference genome.

108
Q

Transposable Element

A

A sequence of DNA that, either via an RNA intermediate (retrotransposons) or a DNA intermediate (DNA transposons), can relocate within a genome.
Active TEs include L1 and Alu elements.

109
Q

Variant Allele Fractions

A

The fraction of sequencing reads in a sample corresponding to the non-reference allele. For bulk sequencing data, this is an estimate of the frequency of DNA molecules carrying the variant.

110
Q

Bulk Sequencing

A

The sequencing of DNA extracted from a large number of cells from the same individual.

111
Q

Mesoderm

A

The middle layer of an embryo in early development, between the endoderm and ectoderm.

112
Q

Ectoderm

A

The outer layer of an embryo in early development.

113
Q

Phasing

A

The process of statistical estimation of the haplotypes of an individual by using the variants in their genome, also called haplotype estimation.

114
Q

Post-mitotic Cell Types

A

Mature muscle and neuronal cells. Post-mitotic cells cannot be stimulated to proliferate by any physiological stimulus, nor by non- physiological stimuli such as carcinogens, irradiation or oncogene expression. In contrast to mitotic cells, post-mitotic cells never undergo tumorigenic transformation.

115
Q

Whole-genome Amplification

A

The amplification of a single genome, or a similarly limited amount of DNA, to generate sufficient DNA
for sequencing. WGA is necessary for single-cell DNA sequencing.

116
Q

Amplification Bias

A

The differential amplification of a region of DNA

relative to another, resulting in unequal coverage across the genome.

117
Q

Allelic Imbalance

A

Allele Dropout. A difference in the sequencing of two
alleles caused by differential amplification (allelic imbalance) or amplification failure (allele dropout) of
one allele. This is a frequent source of error in single-cell DNA sequencing.

118
Q

Artifacts

A

Variations introduced by non-biological processes. Artifacts can arise from various sources, including damaged templates preexisting in FFPE DNA, oxidative DNA damage during sample preparation, DNA polymerase error, pseudogene amplification, adaptor sequences and adaptor chimeras, sequencing chemistry, sequence alignment, and spontaneous deamination of nucleotides during thermocycling.

119
Q

Hemodilute

A

Not having sufficient number of white blood or tumor cells in that draw.

120
Q

Coverage

A

The number of reads overlapping a region in DNA
sequencing, also known as depth. Sequence coverage can also refer to the average number of reads
covering loci across the entire genome.

121
Q

Haplotype

A

A segment of DNA that is inherited as a block from a single parent.

122
Q

Somatic Mosaicism

A

The presence in an individual of at least two genetically distinct populations of cells that arise from somatic mutation(s).

123
Q

Clinicopathologic

A

Relating to or concerned both with the signs and symptoms directly observable by the physician and with the results of laboratory examination.

124
Q

Lobular Carcinomas

A

A type of breast cancer that begins in the milk-producing glands (lobules) of the breast.

125
Q

Mucinous Tumors

A

A very rare type of invasive breast cancer and the mucus along with the cancer cells form a jelly type of tumor inside the breasts. Mastectomy is one such treatment that helps in treating mucinous breast cancer as it results in removing as much of the breast tissues as possible. A simple mastectomy procedure is one where the patient diagnosed with mucinous breast cancer needs to undergo removal of the infected breast without removal of the lymph nodes in the armpit area.

126
Q

Cribriform Breast Cancer

A

A rare type of breast cancer. It’s usually slow growing and low grade. This means generally people with cribriform breast cancer have a good outlook (prognosis) after treatment. Cribriform breast cancer may be mixed with other types of breast cancer. If it’s not mixed with another type, it’s called pure cribriform. Cribriform cancer cells can also be found in a type of early breast cancer called DCIS (ductal carcinoma in situ).

127
Q

Micropapillary

A

A type of otherwise ‘typical‘ invasive ductal carcinoma which exhibits a unique and characteristic growth pattern.

128
Q

Invasive Breast Cancer

A

The cancer cells have broken out of the lobule where they began and have the potential to spread to the lymph nodes and other areas of the body.

129
Q

Ductal Carcinoma

A

The presence of abnormal cells inside a milk duct in the breast. DCIS (Ductal Carcinoma In Situ) is considered the earliest form of breast cancer. DCIS is noninvasive, meaning it hasn’t spread out of the milk duct to invade other parts of the breast.

130
Q

Papillary

A

A malignant epithelial tumor showing evidence of follicular cell differentiation and characterized by distinctive nuclear features.

131
Q

Follicular

A

Of the nature of, composed of, or characteristic of a follicle or follicles.

