Preclinical laboratory studies

Drug development starts with target identification in the laboratory. The target, usually a protein, should play an important and unique role in the cancer cell life. Biomarkers can help identify molecular pathways, that is, a group of genes that acts together and contributes to the development or maintenance of a specific cancer. By narrowing down the list of genes of interest, the process of identifying potential targets becomes more efficient and biologically sound.

Once a target is identified, thousands of compounds are typically screened for potential drug candidates against the target. Biomarkers can aid in selecting the most promising compound (known as lead compound) and gain insight into its mechanism of action.

The lead compound then undergoes a battery of laboratory tests. Biomarkers can help to assess the safety and efficacy of the drug, to understand the drug mechanism of action and aid in dose selection.

An example of a preclinical tool that can be used to predict response to therapy is called the Avatar system. In this system, a small piece of a patient’s tumor is injected into a mouse lacking an immune system, also known as patient-derived xenograft (PDX). The tumor is allowed to grow in the mouse and subsequently re-injected into multiple mice. These PDXs have become a major tool for testing candidates’ drugs as they reflect the genetics of patient tumors seen in the clinic. While this in vivo approach is promising, it should be noted that the process of establishing a PDX is long, expensive, and does not always mimic the tumor heterogeneity in the human cancer. Some investigators are attempting to establish Avatar systems to individualize drug selection, but this remains unproven and very much a subject of ongoing research studies.

A faster and cheaper way to perform drug testing is to use cell cultures (in vitro). In this approach cancer cells from patients are grown in a plastic plate to which drugs are added and tested for efficacy. The main drawback of this approach is that cancer cells do not grow in the artificial conditions of cell cultures which include oxygen levels, nutrients and exposure to plastic. Another difference is that cancer cells in the body are typically surrounded by normal cells termed a microenvironment. Despite these limitations, cell culture studies can be a useful screen and provide valuable information.

Clinical research steps

The steps following preclinical or laboratory studies are known collectively as clinical research. The main purpose of clinical research is to test safety and efficacy of the selected drug in humans.

Phase 1 of clinical trial is aimed at assessing the safety of the drug in humans and also collect data on the appropriate dosing. It typically consists of a relatively small number patients, especially in childhood cancer where many drugs have already been studied in adult trials. Approximately 70% of drugs tested in Phase 1 trial move to the Phase 2 clinical trial in which the efficacy and side effects of the drug are evaluated. About 33% of Phase 2 trials move to the Phase 3 trial (https://www.fda.gov/). The goal of Phase 3 trials is to test the efficacy of the drug and compare it to current therapies for the specific type of cancer. These studies enroll several hundreds to thousands of patients and can continue for many years. Phase 3 trials also provide new safety data about the drug that was not detected in previous phases. Roughly 25 to 30% of the drugs that enter Phase 3 trials are approved by the FDA for marketing and move to Phase 4 trial or a post-market safety monitoring phase.

Biomarkers play an important role in clinical trials and help select patients for enrollment into clinical trials, stratify patients into a subgroup of treatment, guide dose selection, help in assessment of safety and evaluation of drug efficacy, and help to monitor side effects. For example, the presence of NTRK-fusion gene can be a biomarker for selection of patients into a clinical trial that tests the efficacy of Larotrectinib in NTRK-fusion positive tumors. The levels of liver enzymes (aminotransferase) are typically used as safety biomarkers for drugs that can cause liver injury, such as Larotrectinib. The presence of NTRK-fusion gene in cell-free DNA blood samples can be used as biomarkers for response to therapy.