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Oncology Glossary

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Sabin oral polio vaccine (OPV): a live attenuated oral polio vaccine developed by Albert Sabin in 1961.

Salk inactivated poliovirus vaccine (IPV): an inactivated polio vaccine developed in 1955 by Jonas Salk. The IPV is delivered by injection.

SCF (stem cell factor): a growth factor that stimulates the proliferation, differentiation, and survival of hematopoietic cells. SCF is a ligand for c-kit.

Scheuer system: a scoring system originally for chronic viral hepatitis. The Scheuer system is now applied to nonviral hepatitis as well. It gives the portal and lobular components of activity equal weight and evaluates both the necroinflammatory activity and liver fibrosis/cirrhosis in chronic hepatitis.

SCUBE2: gene coding for signal peptide, CUB domain, epidermal growth factor-like 2 protein, an endothelial cell–associated, secreted glycoprotein.

SDHA (succinate dehydrogenase complex subunit): one of the four components of the enzymatic mitochondrial complex II, which is involved in the mitochondrial respiratory chain. It is considered a housekeeping gene because of its essential function in cells.

SDHB: one of four protein subunits forming the succinate dehydrogenase enzyme; the other three are SDHA, SDHC, and SDHD. Germline mutation of the SDHB gene can cause susceptibility to pheochromocytoma, paraganglioma, and renal cell carcinoma.

second-degree family history: the record of a recurring medical condition occurring in family members, including grandparents, half-siblings, grandchildren, aunts/uncles, and nieces/nephews.

selectin: expressed principally on leukocytes and endothelial cells, selectins are cell adhesion molecules that play an important role in host defense mechanisms. Selectins bind to carbohydrate molecules on cells, resulting in weak binding. Thus, selectin-mediated interactions between leukocytes and endothelial cells facilitate rolling of the leukocytes along the endothelium. Endothelial (E) -selectins and platelet (P) -selectins are largely redundant molecules on endothelial cells. Leukocyte (L) -selectin acts as homing receptors for leukocytes.

self-renewal: the process by which a progenitor gives rise to daughter progenitors of equivalent developmental potential (ie, multipotent stem cells self-renew by dividing to generate one or two multipotent daughter cells).

semaphorin: member of a family of secreted and transmembrane proteins that serve as repulsive signals in axonal and neuronal development. These proteins may also play a role in endothelial cell guidance.

seminoma: a type of testicular cancer that arises in the germinal epithelium of the seminiferous tubules.

sensitivity analyses: analyses that evaluate the impact of missing data and possible differences in interval assessments.

sensitivity to endocrine therapy (SET) index: a multigene expression profile that was developed to measure estrogen receptor– related transcription in breast cancer.

sentinel lymph node: the lymph node that is anatomically located such that it is the first site of lymph drainage from the location of the primary tumor. It is suspected and assumed that if a malignancy is going to disseminate via the lymphatic system, metastases will first be evident in the sentinel lymph node. In this manner, this lymph node is said to stand guard or sentinel over the metastatic state of the tumor. For many cancers, the sentinel lymph node is biopsied as part of the staging process and presence of macro- or micrometastases in the sentinel lymph node is a negative prognostic factor.

sequencing: a laboratory process that determines the nucleotide sequence of DNA (can involve the whole genome or whole exome or be targeted to as little as one coding sequence). Unlike somatic mutation genotyping, sequencing can detect previously unknown somatic mutations.

serine protease: enzymes that are involved in the breakdown of proteins. Although unchanged after the enzymatic reaction, at the catalytic site of the enzyme is an essential serine molecule that is intimately involved in the enzymatic reaction.

serine/threonine kinase: generic name for enzymes that phosphorylate serine and/or threonine molecules in proteins.

serous tubal intraepithelial carcinoma: a noninvasive lesion within the fallopian tube epithelium, which is putatively considered to represent a nonobligate precursor of invasive serous carcinoma of the pelvis. The diagnosis of serous tubal itraepithelial carcinoma is based on microscopic identification of tubal epithelium composed of cells with marked cytologic atypia, multilayering and loss of polarity, variably associated with mitotic figures, both normal and abnormal, and evidence of apoptosis.

serpina 5: a tumor-suppressor gene that is a member of the superfamily of serine protease inhibitors. Serpina 5 (also known as PAI3 or PCI) inhibits several plasma proteases involved in blood coagulation, including uPA.

serum human epidermal growth factor receptor 2: serum human epidermal growth factor receptor 2 is a portion or all of the HER2/neu protein that is released into the blood stream and can be detected in serum or a portion of the blood.

