Molecular Genetics of Thyroid Cancer Part 2

Papillary thyroid carcinoma (PTC):
- Is one of the best molecularly understood cancers:
  - With more that 97% of the driver mutations identified
One of the main goals of the cancer genome atlas research network study (TCGA) thyroid project:
- Was to detect cancer-initiating mutations, i.e., driver mutations:
  - In those cases that lacked the well-known PTC driver mutations (BRAF V600E, point mutations of RAS genes, and gene fusions involving RET and NTRK):
    - These cases are referred to by computational biologists as “dark matter” cases
- These very important studies under the umbrella of NCI and NIH analyzed 496 PTCs that permitted several analyses:
  - That showed that approximately 75% of all PTC:
    - Developed through the molecular mechanism of point mutation:
    - The most common been the:
      - BRAF V600E mutation
    - The second most common the:
      - RAS mutation
    - The thyroid most common the:
      - TERT mutation – That constituted a small percentage of tumors but was found to be a marker of aggressive disease
  - Roughly 15% of PTC develop through the mechanism of gene fusions:
    - The most common been RET / PTC,
      NTRK 1/3, ALK, BRAF, PAX8 / PPARG
    - The RET / PTC, NTRK 1/3, ALK have very important therapeutic implications for advanced thyroid cancer:
      - Because of the availability of targeted inhibitors with low toxicity and
        high efficacy for the management of these tumors
  - Roughly 7% of PTC develop exclusively from the molecular mechanism of copy number alterations (CNA) (Figure)

Roughly 45% to 75% of PTC (29% to 83%) have a mutation in the BRAF gene:
- Making it the most frequently known genetic
  alteration in PTC
- Practically all mutations involve:
  - Nucleotide 1799 and result in a valine-to-glutamate substitution at residue 600 (V600E):
    - This point mutation leads to constitutive activation of BRAF kinase:
      - Resulting in a constant phosphorylation of MEK and downstream effectors of the MAPK pathway (Figure)
  - Other mechanisms of BRAF activation in PTC include:
    - K601E point mutation:
      - Small in-frame insertions or deletions surrounding codon 600
    - AKAP9-BRAF rearrangement:
      - Which is more common in PTC associated with radiation exposure
BRAF V600E mutation:
- Is the prevailing mutation in PTC:
  - With classical histology and in the tall cell subtype:
    - But is rare in follicular subtypes tumors
- In multiple studies, the existence of the BRAF mutation:
  - Has been linked with aggressive tumor biology such as:
    - Advanced stage at presentation
    - Extrathyroidal extension (infiltrative)
    - Recurrence
    - Lymph node or distant metastases
- BRAF V600E mutation:
  - Is an independent predictor of tumor recurrence:
    - Even in patients with stage I to stage II disease
- The ability of thyroid cancers to trap
  radioiodine:
  - Has been identified to be decreased in tumors with the BRAF V600E mutations and this may lead to treatment failures of the recurrent disease:
    - Which is due to the dysregulation of the function of sodium iodide
      symporter (NIS) and other genes metabolizing iodide in the thyroid follicular cells
- In thyroid nodules, the V600E BRAF mutation is limited to PTC, poorly differentiated and ATC arising from PTC:
  - Consequently, the identification of the BRAF V600E mutation in FNA cytology of thyroid nodules:
    - Practically confirms the diagnosis of PTC
  - Testing for the BRAF mutation is very useful diagnostically in thyroid FNA samples with indeterminate results:
    - As it can help to determine the diagnosis of PTC in a important portion of these biopsies
Pathologically PTC is one disease and biologically at a minimum PTC has two significantly different groups:
- Based on multiple type of analysis like gene expression alterations, microRNA alterations, DNA methylation, transcriptomics (Figure)
The Cancer Genome Atlas (TCGA) study on PTC highlighted that PTC can be grouped into:
- BRAFV600E-like and RAS-like tumors:
  - BRAFV600E-like tumors:
    - Also harbor RET fusions
  - RAS-like tumors:
    - Show RAS mutations, the BRAFK601E, and PPARG and THADA fusions
- The V600E BRAF–like PTC:
  - Are usually classic PTC and tall cell subtype of PTC
- Clinically when we look at the differentiation score:
  - Which is the expression of genes involved in iodine metabolism and synthesis:
    - BRAF tumors:
      - Loose expression of thyroid differentiation markers
    - RAS-like tumors retain them:
      - Almost at the level of a normal thyroid cell
      - This is important therapeutically because one of the most efficient management options in thyroid cancer is iodine therapy
    - RAS-like tumors:
      - Are usually follicular variant PTC
  - Usually all BRAF mutations are BRAF-like and all RAS mutations are RAS-like:
    - But all other type of molecular alterations can be hidden in either BRAF-like and RAS-like:
      - For example, BRAF K601E mutations are found in RAS-like tumors