Chapter 14: Technology and drugs and diagnostics development (Book, main)

Question 1

What can microarrays (and similar technologies) do?

Answer 1

Enable the expression of tens of thousands of genes to be analyzed tat the same time. Microarrays can identifiy a group of transcripts associated with a specific outcome or phenotype, called a gene signature or profile

Question 2

How is the technique called the supersedes the microarrays in many applications?

Answer 2

Next-generation sequencing

Question 3

How doe microarrays work?

Answer 3

Microarrays are girds, usually made on glass slides or silicon chips. They hold DNA representing thousands of genes that act as probes (sequences that are complementary and can hybridize to specific RNAs) for RNA. Analysis of a sample using a microarray will identify RNAs that are present by hybridization to the probes on the grid and indicate genes that are being expressed (transcribed)

Question 4

How can microarrays be used in the clinic?

Answer 4

Different gene expression signatures can be used to identify molecular subtypes of cancers and lead to the development of more precise diagnosis and treatment

Question 5

What are molecular signatures used for?

Answer 5

For the prediction of disease outcome and prescription of the most efficient treament available for a particular tumor subtype.

Several groups have used microarrays to identify a number of marker genes whose expression can predict metastasis and/or prognosis

Question 6

What is a biomarker?

Answer 6

A biomarker is a biochemical or genetic feature that can be used to estimate risk, detect disease, or measure its progression or the effect of treatment. Biomarkers may include the measurement of specific molecures, genetic alterations, gene expression profiles, cell-based markers, and single nucleotide polymorphisms (SNPs)

Question 7

How can biomarkers be identified?

Answer 7

Through microarray gene expression profiling or thorugh mass spectrometry (allows fro the simultaneous examination of thousands of proteins in a biological sample)

Question 8

The first non-invasive stool-based DNA screening test, Cologuard, was approved by the FDA in 2014. What does it detect?

Answer 8

The presence of DNA mutations (KRAS) and methylation markers (NDRG4 and MP3) associated with colon carcinogenesis. The test also detects haemoglobin for the presence of red blood cells

Question 9

What are three future potential diagnostic and prognostic indicators that may be detected in a simple blood test? Why?

Answer 9

DTCs or tumor DNA, miRNAs and exosomes (discussed Ch9)

• Overall numbers of DTCs, tumor cells that have intravasated into the bloodstream, provide a prognostic indicator of disease outcome in some carcinomas
• Levels of several miRNAs have been correlated to metastatic outcome

Question 10

The study of gene function is very important in oncology. Homologous recombination in embryonic stem cells has low efficiency and takes a lot of time. Expression of cDNA sequences in cells is another way, but levels are difficult to control and are often higher than physiological levles. RNA interference can be used to known down expression, but the control of the degree of inihibition is not precise. What is a technique that overcomes many of the problems describe obve?

Answer 10

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated system), which modifies genomes for functional studies

Question 11

What are different imaging techniques?

Answer 11

CT, MRi, Ultrasound, molecular and functional imaging (MFI), PET and optical imaging

Question 12

What does nanotechnology study?

Answer 12

Nanotechnology is the study of devices (or their essential components) that are made by humans and have at least one dimension of the 1-1000 nm range

Question 13

How can nanotechnology be used in cancer?

Answer 13

Nanotechnology may enable specific cancer drug targeting, leading to better therapeutic results and fewer toxic side effects. It promises to enhance imaging and biomarker detection for improved diagnosis. Used as biomolecular sensors, this technology may replace the need for biopsies

There is a whole page dedicated to all the studies in nanotechnology related to cancer on page 334. Since I don’t think these details are relevant, this is not taken up in the flashcards

Question 14

What is the difference between pre-clinical and clinical trials?

Answer 14

Pre-clinical studies test a drug on animal models and gather data on safety and efficacy for proof of concept. Clinical trials are done on humans

Question 15

What is a true cancer drug target validation?

Answer 15

True cancer drug target validation occurs when a therapeutic agent is shown to act via a molecular target against which it was designed and proved to be clinically effective. However, a more current use of the term “target validation” refers only to the experimental evaluation of the role of a given gene or protein in cancer and its potential as a therapeutic target; that is, target validation may occur before clinical testing

Question 16

What is the three-step approach for a new targeted therapy before it goes to clinic?

Answer 16

1. Identify the molecular targets/pathways that drive tumor growth
2. Creat a genetically equivalent, high-incidence animal model where tumors of interest develop in thier correct anatomical locations ant at a developmetnally relevant time
3. Screen for, or design inhibitors to block the molecular pathway and test their effects in animal models

Question 17

Why is it difficult to reliably predict the effect of a new drug in human patients?

Answer 17

Because it’s hard to find a cancer model that can reliably predict this. A tumor is similar to an organ, with tumor cells interacting with host cells, the immune system, blood vessels and the ECM.

Question 18

What model best replicates the tumor microenvironment for experimentation?

Answer 18

A mouse model. The most widely used approach is the creation of human tumor xenographs, which are generated by injecting human cancer cells under the skin for immunodeficient (nude) mice (necessary so that the immune system of the mice don’t reject the human cells). Another approach is genetically altered mice (transgenic, knock-out, RNA interference, or CRISPR-Cas9)

Question 19

What is the most common approach for drug screening and how does it work?

Answer 19

High-throughput screening because it permits the testing of millions of compounds in a short period of time. Platelets containing hundreds of wells of biological material (e.g. cells) are used to test various chemical compounds for a desired biological effect (e.g. apoptosis). Robotics can analyze up to 100.000 compounds per day

Question 20

One of the problems in the design of clinical trials performed today that result in an inflated number of unsuccessful drug results, is that many new drugs are tested on older patients that have advanced cancer and who have not responded to a range of conventional therapies. Why is this a problem?

Answer 20

Drugs that may be eeffective in early-stage cancer may fail to have an effect on late-stage cancer in clinical trials. The development of such drugs would be wrongly discontinued

Question 21

What are some other problems of the clinical trials, what is a problem in phase II?

Answer 21

although inclusion of controls is stronly recommended, it has not been in included in a majority of phase II trials (comparisons are made to information on previous patient outcome)

Question 22

What shift in clinical trials need to be seen as we more towards personalized medicine?

Answer 22

A shift from population-based unselected approahes to the biomarker-adaptive and hypothesis-testing clinical trial

Question 23

The book emphasizes on using genomic analysis in hospitals and health services. Why?

Answer 23

Because the cancer patients have an unique genome, that is very personalized, and the understanding of this is important for the detection, treatment (before and after). With use of a molecular profile, cancer-specific molecular targets can be identified rapidly

Question 24

There are many potential molecular strategies in development. Can you name some?

Answer 24

Angiogenesis inhibitors, anti-endocrine drugs, apoptotic inducers, cell cycle inhibitors, HDAC inhibitors, inhibitors of cell renewal signaling pathways and immunotherapies.

Others that were not discussed: proteasome inhibitors