SET domain: protein-protein interaction domains found in proteins that modulate chromatin structure (eg, members of the polycomb and trithorax family). The SET (Su[var]39, enhancer of zeste, Trithorax) domain is associated with methyltransferase activity and interacts with several proteins including, N-terminal tails of histones and components of nucleosome remodeling factors.

SH2 (Src-homology 2): modules of approximately 100 amino acids that are motifs in proteins that bind to phosphotyrosine regions (within a specific sequence context) of activated tyrosine kinase receptors. This conserved sequence was first identified between the oncoproteins Src and Fps.

SHH (sonic hedgehog): one of the ligands for the patched 1 protein (PTCH1). Binding of SHH to PTCH1 is one of the early steps in activation of the hedgehog signaling cascade. The hedgehog signaling pathway is important in cell proliferation and differentiation during embryonic development and tumorigenesis.

SHP1: gene that codes for a hematopoietic-specific protein tyrosine phosphatase.

shRNA (short hairpin RNA; short interfering hairpin): shRNA contains sense and antisense sequences from a target gene connected by a loop and is expressed in mammalian cells from a vector by a pol III–type promoter. The shRNA is transported from the nucleus into the cytoplasm, where Dicer processes it. Once in the cell, the shRNA can decrease the expression of a gene with complementary sequences by RNAi.

signature of inheritance: all changes found in a parent genotype must be present in the offspring occurring with a similar frequency. The daughter generation acquires additional genomic imbalances.

significance analysis of microarrays (SAM): a statistical technique using established software that determines the significance in changes of gene expression seen in microarray analysis (eg, cDNA and oligonucleotide microarrays), which measures the expression of thousands of genes and identifies changes in expression between different biologic states. On the basis of changes in gene expression relative to the standard deviation of repeated measurements, SAM assigns a score to each gene. When scores are greater than an adjustable threshold, permutations of repeated measurements are used by SAM to estimate the percentage of such genes identified by chance, the false discovery rate. In addition, SAM correlates gene expression data to a wide range of clinical parameters, including treatment, diagnosis categories, and survival time.

Sin3: see SIN3A.

SIN3A: a transcriptional co-repressor.

SINEs (short interspersed elements): sequences that are repeated, unblocked, and dispersed throughout the genome. They make up roughly 20% of the human genome and are useful as markers for organism classification. An ALU repeat sequence is an example of a SINE.

single nucleotide polymorphism (SNP): natural variations in the genomic DNA sequence present in greater than 1% of the population, with single nucleotide polymorphisms representing DNA variations in a single nucleotide. Single nucleotide polymorphisms are being widely used to better understand disease processes, thereby paving the way for genetic-based diagnostics and therapeutics.

siRNA (short-interfering RNA): used in RNA silencing, a method that allows one to knock down expression of genes in a sequence-specific fashion. Although RNA silencing occurs naturally to protect organisms from aberrant transcription, it is now being exploited to silence genes implicated in diseases and to determine the functions of various genes.

sirolimus: a potent immunosuppressant used in transplantation that inhibits cell cycle progression, preventing cell proliferation. Also called rapamycin.

SIRT2: a NAD-dependent deacetylase (NDAC) that regulates gene silencing, cell cycle, and DNA damage repair. Also known as sirtuin for silent mating type information 2-homolog.

SKI-606: a tyrosine kinase inhibitor designed to inhibit the ATP-binding site of Src and Abl kinases.

skip metastasis: a lymph node metastasis occurring far from the primary tumor, thereby skipping nearby lymph node stations (eg, cancer from the distal esophagus that has spread to the upper mediastinum, or even the neck, without positive local nodes).

