1.2.1 Solid Clinical Samples
In a hospital setting, solid clinical samples are obtained for the primary purposes of either obtaining a clinical diagnosis or to preserve the patient's well-being. In diseases such as cancer, a biopsy is recommended if the clinician determines the patient is at risk of having cancer. The entire biopsy is processed and examined visually under a microscope by a pathologist for the presence of cancer. Depending on the type of cancer, different methods of obtaining biopsies may be conducted. In suspected cases of melanoma, which occurs on the epidermis, a biopsy is typically harvested from the part of the skin where the suspected melanoma is situated through the use of a surgical blade [3]. In other cancers, such as prostate cancer, where the tissue is not easily accessible, needle biopsies are performed. The prostate is first located using ultrasound and a biopsy is obtained transrectally through the use of a biopsy needle and gun. Once the tissue biopsy is harvested, it is placed in fixative and sent to a clinical laboratory for further processing and staining before being examined by a pathologist under the microscope for the presence of cancer [4, 5]. There are other diseases apart from cancer, such as hepatitis, myopathies, or lupus that may require tissue biopsies [6–9]. In hepatitis, a liver biopsy is performed to determine the extent of fibrosis that has occurred in the liver [10]. In myopathy, a muscle biopsy is required to determine the degree of muscle atrophy as well as to make a clinical diagnosis on the type of myopathy the patient might be suffering from [6, 8]. In systemic lupus erythematosus (SLE), a form of autoimmune disease, biopsies can be extracted from multiple tissue types such as skin or kidney to provide better information on whether the patient is suffering from SLE and to determine the severity of the disease [7].
Larger clinical samples can be obtained through surgical resection. Such situations occur when there is a need to remove part or whole organs to preserve the health and well-being of the patient. This is most commonly performed in cancers of the prostate, breast, or colon to name a few examples and is an invaluable resource for studying tumor heterogeneity [11–13]. In prostate cancer, if cancer was detected in the biopsy, a decision may be made by the clinician to perform radical prostatectomy. During this procedure, the entire prostate is removed from the prostate and surrounding lymph nodes may be resected. The harvested prostate and lymph nodes are placed in fixative, stained, and sent to the pathologist for grading. This is an important step as the clinicians need to know whether the surgical margins are clear, indicating full resection of the tumor or whether the cancer had already invaded out of the prostate and into surrounding tissues such as the lymph nodes [14]. Therefore, it is apparent that the purpose of removing solid tissue from a patient is to achieve both clinical diagnosis as well as removing any diseased tissue. If fresh human tissue is desired for research purposes, it often involves coordinating with a pathologist, setting up an internal review board for complying with the ethical implications of using human research subjects as well as informing and obtaining patient consent to participate in the study [15].
In the research setting, fresh tissue samples can be readily obtained from animal sources. Although animal use still requires adherence to ethical treatment of the animals, tissue samples from animals are more abundant and easily accessible as they do not involve patients' clinical diagnoses and the number of animals can be increased easily through purchase. Furthermore, animal facilities can and are often situated closer to a research laboratory, allowing for shorter tissue-processing times.
Animal models are typically used for the sake of studying the progression of normal development or developing treatment strategies against human diseases such as cancer, in a preclinical setting. In studying cancer treatments, the disease is first induced in animals, which can be done through the use of xenograft transplant of human cancer cells, the use of transgenic animals that bear a mutation that makes them susceptible to developing the cancer of interest, or through the use of carcinogens. Once the cancer is initiated, the animal may be treated with different types of drugs to test the efficacy of the drug in treating cancer. This is an important preclinical step as the efficacy and toxicity of the drug need to be demonstrated in animals before it can be possibly considered for future use in human subjects. At the end of the study, the animals are euthanized and various organs, tissues, or the tumor itself are harvested from the animal for downstream cellular enrichment and analysis [16].
1.2.1.1 Cellular Subtypes Found in Solid Clinical Samples
There are many different types of organs and tissues in the body each with different cells. Due to space constraints, we are unfortunately unable to cover everything. Instead, we provide a brief introduction to some of the different cell types typically encountered when working with solid tissue samples. The goal is to highlight the diversity of cellular subtypes found within any tissue sample. Specifically, we discuss the epithelium, a form of tissue that is hig...
