TY - GEN
T1 - Genomic Analysis of Metastatic Breast Cancer
T2 - Exome sequencing of primary tumor, metastasis and circulating tumor DNA
AU - Kavan, Stephanie
PY - 2022/5/31
Y1 - 2022/5/31
N2 - Breast cancer is the most common invasive malignancy and the leading cause of cancer-related deaths among
women. One of the biggest challenges in handling breast cancer is the extensive inter-and intra-tumoral
heterogeneity resulting from a natural or therapeutic selection. Data obtained from various genomic profiling
studies on primary tumors and matched metastases suggested different models of evolutionary patterns that
differ in timing of metastasis-enabling genomic alterations and the degree of genomic concordance between
progression states. Characterizing the evolutionary landscape of breast tumors can provide a biological
understanding of tumor progression from primary cancers to dissemination and may be necessary for directing
effective treatments. Currently, tissue biopsy is considered the gold standard for diagnosis and treatment
guidance in breast cancer, although it may insufficiently represent the entire genomic landscape of a tumor.
Multiple limitations of this technique have led to the proposal of liquid biopsies as an attractive complementary
tool to tissue biopsies. In the form of circulating tumor DNA (ctDNA), liquid biopsy could potentially capture
the inter-and intra-tumoral heterogeneity present in metastatic breast cancer and, through serial blood draws,
track the clonal evolution of the cancer genome.Study I is a literature review focused on intratumor and temporal genetic heterogeneity in breast cancer,
emphasizing studies tracking clonal evolution by global analysis in multiple progression steps from the same
patient. Additionally, we discussed the potential of plasma ctDNA compared to tissue biopsies from primary
tumors and metastases for a complete overview of the molecular tumor landscape. Considering the low number
of papers published in this part using global analysis, we also included studies using targeted sequencing
approaches. Finally, we compared studies focusing on the relevance of genetic heterogeneity and clonal
evolution in the clinical setting and discussed plasma circulating tumor DNA as a powerful real-time approach
for monitoring the clonal landscape of cancer during treatment and recurrence. Breast Cancer is a spatial and temporal dynamic disease where differently evolving genetic clones are
responsible for progression and clinical outcome. Still, the impact of systemic treatment on clonal evolution
and tumor heterogeneity is poorly understood. In Study II, we ought to map the repertoire of genetic
alterations in systemically untreated breast cancer patients with de novo metastatic disease. We analyzed wholeexome sequencing data from the paired primary tumor and metastatic samples from three breast cancer patients
who had not received systemic therapy yet. Point mutations, copy number alterations, potential driver genes,
and mutational cancer cell fractions were identified using state-of-the-art bioinformatics methods. Genomic
differences were observed between primary tumor and metastatic lesion, showing a high level of genetic
divergence. All three patients followed the parallel progression model, with early monoclonal dissemination
from the primary tumor followed by separate clonal evolution. Interestingly, metastasis-specific mutations
involved genes EP300, APOBEC3B, KDM5C, ASXL1, and EPCAM, all associated with cancer migration and
progression. These results were supported by pathway analysis, showing cancer-driving pathways are mainly
significant in stem mutations present in both primary tumor and metastasis. Notably, affected pathways
reflected the patient’s molecular subtype and metastasis location. Lastly, alterations specific to the metastasis
affected driver genes involved in collagen formation, muscle contraction, and nuclear envelope
depolymerizations supporting metastatic tumor cell migration, invasion, and genomic instability. The described patterns of evolution and the polyclonal nature of breast cancer have clinical consequences and
should be considered during patient diagnosis and treatment selection. Current studies focusing on the
relevance of clonal evolution in the clinical setting elucidate the role of liquid biopsy as a noninvasive biomarker
for monitoring clonal progression and response to treatment. In the clinical setting, circulating tumor DNA
may constitute ideal support for tumor biopsies to characterize the genetic landscape of metastatic disease. This
might improve longitudinal monitoring of disease dynamics and treatment effectiveness to detect any residual
tumor after resection, relapse, or metastasis within a particular patient.In Study III, we performed copy number profiling and somatic mutation detection based on whole-exome
sequencing of primary tumors, distant metastasis, and plasma circulating tumor DNA from eight metastatic
breast cancer patients. Our data showed diverse patterns of tumor evolution. Although linear evolution with
late dissemination of metastatic cells was detected in some cases, we mainly observed parallel evolution with
early dissemination from primary tumors to distant sites. Comparing tissue biopsies with plasma samples, we
detected variants mirroring primary tumor and/or metastasis, depending on the period between the progression
steps. The old mutations from the early tumor clone dominate in plasma, followed by metastasis-specific
mutations. However, different patterns were observed. The genomic discordance between the various stages
of tumor evolution emphasizes the importance of molecular profiling of metastatic tissue and the possibilities
of liquid biopsies for real-time tracking of tumor dynamics.