SLAM (signaling lymphocytic activation molecule): lymphocyte found on activated T cells, B cells, macrophages, and dendritic cells. SLAM (also called CD150) is a costimulator in T-cell receptor–induced T-cell proliferation and controls the production of Th1 cytokines. It also mediates intracellular protein tyrosine phosphorylation signals by binding with SLAM-associated protein (SAP).

SLCO2B1: a member of the organic anion-transporting polypeptide family (OATP) and mediates the transport of montelukast and various sulfated steroids.

Smac: a mitochondrial protein that is the mammalian inhibitor of IAP (inhibitor of apoptosis) and a master regulator of apoptosis.

small round blue-cell tumors: a class of tumors united by the appearance of characteristic small, round, blue tumor cells. Besides rhabdomyosarcoma, desmoplastic small round blue-cell tumor, Ewing sarcoma, lymphoma, small-cell mesothelioma, neuroblastoma, primitive neuroectodermal tumor, and Wilms tumor belong to this class.

SMO (smoothened): a receptor that is inhibited by PTCH1. When one of the hedgehog ligands binds PTCH1, PTCH1 releases the inhibition of SMO and SMO activates the hedgehog signal transduction cascade. Downstream of SMO is a family of transcription factors, GLI, which are key proteins in mediating the hedgehog signal. The hedgehog signaling pathway is important in cell proliferation and differentiation during embryonic development and tumorigenesis.

SMRT (silencing mediator of retinoid and thyroid receptors): a transcriptional co-repressor.

SN-38: the active metabolite of irinotecan, which is the in vivo substrate for carboxylesterase.

SOCS (suppressor of cytokine signaling): gene that may have regulatory roles in T cell differentiation. It is also postulated to negatively regulate activated T-cells. Absence of the gene permits activated T cells to make interferon gamma.

solid stresses: the stresses exerted by the solid components of a tissue and accumulated within solid structural components (ie, cancer and stromal cells, collagen, and hyaluronan) during growth and progression. Solid stress is elevated in tumors because of growth and is independent of the high interstitial fluid pressure.

somatic alterations: alterations in DNA that occur in an individual after conception, used here to denote alterations that occur uniquely in a tumor cell.

somatic mutation: a change in the genotype of a cancer cell. This is distinguished from a germline mutation, which is a change in the genotype of all the normal cells in a patient's body. Germline mutations may be passed to offspring, but somatic mutations may not.

somatostatin analogs: analogs of somatostatin, a ubiquitous hormonal peptide that displays inhibitory properties on various endocrine and exocrine secretions. AS a result of the very short half-life of the natural somatostatins SRIF-14 and SRIF-28, stable synthetic analogs with prolonged half-life, have been developed. Two of them are clinically used via subcutaneous or intramuscular routes (octreotide and lanreotide) especially in endocrine tumors for medical treatment of acromegaly and carcinoid syndrome. Radiolabeled analogs are also applied in clinical practice to detect primary endocrine tumors as well as their metastasis by means of in vivo scintigraphy. A distinct affinity profile of somatostatin analogs for the five somatostatin receptors has been well demonstrated; both analogs bind with high affinity to SST2, with moderate affinity to SST5 and SST3, and with low affinity to SST1 and SST4.

somatostatin receptors: receptors that interact with the natural somatostatins (SRIF-14 and SRIF-28) and the stable somatostatin analogs of somatostatin to induce their physiologic affects. These receptors belong to the family of seven transmembrane domain G protein-coupled receptors and are distributed throughout the human endocrine and nonendocrine tissues. Five subtypes are known named SST1, SST2, SST3, SST4, and SST5. Some tumor tissues express somatostatin receptors, including endocrine tumors, and this provides the basis of the use of somatostatin analog for staging and treatment of these tumors.

sorafenib: a substance belonging to the family of drugs called RAF kinase inhibitors and anti–vascular endothelial growth factor that is being studied in the treatment of cancer.

SOS (son of sevenless): an exchange factor that stimulates GDP release from GDP bound to Ras. This allows for the activation of Ras that occurs as a consequence of GTP binding. As a first step, SOS must be directed to the membrane where Ras resides. This occurs when SOS (via its proline-rich regions) binds to Grb2 via Src-homology 3 (SH3) domains in Grb2. Other activities of SOS governed by its dbl homology and pleckstrin homology domains correspond to a stimulation of GDP/GTP exchange on Rac and regulation of Rac exchange activity, respectively.

