A system for detecting high impact-low frequency mutations in primary tumors and metastases

M. Anjanappa, Y. Hao, E. R. Simpson, P. Bhat-Nakshatri, J. B. Nelson, S. A. Tersey, Raghu Mirmira, Aaron Cohen-Gadol, M. R. Saadatzadeh, L. Li, F. Fang, Kenneth Nephew, Kathy Miller, Yunlong Liu, Harikrishna Nakshatri

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50% of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.

Original languageEnglish (US)
Pages (from-to)185-196
Number of pages12
JournalOncogene
Volume37
Issue number2
DOIs
StatePublished - Jan 11 2018

Fingerprint

Mutation Rate
Neoplasm Metastasis
Mutation
Neoplasms
Liver
Epithelial Cells
Breast Neoplasms
Cultured Tumor Cells
DNA
Transforming Growth Factors
HLA-DR Antigens
Genomics
Computational Biology
Epigenomics
Genes
Sequence Analysis
Hepatocellular Carcinoma
Clone Cells
Tumor Necrosis Factor-alpha
Genome

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Cancer Research

Cite this

Anjanappa, M., Hao, Y., Simpson, E. R., Bhat-Nakshatri, P., Nelson, J. B., Tersey, S. A., ... Nakshatri, H. (2018). A system for detecting high impact-low frequency mutations in primary tumors and metastases. Oncogene, 37(2), 185-196. https://doi.org/10.1038/onc.2017.322

A system for detecting high impact-low frequency mutations in primary tumors and metastases. / Anjanappa, M.; Hao, Y.; Simpson, E. R.; Bhat-Nakshatri, P.; Nelson, J. B.; Tersey, S. A.; Mirmira, Raghu; Cohen-Gadol, Aaron; Saadatzadeh, M. R.; Li, L.; Fang, F.; Nephew, Kenneth; Miller, Kathy; Liu, Yunlong; Nakshatri, Harikrishna.

In: Oncogene, Vol. 37, No. 2, 11.01.2018, p. 185-196.

Research output: Contribution to journalArticle

Anjanappa, M, Hao, Y, Simpson, ER, Bhat-Nakshatri, P, Nelson, JB, Tersey, SA, Mirmira, R, Cohen-Gadol, A, Saadatzadeh, MR, Li, L, Fang, F, Nephew, K, Miller, K, Liu, Y & Nakshatri, H 2018, 'A system for detecting high impact-low frequency mutations in primary tumors and metastases', Oncogene, vol. 37, no. 2, pp. 185-196. https://doi.org/10.1038/onc.2017.322
Anjanappa M, Hao Y, Simpson ER, Bhat-Nakshatri P, Nelson JB, Tersey SA et al. A system for detecting high impact-low frequency mutations in primary tumors and metastases. Oncogene. 2018 Jan 11;37(2):185-196. https://doi.org/10.1038/onc.2017.322
Anjanappa, M. ; Hao, Y. ; Simpson, E. R. ; Bhat-Nakshatri, P. ; Nelson, J. B. ; Tersey, S. A. ; Mirmira, Raghu ; Cohen-Gadol, Aaron ; Saadatzadeh, M. R. ; Li, L. ; Fang, F. ; Nephew, Kenneth ; Miller, Kathy ; Liu, Yunlong ; Nakshatri, Harikrishna. / A system for detecting high impact-low frequency mutations in primary tumors and metastases. In: Oncogene. 2018 ; Vol. 37, No. 2. pp. 185-196.
@article{d9f7e8455075412fa2895da31533bbc9,
title = "A system for detecting high impact-low frequency mutations in primary tumors and metastases",
abstract = "Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50{\%} of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.",
author = "M. Anjanappa and Y. Hao and Simpson, {E. R.} and P. Bhat-Nakshatri and Nelson, {J. B.} and Tersey, {S. A.} and Raghu Mirmira and Aaron Cohen-Gadol and Saadatzadeh, {M. R.} and L. Li and F. Fang and Kenneth Nephew and Kathy Miller and Yunlong Liu and Harikrishna Nakshatri",
year = "2018",
month = "1",
day = "11",
doi = "10.1038/onc.2017.322",
language = "English (US)",
volume = "37",
pages = "185--196",
journal = "Oncogene",
issn = "0950-9232",
publisher = "Nature Publishing Group",
number = "2",

}

TY - JOUR

T1 - A system for detecting high impact-low frequency mutations in primary tumors and metastases

AU - Anjanappa, M.

AU - Hao, Y.

AU - Simpson, E. R.

AU - Bhat-Nakshatri, P.

AU - Nelson, J. B.

AU - Tersey, S. A.

AU - Mirmira, Raghu

AU - Cohen-Gadol, Aaron

AU - Saadatzadeh, M. R.

AU - Li, L.

AU - Fang, F.

AU - Nephew, Kenneth

AU - Miller, Kathy

AU - Liu, Yunlong

AU - Nakshatri, Harikrishna

PY - 2018/1/11

Y1 - 2018/1/11

N2 - Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50% of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.

AB - Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50% of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.

UR - http://www.scopus.com/inward/record.url?scp=85040515703&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85040515703&partnerID=8YFLogxK

U2 - 10.1038/onc.2017.322

DO - 10.1038/onc.2017.322

M3 - Article

VL - 37

SP - 185

EP - 196

JO - Oncogene

JF - Oncogene

SN - 0950-9232

IS - 2

ER -