The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers

Michael Barrett, Elizabeth Lenkiewicz, Smriti Malasi, Anamika Basu, Jennifer Holmes Yearley, Lakshmanan Annamalai, Ann E. McCullough, Heidi E. Kosiorek, Pooja Narang, Melissa A. Wilson Sayres, Meixuan Chen, Karen S. Anderson, Barbara A Pockaj

Research output: Contribution to journalArticle

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Abstract

Background: Elevated PD-L1 expression on tumor cells, a context associated with an adaptive immune response, has been linked to the total burden of copy number variants (CNVs) in aneuploid tumors, to microsatellite instability (MSI), and to specific genomic driver lesions, including loss of PTEN, MYC amplification, and activating mutations in driver oncogenes such as KRAS and PIK3CA. Triple-negative breast cancers (TNBCs) typically have high levels of CNVs and diverse driver lesions in their genomes. Thus, there is significant interest in exploiting genomic data to develop predictive immunotherapy biomarkers for patients with TNBC. Methods: Whole tissue samples from 55 resected TNBCs were screened by immunohistochemistry (IHC) for PD-1 and PD-L1 by using validated antibodies and established scoring methods for staining of tumor and non-tumor cells. In parallel, we interrogated biopsies from each resection with DNA content flow cytometry and sorted the nuclei of diploid, tetraploid, and aneuploid cell populations. CNVs were mapped with CNV oligonucleotide arrays by using purified (>95%) tumor populations. We generated whole exome data for 12 sorted tumor samples to increase the resolution within loci of interest and to incorporate somatic mutations into our genomic signatures. Results and Conclusions: PD-L1 staining was detected on tumor cells in 29 out of 54 (54%) evaluable cases and was associated with increased overall survival (P = 0.0024). High levels of PD-1 and PD-L1 (IHC ≥4) were present in 11 out of 54 (20%) and 20 out of 54 (37%) cases with staining of PD-L1 primarily on tumor cells for 17 out of 20 (85%) cases. The latter included tumors with both high (>50) and low (<20) numbers of CNVs. Notably, homozygous deletion of PTEN (n = 6) or activating mutation in PIK3CA (n = 1) was not associated with increased expression of either immune checkpoint activator in TNBC. In contrast, two treatment-naïve cases with EGFR driver amplicons had high PD-L1 tumor staining. High mutational load and predicted neoepitopes were observed in MSI+ and high CNV burden TNBCs but were not associated with high PD-L1 expression on tumor cells. Our results challenge current models of genomic-based immunotherapy signatures yet suggest that discrete genomic lesions may complement existing biomarkers to advance immune checkpoint therapies for patients with TNBC.

Original languageEnglish (US)
Article number71
JournalBreast Cancer Research
Volume20
Issue number1
DOIs
StatePublished - Jul 11 2018

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Triple Negative Breast Neoplasms
Neoplasms
Staining and Labeling
Microsatellite Instability
Aneuploidy
Immunotherapy
Mutation
Biomarkers
Immunohistochemistry
Exome
Tetraploidy
Adaptive Immunity
Oligonucleotide Array Sequence Analysis
Diploidy
Oncogenes
Population
Flow Cytometry
Research Design
Genome

Keywords

  • Copy number
  • Flow sorting
  • IHC
  • PD-1
  • PD-L1
  • Somatic mutations
  • Triple-negative breast cancer

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers. / Barrett, Michael; Lenkiewicz, Elizabeth; Malasi, Smriti; Basu, Anamika; Yearley, Jennifer Holmes; Annamalai, Lakshmanan; McCullough, Ann E.; Kosiorek, Heidi E.; Narang, Pooja; Wilson Sayres, Melissa A.; Chen, Meixuan; Anderson, Karen S.; Pockaj, Barbara A.

In: Breast Cancer Research, Vol. 20, No. 1, 71, 11.07.2018.