SP1: a transcriptional factor.

Spearman’s Rho (Spearman’s rank correlation coefficient): a nonparametric measure of statistical dependence between two ordinal or continuous variables assessing how well their relationship can be described by a monotone function. It is defined as the Pearson’s correlation coefficient between the ranks of the variables. Values lie between 1 and 1, whereas a value of 1 or 1 implies a perfect monotone relationship.

spectral karyotyping: a new method for karyotyping that uses fluorescent dyes that bind to specific regions of chromosomes. Spectral karyotyping has been used to detect chromosomal translocations not recognizable by traditional binding methods. Because a series of specific probes, each with varying amounts of the dyes, are used, different pairs of chromosomes have unique spectral characteristics. An interferometer recognizes slight variations in color undetectable to the human eye and assigns an easy-to-distinguish color to each pair of chromosomes, generating a digital image. Thus, pairing of the chromosomes is simpler as homologous pairs are the same color, and aberrations and crossovers are more easily recognizable.

splice site mutation: mutation that changes the specific sites at which the splicing of an intron takes place.

split-sample validation: a method used for internal validation in which the sample is split into two portions; one is used as a training set and the other as a test set.

sporadic human tumors: tumors in which the mutations or epigenetic events predisposing to cancer occur spontaneously, as opposed to in hereditary tumors, when gene mutations are inherited.

Src: see c-Src.

SRL172: a suspension of heat-killed Mycobacterium vaccae. SRL172 has been developed both as an adjuvant used in vaccine administration and for the treatment of cancer. SRL172 has several functions that make it relevant in cancer treatment protocols. It stimulates innate immunity through activation of antigen-presenting cells and precursor T-helper cells; it is a nonspecific modulator and promoter of T-helper type 1 responses; it suppresses pre-existing T-helper type 2 responses; and it activates natural killer cells. It is being evaluated in combination with conventional chemotherapy and as a vaccine adjunct.

SST2 somatostatin receptor: somatostatin receptor implicated in various pharmacologic and biologic functions both in normal and tumor tissues. SST2 binds the analogs clinically used (octreotide and lanreotide) with a higher affinity than the other somatostatin receptors. SST2 mediates the antiproliferative and many antisecretory effects of somatostatin analogs. Its expression is often high and frequent in many endocrine tumors such as pituitary adenomas, gastrinomas, carcinoid tumors, and nonfunctioning islet cell tumors. In such tumors, a positive correlation is found between tumor expression of SST2 and positive results (positive fixation of primary and metastasis) at in vivo scintigraphy, using radiolabeled octreotide.

stable nucleic acid lipid particles: microscopic particles approximately 120 nanometers in diameter. They have been used to deliver short-interfering RNAs (siRNAs) therapeutically to mammals in vivo. In SNALPs the siRNA is surrounded by a lipid bilayer containing a mixture of cationic and fusogenic lipids, coated with diffusible polyethylene glycol.

standardized competitive reverse transcriptase–polymerase chain reaction: quantitative polymerase chain reaction that measures absolute expression levels of multiple genes using competitive templates of the target and reference (β-actin) genes incorporated into standardized mixtures of internal standards. Use of the same standardized mixtures potentially allows comparability of data across experiments and laboratories.

standardized incidence ratio: a comparison measure to compare the incidence of a disease in a small population with the incidence in a larger (general) population. The standardized incidence ratio is obtained by dividing the observed number of cases by the expected number of cases. The expected number is the number of cases that would occur in a population with the same age and sex distribution.

standardized uptake value (SUV): in positron emission tomography imaging, the semiquantitative measure of the degree of fixation of a radiotracer (eg, [18F]fluorodeoxyglucose). The SUVmax corresponds to the most intense fixation value at tumor site.

