Molecular Medicine

DNA and Genetic Material

DNA stands for “deoxyribonucleic acid”, a complex string of nucleotides found inside your body in chromosomes. The information in this DNA determines unique biological characteristics, such as eye color, hair color, and age. 

Molecular biology techniques utilize DNA, RNA, and enzymes that interact with nucleic acids to develop a greater understanding of biology on a molecular level; one example of this technique is molecular pathology. In this subspecialty, molecular biology techniques are utilized to diagnose and prognose (predict disease progression). Genetic diseases, such as cystic fibrosis, sickle cell anemia, and predispositions to cancer are typically detected via molecular biology techniques. Molecular pathology techniques are used in fields such as forensics and in identity testing (HLA and parentage). 

Nucleic acid is the genetic material in organisms, appearing through either double-stranded DNA (read in a 5’-3’ direction) or single-stranded RNA (ribonucleic acid)(typically appears in prokaryotes). DNA/RNA consist of chemically linked sequences of nucleotides, which are made up of nitrogenous bases (adenine, thymine, guacine, cytosine, and in RNA uracil replaces thymine), as well as pentose (5-carbon) sugars and a phosphate group. The sequences of the nitrogenous bases provide the genetic information. As for the bases specifically, they are separated into two categories. Purines have fused five- and six-membered rings (adenine and guanine), while pyrimidines have six-membered rings (cytosine, thymine, and uracil). Purines are more stable than pyrimidines because they have two rings, while pyrimidines only have one. Hydrogen bonds are relatively weak bonds compared to covalent bonds and can form between pyrimidines and purines. The nucleotides also follow Watson-Crick base-pairing rules, in which adenine bonds to either thymine or uracil, while guanine bonds to cytosine.


Hallmarks of Cancer


Hallmarks of Cancer: The characteristic abnormal division of cancer cells occurs due to the presence of oncogenes, mutated forms of normal genes that promote cell proliferation. Tumor suppressor genes are also involved in cancer. These tumor suppressor genes that play a crucial role in tumor growth suppression are the TP53 gene, which senses the need to halt cell cycle progression and can trigger apoptosis, and the RB gene, which monitors the stages of cell cycle progression. Mutation of these genes, however, can lead to the devastating progression of cancer. At least 50% of tumors have a mutation in the TP53 gene, and mutation of the gene can also become hereditary and lead to Li-Fraumeni Syndrome, a genetic condition in which the individual has roughly a 50% chance of developing cancer by age 30.

Cell cycles regulate proliferation by ordering the genes to stop making new cells; when they become mutated, the cells are not given the order to stop increasing. Cancer cells have unlimited replicative potential and avoid cell death by evading cell-regulation stages and creating more telomerase to keep their telomeres longer and, thus, keep themselves alive. Telomeres are compound structures at the end of chromosomes that signal cell death once they become too short; however, in cancer cells, telomeres can be lengthened infinitely so the cell will never reach death. The main difference between cancer cells and normal cells is that cancer cells do not stop reproducing, while normal cells carefully regulate their growth and division. Tumors deregulate these measures by bypassing stages that check for cell growth, usually through apoptosis (deliberate cell death), senescence (deterioration of cell through age), DNA damage response (the response to which DNA creates an abnormal nucleotide, causing a break in the DNA), cell cycle inhibition (where cells are given the command to stop proliferating), and contact inhibition (where cells stop proliferation when they come in contact with each other). Cancerous cells can ignore these programs, leading to their continued production despite evidence of DNA damage or overgrowth. They support themselves via angiogenesis, the formation of new blood vessels by cancerous cells, as tumors require oxygen, nutrients, and the ability to evacuate metabolic wastes and carbon dioxide. These new blood vessels are hastily constructed and are thus fragile, which usually leads to internal bleeding of the tumor.


Cancer Staging and Types


Cancer is a term used for diseases in which abnormal cells divide without control and can invade other tissues. They can metastasize (spread) to other body parts through the blood and lymph systems.

Broadly cancers can be classified into five main categories based on the origin of tissue, the first being carcinoma, in which cancer begins in the skin or tissues that line or cover internal organs; for example, adenocarcinoma and squamous cell carcinoma. Second, a sarcoma may arise, a cancer beginning in bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. Thirdly, cancer may be leukemia, a cancer that begins in blood-forming tissue such as bone marrow and causes large numbers of abnormal blood cells to be produced and enter the blood, which is dangerous as it allows the cancer to metastasize easily as it is already in the blood vessels. Fourthly, there is lymphoma and myeloma, which describe cancels that begin in the cells of the immune system. Lastly, there are central nervous system cancers, which begin in the tissues of the brain and spinal cord.


