9.7: Genetic testing for targeted cancer treatment

While each cancer is caused by random mutations -- and thus every cancer is in some sense a unique disease -- there are only a limited number of tumor suppressors and proto-oncogenes whose mutations cause the transformation from a non-cancer cell into a cancer cell. (This is how we discovered tumor suppressors and proto-oncogenes in the first place: they are mutated over and over in common cancers like B-cell lymphoma!) As DNA technologies -- PCR, microarrays and DNA sequencing in particular -- have become less expensive and more wide-spread, oncologists have begun using them to search for markers associated with specific sub-types of cancer (called tumor biomarkers) and use that information to guide treatment.

Classifying cancers

Cancers are classified by the type of cell that the tumor cells resemble and is therefore presumed to be the origin of the tumor. These types include:

• Carcinoma: Cancers derived from epithelial cells. This group includes many of the most common cancers and include nearly all those in the breast, prostate, lung, pancreas and colon. Most of these are of the adenocarcinoma type, which means that the cancer has gland-like differentiation.
• Sarcoma: Cancers arising from connective tissue (i.e. bone, cartilage, fat, nerve), each of which develops from cells originating in mesenchymal cells outside the bone marrow.
• Lymphoma and leukemia: These two classes arise from hematopoietic (blood-forming) cells that leave the marrow and tend to mature in the lymph nodes and blood, respectively.
• Germ cell tumor: Cancers derived from pluripotent cells, most often presenting in the testicle or the ovary (seminoma and dysgerminoma, respectively).
• Blastoma: Cancers derived from immature "precursor" cells or embryonic tissue.

Because cancer cells maintain (some) of the patterns of gene expression of the tissue they originated from, these classifications can guide an oncologist to use a treatment that works more reliably for that type of cancer. However, as mentioned above, the mutations that drive carcinogenesis are random -- and, as described in the previous section, cancers acquire mutations rapidly. Thus, which genes are being expressed by cells in a tumor may vary from individual to individual.

A classic example is breast cancer. Breast cancers are commonly grouped into categories based on the tumor cells' expression of different hormone receptors: estrogen receptor-positive (ER+), progesterone receptor positive (PR+), human epidermal growth factor positive (HER2+), and triple-negative (TNBC). These subclassifications are used to guide therapeutic choices, such as whether hormonal therapy is used as an adjunct to chemotherapy. Molecular markers are often tested using immunohistochemistry -- that is, staining biopsied tissue with antibodies, such as in the image below.

Immunohistochemistry of HER2 invasive breast carcinoma. A, estrogen receptor positive, nuclear staining. B, progesterone receptor positive, nuclear staining. C, HER2 3+ positive, membrane staining. D, Ki-67 positive 5%, nuclear staining. From Orrantia-Borunda et al, Breast Cancer. Mayrovitz HN, ed. Exon Publications 2022.

Genetic testing for targeted cancer therapy

As PCR, microarrays and DNA sequencing have become less expensive and more common, it is becoming easier to measure the gene expression and to sequence specific genes commonly involved in cancer to look for therapeutically relevant mutations. The expression of a gene, or the mutations present in it, may indicate or counterindicate particular treatments, as exemplified in the following table from https://testing.com:

Type of Cancer	Gene Tested*	Interpretation of Test Result
Breast cancer	Her2/neu	When present, likely response to trastuzumab
Chronic myelogenous leukemia (CML)	ABL1	Nonresponsive to imatinib when mutation(s) present
	BCR-ABL	When present, can be measured periodically to monitor response to targeted drug
Colon cancer	KRAS	When mutation present, likely resistance to tyrosine kinase inhibitor
	BRAF	Poor prognosis when mutation present
Gastrointestinal stromal tumor (GIST)—rare tumors of the digestive tract	KIT	Depending on mutation present, better response to imatinib therapy, increased dose of imatinib likely necessary and better response to sunitinib, or possible resistance to imatinib
	PDGFRA	When mutation present, less likely to respond to imatinib
Melanoma	BRAF	Better response to vemurafenib when mutation present with metastatic melanoma
Myeloproliferative neoplasms (MPNs)	JAK2	When mutation present, may be measured periodically to monitor responsiveness to treatment (e.g., Ruxolitinib)
Non-small cell lung cancer (NSCLC)	EGFR	Best response to tyrosine kinase inhibitors such as gefitinib and erlotinib in those with certain mutations
	EML4-ALK	If ALK is present, may respond to ALK kinase inhibitors, such as crizotinib
	ROS1	If ROS1 is present, ALK kinase inhibitors, such as crizotinib
	KRAS	Poorer prognosis when certain mutations present, resistance to tyrosine kinase inhibitors, and poor response to platinum/vinorelbine therapy
	PDL1	Likely response to immunotherapy

A useful example is the KRAS gene which encodes the K-Ras protein -- it is commonly mutated in lung cancer, ductal carcinoma and colon cancer. K-Ras is a GTPase, a class of enzymes which convert the nucleotide guanosine triphosphate (GTP) into guanosine diphosphate (GDP). Driver mutations in KRAS seem to underlie the pathogenesis of up to 20% of human cancers! Because K-Ras is a small protein, single mutations have major impacts on its shape and function -- and thus which therapeutic to use:

• G12C mutation. One fairly frequent driver mutation is KRASG12C which is adjacent a shallow binding site. As of 2019, this allowed the development of electrophilic KRAS inhibitors that can form irreversible covalent bonds with nucleophilic sulfur atom of Cys-12 and hence selectively target KRASG12C and leave wild-type KRAS untouched. In 2021, the U.S. FDA approved one KRASG12C mutant covalent inhibitor, sotorasib (AMG 510, Amgen) for the treatment of non-small cell lung cancer (NSCLC), the first KRAS inhibitor to reach the market and enter clinical use.
• G12D mutation. The most common KRAS mutation is G12D which is estimated to be present in up to 37% pancreatic cancers and over 12% of colorectal cancers. Normally amino acid position 12 of the KRAS protein is occupied by glycine but in G12D it is occupied by aspartic acid. As of 2023, there are no commercial drug candidates targeting the KRAS G12D mutation, though a number are in pre-clinical stages.

 

Sources:

https://www.ncbi.nlm.nih.gov/books/NBK583808/

https://www.testing.com/tests/geneti...ancer-therapy/

https://en.wikipedia.org/wiki/KRAS