132
Q

Follicle

A

A small secretory cavity, sac, or gland.

133
Q

Cellular Differentiation

A

The process in which a cell changes from one cell type to another. Usually, the cell changes to a more specialized type. Differentiation occurs numerous times during the development of a multicellular organism as it changes from a simple zygote to a complex system of tissues and cell types. Differentiation continues in adulthood as adult stem cells divide and create fully differentiated daughter cells during tissue repair and during normal cell turnover. Some differentiation occurs in response to antigen exposure. Differentiation dramatically changes a cell’s size, shape, membrane potential, metabolic activity, and responsiveness to signals. These changes are largely due to highly controlled modifications in gene expression and are the study of epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself. Although metabolic composition does get altered quite dramatically where stem cells are characterized by abundant metabolites with highly unsaturated structures whose levels decrease upon differentiation. Thus, different cells can have very different physical characteristics despite having the same genome.

134
Q

Tubular Breast Cancer

A

A type of invasive ductal breast cancer that accounts for less than 2% of all breast cancers. Like other types of invasive ductal cancer, tubular breast cancer begins in the milk duct of the breast before spreading to the tissues around the duct. When the cells of a tubular breast tumor are examined under a microscope, they look like tubes, which gives this cancer its name.

135
Q

Medullary Breast Cancer

A

A very rare type of invasive ductal breast cancer which accounts less than 5% of all breast cancers. Medullary breast cancer is somewhat more common in people who are carriers of a genetic mutation known as BRCA-1. Like other types of invasive ductal cancer, medullary breast cancer begins in the milk duct of the breast before spreading to the tissues around the duct. It is called “medullary” because when pathologists first looked at these tumors, they were reminded of the grayish soft tissue in the brainstem, or medulla.

136
Q

Metaplastic Breast Cancer

A

A very uncommon type of breast cancer. It is a form of invasive ductal cancer, meaning that it forms in the milk ducts and then moves into other tissues of the breast.

137
Q

Apocrine Breast Cancer

A

A specific type of invasive ductal carcinoma (or infiltrating ductal carcinoma) of breast that initially affects the milk ducts and moves on to involve other parts of the breast. Apocrine Carcinoma of Breast is called as such because of the “apocrine” pattern, which is visible when a breast biopsy specimen is examined by a pathologist under a microscope. It is a very rare type of breast cancer.

138
Q

Pleomorphism

A

The occurrence of more than one distinct form of a natural object, such as the cells in a tumor at different stages of the life cycle.

139
Q

Basal-like Breast Cancer

A

A particularly aggressive molecular subtype defined by a robust cluster of genes expressed by epithelial cells in the basal or outer layer of the adult mammary gland.

140
Q

Proteomic

A

The large-scale study of proteins.

141
Q

Mesechyme

A

A loosely organized, mainly mesodermal embryonic tissue which develops into connective and skeletal tissues, including blood and lymph.

142
Q

Mucin

A

A family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most animals. Key characteristic is their ability to form gels; therefore, they are a key component in most gel-like secretions, serving functions from lubrication to cell signaling to forming chemical barriers. They often take an inhibitory role. Some mucins are associated with controlling mineralization, including bone formation in vertebrates. They bind to pathogens as part of the immune system. Overexpression of the mucin proteins, especially MUC1, is associated with many types of cancer.

143
Q

Cytokeratins

A

Keratin proteins found in the intracytoplasmic cytoskeleton of epithelial tissue. They are an important component of intermediate filaments, which help cells resist mechanical stress. Expression of these cytokeratins within epithelial cells is largely specific to particular organs or tissues. Thus, they are used clinically to identify the cell of origin of various human tumors.

144
Q

Keratin Proteins

A

One of a family of structural fibrous proteins also known as scleroproteins. Alpha-keratin (α-keratin) is a type of keratin found in vertebrates. It is the key structural material making up scales, hair, nails, feathers, horns, claws, hooves, and the outer layer of skin among vertebrates. Keratin also protects epithelial cells from damage or stress. Keratin is extremely insoluble in water and organic solvents. Keratin monomers assemble into bundles to form intermediate filaments, which are tough and form strong unmineralized epidermal appendages found in reptiles, birds, amphibians, and mammals. Excessive keratinization participates in fortification of certain tissues such as in horns of cattle and rhinos, and armadillos’ osteoderm. The only other biological matter known to approximate the toughness of keratinized tissue is chitin. Keratin comes in two types, the primitive, softer forms found in all vertebrates and harder, derived forms found only among sauropsids (reptiles and birds). Keratin resists digestion, which is why cats regurgitate hairballs.