Research output: Contribution to journalArticle

Barrett, M, Lenkiewicz, E, Malasi, S, Basu, A, Yearley, JH, Annamalai, L, McCullough, AE, Kosiorek, HE, Narang, P, Wilson Sayres, MA, Chen, M, Anderson, KS & Pockaj, BA 2018, 'The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers', Breast Cancer Research, vol. 20, no. 1, 71. https://doi.org/10.1186/s13058-018-1004-0
Barrett, Michael ; Lenkiewicz, Elizabeth ; Malasi, Smriti ; Basu, Anamika ; Yearley, Jennifer Holmes ; Annamalai, Lakshmanan ; McCullough, Ann E. ; Kosiorek, Heidi E. ; Narang, Pooja ; Wilson Sayres, Melissa A. ; Chen, Meixuan ; Anderson, Karen S. ; Pockaj, Barbara A. / The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers. In: Breast Cancer Research. 2018 ; Vol. 20, No. 1.
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abstract = "Background: Elevated PD-L1 expression on tumor cells, a context associated with an adaptive immune response, has been linked to the total burden of copy number variants (CNVs) in aneuploid tumors, to microsatellite instability (MSI), and to specific genomic driver lesions, including loss of PTEN, MYC amplification, and activating mutations in driver oncogenes such as KRAS and PIK3CA. Triple-negative breast cancers (TNBCs) typically have high levels of CNVs and diverse driver lesions in their genomes. Thus, there is significant interest in exploiting genomic data to develop predictive immunotherapy biomarkers for patients with TNBC. Methods: Whole tissue samples from 55 resected TNBCs were screened by immunohistochemistry (IHC) for PD-1 and PD-L1 by using validated antibodies and established scoring methods for staining of tumor and non-tumor cells. In parallel, we interrogated biopsies from each resection with DNA content flow cytometry and sorted the nuclei of diploid, tetraploid, and aneuploid cell populations. CNVs were mapped with CNV oligonucleotide arrays by using purified (>95{\%}) tumor populations. We generated whole exome data for 12 sorted tumor samples to increase the resolution within loci of interest and to incorporate somatic mutations into our genomic signatures. Results and Conclusions: PD-L1 staining was detected on tumor cells in 29 out of 54 (54{\%}) evaluable cases and was associated with increased overall survival (P = 0.0024). High levels of PD-1 and PD-L1 (IHC ≥4) were present in 11 out of 54 (20{\%}) and 20 out of 54 (37{\%}) cases with staining of PD-L1 primarily on tumor cells for 17 out of 20 (85{\%}) cases. The latter included tumors with both high (>50) and low (<20) numbers of CNVs. Notably, homozygous deletion of PTEN (n = 6) or activating mutation in PIK3CA (n = 1) was not associated with increased expression of either immune checkpoint activator in TNBC. In contrast, two treatment-na{\"i}ve cases with EGFR driver amplicons had high PD-L1 tumor staining. High mutational load and predicted neoepitopes were observed in MSI+ and high CNV burden TNBCs but were not associated with high PD-L1 expression on tumor cells. Our results challenge current models of genomic-based immunotherapy signatures yet suggest that discrete genomic lesions may complement existing biomarkers to advance immune checkpoint therapies for patients with TNBC.",
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T1 - The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers

AU - Barrett, Michael

AU - Lenkiewicz, Elizabeth

AU - Malasi, Smriti

AU - Basu, Anamika

AU - Yearley, Jennifer Holmes

AU - Annamalai, Lakshmanan

AU - McCullough, Ann E.

AU - Kosiorek, Heidi E.

AU - Narang, Pooja

AU - Wilson Sayres, Melissa A.

AU - Chen, Meixuan

AU - Anderson, Karen S.

