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Juhlin. Cancer Drug Resist 2020;3:992-1000 I http://dx.doi.org/10.20517/cdr.2020.66 Page 995

overrepresentation of rare variants in genes responsible for DNA repair, including mismatch repair (MMR)
genes such as MSH6, nucleotide excision repair genes (e.g., XPC, ERCC5, CCNH) as well as genes involved
in homologous recombination repair (HRR) (e.g., XRCC3, ATM, BRCA1, CHEK2) [20-22] . Moreover, MMR
gene dysregulation and microsatellite instability (MSI) have been found in subsets of WDTCs, adding fuel
to the hypothesis that aberrant DNA repair is an important component in thyroid tumorigenesis [23,24] .

Through NGS studies in ATC, somatic mutations in DNA repair genes has been reported [13,14] . MSI is not
uncommon, and subsets of ATCs seem to exhibit a hypermutator phenotype with an immense increase
in somatic mutations - most often in tumors with defects in MMR genes, such as MLH1, MLH3, MSH5,
[13]
and MSH6 . Moreover, these MMR deficient, hypermutated ATCs might display a slightly better overall
prognosis than MMR competent ATCs, possibly reflecting a prognostic significance of this genetic
[25]
feature in clinical practice . Overall, ATCs are generally genetically unstable compared to their WDTC
counterparts with a massive overrepresentation of gross genetic aberrations, but a specific coupling
between ATCs and defective HRR has not yet been established [12,13] . As of this, the reason for the increase
in gross structural abnormalities observed in ATCs compared to WDTCs is not fully established.

WHOLE-GENOME SEQUENCING AS A TOOL TO PINPOINT CLONAL EVOLUTION AND DNA
REPAIR DEFICIENCY IN THYROID CANCER DEDIFFERENTIATION
Aim of the study
In order to deepen the understanding of the phylogenetic relations between WDTCs and ATCs as well as
[26]
to investigate the role of DNA repair in this process, Paulsson et al. recently employed WGS to analyze
synchronous manifestations of primary FTC, PDTC, and ATC, as well as regional lymph node metastases
of the PDTC and ATC components from a single patient. The main aim was to obtain high-resolution
phylogenetic data through the interrogation of both mutations as well as copy number alterations on a
genome-wide scale, as previous studies focused solely on WES, allowing for a less comprehensive copy
number coverage. Moreover, as the tumors analyzed were diagnosed synchronously in the same thyroid
lobe from the same patient and operation, this gave the authors a unique opportunity to study the genomic
progression of each tumor component without the risk of sampling bias or unrelated patient comparisons.
Herein, the overall results from this study as well as associated interpretations are highlighted from both
tumor progression and DNA repair perspectives.

The progression of thyroid cancer as a chained clonal event
In order to obtain material for a comparative analysis between the different thyroid tumor types derived
from the single patient, Paulsson et al. successfully extracted DNA from normal thyroid tissue as well
[26]
as neighboring FTC, PDTC, and ATC components, in addition to disseminated PDTC and ATC lymph
node metastases. This strategy required the material to be scraped from sections derived from formalin-
fixated paraffin-embedded tissues rather than fresh-frozen ones, as the primary FTC, PDTC, and ATC
components were bordering each other and only properly visualized using light microscopy.

Following successful whole-genome sequencing and bioinformatics analyses, Paulsson et al. identified
[26]
a number of coding mutational events in cancer-associated genes from each tumor component, which
were identified as somatic after correcting for variants also present in constitutional tissue. Some of these
mutations were carried along from the FTC all the way to the metastatic ATC, potentially suggesting they
provided the tumor components with a selective advantage (i.e., CALR, MSH2, and RB1). Additional
tumor-related genes were mutated at the level of the PDTC component, also identified in the neighboring
ATC and both metastatic lesions (i.e., APC, DROSHA, TP53, TERT, KMT2A, and ASXL1), implying that
one or several of these contributed to the dedifferentiation process. Furthermore, mutations in TSC1, TSC2,
JAK1, and DAXX appeared at the level of ATC, making it likely that some of these genetic events influenced