145
Q

Neoadjuvant

A

Of, relating to, or being treatment (such as chemotherapy or hormone therapy) administered before primary cancer treatment (such as surgery) to enhance the outcome of primary treatment.

146
Q

Leptomeninges

A

The inner two meninges between which circulates the cerebrospinal fluid.

147
Q

Meninges

A

A layered unit of membranous connective tissue that covers the brain and spinal cord. These coverings encase central nervous system structures so that they are not in direct contact with the bones of the spinal column or skull. Each layer of the meninges serves a vital role in the proper maintenance and function of the central nervous system.

148
Q

Cerebrospinal Fluid

A

A clear, colorless body fluid found within the tissue that surrounds the brain and spinal cord of all vertebrates. There is about 125 mL of CSF at any one time, and about 500 mL is generated every day. CSF acts as a cushion or buffer, providing basic mechanical and immunological protection to the brain inside the skull.

149
Q

Adenosquamous

A

A rare variant of metaplastic breast cancer characterized by well-developed gland formation mixed with solid nests of squamous cells in a spindle cell background.

150
Q

Basaloid

A

Resembling that which is basal, but not necessarily basal in origin or position.

151
Q

Basal

A

Forming or belonging to a bottom layer or base.

152
Q

PSA

A

Prostate Specific Antigen. A protein produced by normal, as well as malignant, cells of the prostate gland. The PSA test measures the level of PSA in a man’s blood.

153
Q

Protease

A

An enzyme which breaks down proteins and peptides.

154
Q

Benign Prostatic Hyperplasia

A

BPH. Enlarged prostate. A condition in which the flow of urine is blocked due to the enlargement of prostate gland. The symptoms include increased frequency of urination at night and difficulty in urinating.

155
Q

Circulating Tumor Cell

A

A cell that has shed into the vasculature or lymphatics from a primary tumor and is carried around the body in the blood circulation. CTCs can extravasate and become seeds for the subsequent growth of additional tumors (metastases) in distant organs, a mechanism that is responsible for the vast majority of cancer-related deaths. The detection and analysis of CTCs can assist early patient prognoses and determine appropriate tailored treatments.

156
Q

Prostatectomy

A

Surgery to remove part or all of the prostate gland.

157
Q

Tumorigenesis

A

The production or formation of a tumor or tumors.

158
Q

Tumor Microenvironment

A

TME. Different cellular, including immune cells, and non-cellular components in and around the tumor. The TME has been recognized to play a significant role in tumor progression.

159
Q

Micrometastasis

A

A small collection of cancer cells that has been shed from the original tumor and spread to another part of the body through the lymphovascular system. Micrometastases are too few, in size and quantity, to be picked up in a screening or diagnostic test, and therefore cannot be seen with imaging tests.

160
Q

Extracellular Matrix

A

A three-dimensional network consisting of extracellular macromolecules and minerals, such as collagen, enzymes, glycoproteins and hydroxyapatite that provide structural and biochemical support to surrounding cells. Because multicellularity evolved independently in different multicellular lineages, the composition of ECM varies between multicellular structures; however, cell adhesion, cell-to-cell communication and differentiation are common functions of the ECM.

161
Q

Fibroblasts

A

A type of biological cell that synthesizes the extracellular matrix and collagen, produces the structural framework for animal tissues, and plays a critical role in wound healing. Fibroblasts are the most common cells of connective tissue in animals.

162
Q

Myofibroblasts

A

A cell phenotype that was first described as being in a state between a fibroblast and a smooth muscle cell.

163
Q

Mesenchymal Stem Cells

A

(MSCs) also known as mesenchymal stromal cells or medicinal signaling cells. Multipotent stromal cells that can differentiate into a variety of cell types, including osteoblasts (bone cells), chondrocytes (cartilage cells), myocytes (muscle cells) and adipocytes (fat cells which give rise to marrow adipose tissue).

164
Q

Neuroendocrine Cells

A

Cells that receive neuronal input and, as a consequence of this input, release message molecules into the blood. In this way they bring about an integration between the nervous system and the endocrine system, a process known as neuroendocrine integration.

165
Q

Adipose Cells

A

Body fat, or simply fat is a loose connective tissue composed mostly of adipocytes. In addition to adipocytes, adipose tissue contains the stromal vascular fraction (SVF) of cells including preadipocytes, fibroblasts, vascular endothelial cells and a variety of immune cells such as adipose tissue macrophages.

166
Q

PTEN

A

Phosphatase and tensin homolog is a phosphatase, in humans, is encoded by the PTEN gene. Mutations of this gene are a step in the development of many cancers, specifically glioblastoma, lung cancer, breast cancer, and prostate cancer.