AU - Pockaj, Barbara A

PY - 2018/7/11

Y1 - 2018/7/11

N2 - Background: Elevated PD-L1 expression on tumor cells, a context associated with an adaptive immune response, has been linked to the total burden of copy number variants (CNVs) in aneuploid tumors, to microsatellite instability (MSI), and to specific genomic driver lesions, including loss of PTEN, MYC amplification, and activating mutations in driver oncogenes such as KRAS and PIK3CA. Triple-negative breast cancers (TNBCs) typically have high levels of CNVs and diverse driver lesions in their genomes. Thus, there is significant interest in exploiting genomic data to develop predictive immunotherapy biomarkers for patients with TNBC. Methods: Whole tissue samples from 55 resected TNBCs were screened by immunohistochemistry (IHC) for PD-1 and PD-L1 by using validated antibodies and established scoring methods for staining of tumor and non-tumor cells. In parallel, we interrogated biopsies from each resection with DNA content flow cytometry and sorted the nuclei of diploid, tetraploid, and aneuploid cell populations. CNVs were mapped with CNV oligonucleotide arrays by using purified (>95%) tumor populations. We generated whole exome data for 12 sorted tumor samples to increase the resolution within loci of interest and to incorporate somatic mutations into our genomic signatures. Results and Conclusions: PD-L1 staining was detected on tumor cells in 29 out of 54 (54%) evaluable cases and was associated with increased overall survival (P = 0.0024). High levels of PD-1 and PD-L1 (IHC ≥4) were present in 11 out of 54 (20%) and 20 out of 54 (37%) cases with staining of PD-L1 primarily on tumor cells for 17 out of 20 (85%) cases. The latter included tumors with both high (>50) and low (<20) numbers of CNVs. Notably, homozygous deletion of PTEN (n = 6) or activating mutation in PIK3CA (n = 1) was not associated with increased expression of either immune checkpoint activator in TNBC. In contrast, two treatment-naïve cases with EGFR driver amplicons had high PD-L1 tumor staining. High mutational load and predicted neoepitopes were observed in MSI+ and high CNV burden TNBCs but were not associated with high PD-L1 expression on tumor cells. Our results challenge current models of genomic-based immunotherapy signatures yet suggest that discrete genomic lesions may complement existing biomarkers to advance immune checkpoint therapies for patients with TNBC.

AB - Background: Elevated PD-L1 expression on tumor cells, a context associated with an adaptive immune response, has been linked to the total burden of copy number variants (CNVs) in aneuploid tumors, to microsatellite instability (MSI), and to specific genomic driver lesions, including loss of PTEN, MYC amplification, and activating mutations in driver oncogenes such as KRAS and PIK3CA. Triple-negative breast cancers (TNBCs) typically have high levels of CNVs and diverse driver lesions in their genomes. Thus, there is significant interest in exploiting genomic data to develop predictive immunotherapy biomarkers for patients with TNBC. Methods: Whole tissue samples from 55 resected TNBCs were screened by immunohistochemistry (IHC) for PD-1 and PD-L1 by using validated antibodies and established scoring methods for staining of tumor and non-tumor cells. In parallel, we interrogated biopsies from each resection with DNA content flow cytometry and sorted the nuclei of diploid, tetraploid, and aneuploid cell populations. CNVs were mapped with CNV oligonucleotide arrays by using purified (>95%) tumor populations. We generated whole exome data for 12 sorted tumor samples to increase the resolution within loci of interest and to incorporate somatic mutations into our genomic signatures. Results and Conclusions: PD-L1 staining was detected on tumor cells in 29 out of 54 (54%) evaluable cases and was associated with increased overall survival (P = 0.0024). High levels of PD-1 and PD-L1 (IHC ≥4) were present in 11 out of 54 (20%) and 20 out of 54 (37%) cases with staining of PD-L1 primarily on tumor cells for 17 out of 20 (85%) cases. The latter included tumors with both high (>50) and low (<20) numbers of CNVs. Notably, homozygous deletion of PTEN (n = 6) or activating mutation in PIK3CA (n = 1) was not associated with increased expression of either immune checkpoint activator in TNBC. In contrast, two treatment-naïve cases with EGFR driver amplicons had high PD-L1 tumor staining. High mutational load and predicted neoepitopes were observed in MSI+ and high CNV burden TNBCs but were not associated with high PD-L1 expression on tumor cells. Our results challenge current models of genomic-based immunotherapy signatures yet suggest that discrete genomic lesions may complement existing biomarkers to advance immune checkpoint therapies for patients with TNBC.

KW - Copy number

KW - Flow sorting

KW - IHC

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KW - PD-L1

KW - Somatic mutations

KW - Triple-negative breast cancer

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