Cancer staging is based on the size or extent of the primary tumor and whether it has already metastasized to other areas of the body. Summary staging (in situ, local, regional, and distant) is used for descriptive and statistical analysis of the tumor registry data. When the cancer cells are present only in the layer of cells where they have developed and have not spread yet, the stage is in situ; however, if they have penetrated beyond the original layer of tissue, the cancer is invasive and categorized as begin in the local, regional, or distant stage based on the extent of the spread. TNM staging assesses tumors in three ways, the T standing for the extent of the primary tumor, the N being the absence or presence of regional lymph node involvement, and M being the absence or presence of distant metastases. As soon as these categories are determined, a stage of 0 (in situ), I (early), II, III, or IV (most advanced) is assigned. Cancer is defined as when normal body cells begin to divide without stopping and simultaneously spread into surrounding tissues. 


Cancer Therapeutics


In chemotherapy, toxic drugs (such as melphalan, busulfan, capecitabine, and 5-fluorouracil) are given to the cancer patient to interfere with the growth of the cancer cells. The goal of chemotherapy is to eliminate all cancer cells as well as slow the growth of cancer and prevent spreading; in later stages, chemotherapy may also be used to provide palliative care, which means to shrink the tumor to relieve pressure on the patient. 


In radiation therapy, beams of intense energy, typically X-rays, are used to kill cancer cells, and the therapy can be accomplished via either external beam radiation therapy or brachytherapy. Protons and other energy types may also be used in the place of X-rays. During external beam radiation therapy, high-energy beams are discharged from an external machine that targets specific areas of your body where the cancer is prevalent. In brachytherapy, the radiation is placed inside your body. 


In targeted therapy, medicine targets the proteins that control the replication and growth of cancer cells. Most of these therapies are given via small-molecule drugs (minuscule drugs that target anomalies inside cells) or monoclonal antibodies (lab-made antibodies that mark cancer cells for easier recognition and destruction by the body’s immune system). Monoclonal antibodies are especially flexible in that they can also directly cause cancer cells to self-destruct or cease growth, and others may carry toxins to cancer cells.


In immunotherapy, drugs are used to stimulate the body’s immune system to recognize and attack cancer cells. These drugs include checkpoint inhibitors (drugs that allow the immune system to create responses without checkpoints) and chimeric antigen receptor T-cell therapy (drawing the patient’s blood and teaching them to attach to tumor cells, followed by injecting the blood back into the patient).




Drug Discovery and Development

Drug development is a process that typically occurs where a disease must be chosen as well as a drug target identified. Bioassay (a test used to determine biological activity) should also be recognized to test the activity of the drug. Once this is done the properties of the drug should then be improved. It is then important to understand the pharmacokinetics and pharmacodynamics of the drug before assessing it through clinical trials.

Broadly, the process as a whole can be summarized in the following steps

Oncology: Clinical Trials

Clinical trials assess the patient and the treatment to conclude how the patient should be treated so that they may receive the most effective care possible. 

Patient Inclusion and Exclusion: Patients are selected through disease type, prior treatment, age, sex, organ function, disease status, performance status, pain score, and other variables. 

The treatment’s type, dose, and schedule should also be discussed as well as how long it should last. 

In Phase I trials, the objective is to determine the drug's safety in humans. This is where the drug is determined for toxicities and range of doses, as well as identifying the drug's Pharmacokinetics (PK) and Pharmacodynamics (PD). 

In Phase II trials, possible benefits to the patients from the drug are evaluated. Once the drug's activity is screened in Phase II trials, Phase III trials are initiated. 

In Phase III trials, results from Phase II studies are confirmed and it is also confirmed that there is a benefit for a large number of patients across multiple countries. 

It is also important to take into account the safety of the treatment itself and evaluate its toxicity and if that toxicity level is safe for the patient to use. Key concepts of clinical trials include pharmacokinetics (PK), otherwise defined as what the body does to the drug. It evaluates the body’s absorption, distribution, metabolism, and excretion of the treatment. The other concept is pharmacodynamics (PD), defined as what the drug does to the body; this evaluates the nadir counts (blood cell counts), non-hematologic toxicity, molecular correlates, biomarker changes, and imaging endpoints.