STAT: proteins present in the cytoplasm in their inactive form that are transcription factors that become activated after recruitment to an activated receptor complex at the cell surface. After activation, STAT (signal transducer and activators of transcription) proteins form homo- or heterodimers and, as such, translocate to the nucleus, where they induce unique gene expression programs by binding to specific DNA-response elements in the promoters of target genes. Currently seven STAT proteins have been identified in mammalian cells.

STAT3: see STAT.

STAT5β-RARα: a fusion protein that acts as a transcriptional repressor, in which the self-association domain of STAT5 is retained in the fusion protein and is necessary to induce aberrant transcriptional repression of target genes by retinoic acid receptor α (RARα), which is critical for leukemogenesis.

stereologic counting technique: a computer-based counting technique used to achieve a cell-density measure or a certain measure of volume in immunohistochemical sections. A computer places a counting frame in several different positions within the tumor sections, and each cell of interest has the same probability of being sampled, irrespective of distribution within the particular tissue block. The estimate given is highly reproducible and not biased by a distinct pattern of distribution within the tumor sections.

stereotactic ablative radiotherapy: a more contemporary term for stereotactic body radiation therapy. See stereotactic body radiation therapy.

stereotactic body radiation therapy: a tumor-ablative radiation modality using essential technologies capable of accurately and precisely damaging targets with a high dose while geometrically sparing innocent normal tissues (Timmerman RD, et al: J Clin Oncol [epub online ahead of print on August 11, 2014]).

STK15: also called STK6 or auroraA. See aurora kinase inhibitors.

sTNF-RII: soluble form of tumor necrosis factor–receptor II.

stratification factor: afactor used to separate data into subgroups to determine whether that factor is significant.

streptavidin: an approximately 50- to 60-kD protein isolated from bacteria and has four high-affinity binding sites for biotin. See avidin.

stress kinase signaling: pathways activated by stress signals, which are extracellular in nature and varied (eg, hypoxia, exposure to high salt, ionizing radiation, osmotic shock), including cellular cell survival pathways that involve the signaling molecules, p38-MAPK and JNK/SAPK. See MAPK (mitogen-activated protein kinase) and JNK/SAPK.

stromal cells: the noncancer cells in tumors. The stroma is distinct from the parenchyma, which consists of the key functional elements of an organ.

stromal response genes: genes within the surrounding tissues that control the reaction of the supporting stromal cells to the presence of cancer cells.

stromelysin 3: also known as MMP11. See MMP (matrix metalloprotease [metalloproteinases]).

SU011248: see SU11248.

SU101: a small molecule inhibitor that inhibits the tyrosine kinase activity of the platelet-derived growth factor receptor.

SU10944: a vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitor. SU10944 inhibits the activities of VEGFR-1 and VEGFR-2.

SU11248: a receptor tyrosine kinase inhibitor of vascular endothelial growtch factor receptor, platelet-derived growth factor receptor, c-kit, and FLT-3 that was developed as a small molecule with antiangiogenic properties.

SU6668: a receptor tyrosine kinase inhibitor of vascular endothelial growth factor receptor, fibroblast growth factor receptor, and platelet-derived growth factor receptor that was developed as a small molecule with antiangiogenic properties.

suberoylanilide hydroxamic acid (SAHA): a derivative of hydroxamic acid, which is a histone deacetylase inhibitor.

subgroup analysis: an analysis in which the intervention effect is evaluated in a defined subset of the participants in the trial, or in complementary subsets, such as by sex or in age categories. Sample sizes in subgroup analyses are often small and subgroup analyses therefore usually lack statistical power. Comparison of subgroups should be done by test of interaction rather than by comparison of P values. They are also subject to the multiple comparisons problem, which increases the probability of making a type I error (ie, attributing a difference to an intervention when chance is the more likely explanation).

substitution mutation: a change of one base in a nucleotide sequence that may result in a change in the amino acid sequence.