AB - Breast cancer is the most common invasive malignancy and the leading cause of cancer-related deaths among
women. One of the biggest challenges in handling breast cancer is the extensive inter-and intra-tumoral
heterogeneity resulting from a natural or therapeutic selection. Data obtained from various genomic profiling
studies on primary tumors and matched metastases suggested different models of evolutionary patterns that
differ in timing of metastasis-enabling genomic alterations and the degree of genomic concordance between
progression states. Characterizing the evolutionary landscape of breast tumors can provide a biological
understanding of tumor progression from primary cancers to dissemination and may be necessary for directing
effective treatments. Currently, tissue biopsy is considered the gold standard for diagnosis and treatment
guidance in breast cancer, although it may insufficiently represent the entire genomic landscape of a tumor.
Multiple limitations of this technique have led to the proposal of liquid biopsies as an attractive complementary
tool to tissue biopsies. In the form of circulating tumor DNA (ctDNA), liquid biopsy could potentially capture
the inter-and intra-tumoral heterogeneity present in metastatic breast cancer and, through serial blood draws,
track the clonal evolution of the cancer genome.Study I is a literature review focused on intratumor and temporal genetic heterogeneity in breast cancer,
emphasizing studies tracking clonal evolution by global analysis in multiple progression steps from the same
patient. Additionally, we discussed the potential of plasma ctDNA compared to tissue biopsies from primary
tumors and metastases for a complete overview of the molecular tumor landscape. Considering the low number
of papers published in this part using global analysis, we also included studies using targeted sequencing
approaches. Finally, we compared studies focusing on the relevance of genetic heterogeneity and clonal
evolution in the clinical setting and discussed plasma circulating tumor DNA as a powerful real-time approach
for monitoring the clonal landscape of cancer during treatment and recurrence. Breast Cancer is a spatial and temporal dynamic disease where differently evolving genetic clones are
responsible for progression and clinical outcome. Still, the impact of systemic treatment on clonal evolution
and tumor heterogeneity is poorly understood. In Study II, we ought to map the repertoire of genetic
alterations in systemically untreated breast cancer patients with de novo metastatic disease. We analyzed wholeexome sequencing data from the paired primary tumor and metastatic samples from three breast cancer patients
who had not received systemic therapy yet. Point mutations, copy number alterations, potential driver genes,
and mutational cancer cell fractions were identified using state-of-the-art bioinformatics methods. Genomic
differences were observed between primary tumor and metastatic lesion, showing a high level of genetic
divergence. All three patients followed the parallel progression model, with early monoclonal dissemination
from the primary tumor followed by separate clonal evolution. Interestingly, metastasis-specific mutations
involved genes EP300, APOBEC3B, KDM5C, ASXL1, and EPCAM, all associated with cancer migration and
progression. These results were supported by pathway analysis, showing cancer-driving pathways are mainly
significant in stem mutations present in both primary tumor and metastasis. Notably, affected pathways
reflected the patient’s molecular subtype and metastasis location. Lastly, alterations specific to the metastasis
affected driver genes involved in collagen formation, muscle contraction, and nuclear envelope
depolymerizations supporting metastatic tumor cell migration, invasion, and genomic instability. The described patterns of evolution and the polyclonal nature of breast cancer have clinical consequences and
should be considered during patient diagnosis and treatment selection. Current studies focusing on the
relevance of clonal evolution in the clinical setting elucidate the role of liquid biopsy as a noninvasive biomarker
for monitoring clonal progression and response to treatment. In the clinical setting, circulating tumor DNA
may constitute ideal support for tumor biopsies to characterize the genetic landscape of metastatic disease. This
might improve longitudinal monitoring of disease dynamics and treatment effectiveness to detect any residual
tumor after resection, relapse, or metastasis within a particular patient.In Study III, we performed copy number profiling and somatic mutation detection based on whole-exome
sequencing of primary tumors, distant metastasis, and plasma circulating tumor DNA from eight metastatic
breast cancer patients. Our data showed diverse patterns of tumor evolution. Although linear evolution with
late dissemination of metastatic cells was detected in some cases, we mainly observed parallel evolution with
early dissemination from primary tumors to distant sites. Comparing tissue biopsies with plasma samples, we
detected variants mirroring primary tumor and/or metastasis, depending on the period between the progression
steps. The old mutations from the early tumor clone dominate in plasma, followed by metastasis-specific
mutations. However, different patterns were observed. The genomic discordance between the various stages
of tumor evolution emphasizes the importance of molecular profiling of metastatic tissue and the possibilities
of liquid biopsies for real-time tracking of tumor dynamics.
U2 - 10.21996/tmns-bs18
DO - 10.21996/tmns-bs18
M3 - Ph.D. thesis
PB - Syddansk Universitet. Det Sundhedsvidenskabelige Fakultet
ER -