167
Q

Cytokines

A

A broad and loose category of small proteins important in cell signaling. Cytokines are peptides and cannot cross the lipid bilayer of cells to enter the cytoplasm. Cytokines have been shown to be involved in autocrine, paracrine and endocrine signaling as immunomodulating agents.

168
Q

Chemokines

A

Any of a class of cytokines with functions that include attracting white blood cells to sites of infection.

169
Q

Ubiquintation

A

A form of post-translational modification in which the ubiquitin-protein is attached to a substrate protein.

170
Q

Ubiquitin

A

A small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ubiquitously.Four genes in the human genome code for ubiquitin: UBB, UBC, UBA52 and RPS27A.

171
Q

DNA Oxidation

A

The process of oxidative damage of DNA. It occurs most readily at guanine residues due to the high oxidation potential of this base relative to cytosine, thymine, and adenine. It is widely believed to be linked to certain disease and cancers.

172
Q

DNA Phosphorylation

A

The process by which phosphate groups are added to a molecule by a kinase. The phosphorylation status of a fragment of DNA can influence its ability to proceed in reactions.

173
Q

Sumoylation

A

A critical regulator of many diverse cellular processes, including transcription, DNA replication, cell-cycle progression, mitochondrial dynamics, ribosome biogenesis, DNA repair, apoptosis and stress responses.

174
Q

Sporadic Cancer

A

Certain cells in the body developed mutations that led to cancer. In sporadic cancer, only the tumor cells have mutations. In hereditary cancer, every cell in the person’s body has a mutation. Most cancers are considered sporadic.

175
Q

PTEN Harmartoma Tumor Syndrome

A

A genetic condition in which non-cancerous growths, called hamartomas, develop in different areas of the body. In addition to hamartomas, patients can have other physical findings, including larger-than-average head size, abnormal skin growths, and intellectual disabilities.

176
Q

Haploinsufficiency of Tumor Suppressor Genes

A

Indicates that the reduced levels of proteins in cells that lack one allele of the genomic locus results in the inability of the cell to execute normal cellular functions contributing to tumor development.

177
Q

Hyplomorphic

A

Genetics showing a loss of gene function.

178
Q

Metazoan

A

Prostate cancer antigen 3 is a gene that expresses a non-coding RNA. PCA3 is only expressed in human prostate tissue, and the gene is highly overexpressed in prostate cancer.

179
Q

Adenosine Deaminase

A

An enzyme (EC 3.5.4.4) involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues.

180
Q

DHT

A

Dihydrotestosterone, which is an endogenous androgen sex hormone. This hormone, which is converted from testosterone (another androgen, which basically means “male hormone”), is associated with many masculine physical characteristics.

181
Q

Angiogenesis

A

The development of new blood vessels.

182
Q

Prostatitis

A

Prostate inflammation.

183
Q

BPH

A

Benign Prostatic Hyperplasia. A condition in which the flow of urine is blocked due to the enlargement of prostate gland. The symptoms include increased frequency of urination at night and difficulty in urinating.

184
Q

Parenchyma

A

The functional tissue of an organ as distinguished from the connective and supporting tissue.

185
Q

HG-PIN

A

High-grade prostatic intraepithelial neoplasia. An abnormality of prostatic glands and believed to precede the development of prostate adenocarcinoma (the most common form of prostate cancer). It may be referred to simply as prostatic intraepithelial neoplasia (PIN).

186
Q

Pathogenesis

A

The process by which a disease or disorder develops. It can include factors which contribute not only to the onset of the disease or disorder, but also to its progression and maintenance.

187
Q

PI 3-kinase

A

A family of enzymes involved in cellular functions such as cell growth, proliferation, differentiation, motility, survival and intracellular trafficking, which in turn are involved in cancer.

188
Q

Elucidation

A

Clarification.

189
Q

Double-holiday Junction

A

Important intermediates of homologous recombination. The separate junctions can each be cleaved by DNA structure-selective endonucleases known as Holliday junction resolvases.

190
Q

Synthesis-dependent Strand Annealing

A

A major mechanism of homology-directed repair of DNA double-strand breaks (DSBs).

191
Q

Double Minute Chromosomes

A

Small fragments of extrachromosomal DNA, which have been observed in a large number of human tumors including breast, lung, ovary, colon, and most notably, neuroblastoma. They are a manifestation of gene amplification as a result of chromothripsis, during the development of tumors, which give the cells selective advantages for growth and survival.

Molecular Diagnostics (20 decks)

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