SUMOlyation: a post-translational modification of proteins involving the covalent attachment of SUMO (small ubiquitin-related modifier) to proteins and affecting biologic processes including those of protein localization and stability, transcriptional activities, nucleocytoplasmic signalling and transport, and genome replication as well as the regulation of gene expression.

sunitinib: an oral small molecular tyrosine kinase inhibitor that exhibits potent antiangiogenic and antitumor activity. Also known as SU011248 or Sutent (Pfizer, New York, NY).

supervised analysis: analysis of gene expression profiling data in which external information such as survival status is used as a guide to select genes from microarray data.

supervised classification: the process of deriving a mathematical function that can predict the membership of a class on the basis of input data. The function (classifier) is derived from examples given by a supervisor or expert and is designed to mimic the given behavior.

support vector machine (SVM): a supervised learning method for solving classification and regression problems. It is used to develop a model based on a set of training data (the training samples and their labels) and then this model is used to predict the label when a new input sample is given.

surface-enhanced laser desorption and ionization (SELDI): an ionization method in time of flight mass spectrometry that is used for the analysis of protein mixtures in tissue samples, blood, urine, or other clinical samples. Comparison of protein levels between patients with and without a disease can be used for biomarker discovery. Compared with MALDI, SELDI uses a target modified to achieve biochemical affinity with the analyte compound (eg, protein chips).

surface-enhanced laser desorption and ionization–time of flight mass spectrometry (SELDI-TOF-MS): a powerful analytic tool that profiles proteins in a biologic sample. In contrast to cDNA microarrays, SELDI uses aluminum chips (1 to 2 mm in diameter) that are spotted with baits to capture proteins. The baits vary and may consist of affinity resins, small molecules, antibodies, DNA, or enzymes. Analysts apply crude biologic samples to the chip, allowing the baits to capture appropriate molecules that bind to their surfaces. After extensive washes, the analytes are laser desorbed from the chip, ionized, and analyzed by mass spectroscopy. Mass spectral fingerprints are thus obtained. Proteomic researchers use the technique to understand the involvement of specific proteins in the disease process or to define/follow biomarkers for diseases.

surrogate: a biologic marker evaluated in place of the actual marker of interest. For example, studying a marker for drug effect in blood instead of tumor. The relationship between the marker under study and the marker of interest needs to be established before using the term surrogate.

surveillance: monitoring patients for cancer recurrence after treatment with physical exam, laboratory and imaging studies, and minor procedures (ie, cystoscopy, colonoscopy, prostate biopsy). The specific interval and type of testing used for monitoring are specific to the type of cancer. Recommendations are typically provided by national cancer organizations/associations.

surveillance bias: a nonrandom type of information bias that occurs when some patients are observed more closely or have more diagnostic tests performed than others, often leading to an outcome diagnosed more frequently in the more closely monitored group (Haut ER, et al: JAMA 305:2462-2463, 2011).

Surveillance, Epidemiology, and End Results (SEER): a national cancer registry that collects information from all incident malignancies in multiple geographic areas of the United States.

surveillance scans: scans performed routinely after the conclusion of treatment to assess for residual or recurrent disease.

survivin: see IAP (inhibitors of apoptosis proteins).

survivorship care plan: a personalized document ideally provided to a patient with cancer by the coordinating oncology clinician that summarizes the patient's diagnosis and treatment, delineates risks for possible late effects and health screening and surveillance recommendations for those late effects, outlines resources for addressing practical and other issues in survivorship care, and specifies the roles of multiple providers overseeing survivorship and primary care.

SUV39H1: a histone lysine methyltransferase.

SV40 (simian virus 40): virus that establishes a low-level infection in its host where it persists in the kidneys without apparent effect. It is thought that SV40 may be excreted through the urine of the infected host and transmitted through the oral or respiratory route. SV40 is closely related to two human polyomaviruses—JC virus and BK virus.

sVEGFR1: soluble form of vascular endothelial growth factor receptor (VEGFR) -1 (also known as sFLT-1), a truncated version of the cell membrane–spanning VEGFR-1, that can bind to circulating VEGF and placental growth factor.

Swi/Snf: chromatin remodeling multiprotein complexes that are involved in global transcriptional activation because of their ability to bind DNA, disrupt nucleosomes, and provide transcription factors with access to nucleosomal DNA.

synthetic lethality: a situation that occurs when a DNA repair pathway is inhibited in cells already compromised in a second repair pathway. This prevents repair of DNA breaks, thereby leading to cell death.

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