Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank

Ivanesa Pardo, Heather A. Lillemoe, Rachel J. Blosser, MiRan Choi, Candice A M Sauder, Diane K. Doxey, Theresa Mathieson, Bradley A. Hancock, Dadrie Baptiste, Rutuja Atale, Matthew Hickenbotham, Jin Zhu, Jarret Glasscock, Anna Maria Storniolo, Faye Zheng, RW W. Doerge, Yunlong Liu, Sunil Badve, Milan Radovich, Susan E. Clare

Research output: Contribution to journalArticle

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Abstract

Introduction: Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined.Methods: Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq).Results: In total, 255 genes representing 1.4% of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87%) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase.Conclusions: We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle.

Original languageEnglish
Article numberR26
JournalBreast Cancer Research
Volume16
Issue number2
DOIs
StatePublished - Mar 17 2014

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Tissue Banks
Menstrual Cycle
Transcriptome
Breast
Epithelium
Human Mammary Glands
Luteal Phase
Contraception
Genes
Tissue Donors
RNA Sequence Analysis
Developmental Biology
Contraceptive Agents
Molecular Biology
Volunteers
Breast Neoplasms
Messenger RNA
DNA
Research

ASJC Scopus subject areas

  • Cancer Research
  • Oncology
  • Medicine(all)

Cite this

Pardo, I., Lillemoe, H. A., Blosser, R. J., Choi, M., Sauder, C. A. M., Doxey, D. K., ... Clare, S. E. (2014). Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank. Breast Cancer Research, 16(2), [R26]. https://doi.org/10.1186/bcr3627

Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank. / Pardo, Ivanesa; Lillemoe, Heather A.; Blosser, Rachel J.; Choi, MiRan; Sauder, Candice A M; Doxey, Diane K.; Mathieson, Theresa; Hancock, Bradley A.; Baptiste, Dadrie; Atale, Rutuja; Hickenbotham, Matthew; Zhu, Jin; Glasscock, Jarret; Storniolo, Anna Maria; Zheng, Faye; Doerge, RW W.; Liu, Yunlong; Badve, Sunil; Radovich, Milan; Clare, Susan E.

In: Breast Cancer Research, Vol. 16, No. 2, R26, 17.03.2014.

Research output: Contribution to journalArticle

Pardo, I, Lillemoe, HA, Blosser, RJ, Choi, M, Sauder, CAM, Doxey, DK, Mathieson, T, Hancock, BA, Baptiste, D, Atale, R, Hickenbotham, M, Zhu, J, Glasscock, J, Storniolo, AM, Zheng, F, Doerge, RWW, Liu, Y, Badve, S, Radovich, M & Clare, SE 2014, 'Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank', Breast Cancer Research, vol. 16, no. 2, R26. https://doi.org/10.1186/bcr3627
Pardo, Ivanesa ; Lillemoe, Heather A. ; Blosser, Rachel J. ; Choi, MiRan ; Sauder, Candice A M ; Doxey, Diane K. ; Mathieson, Theresa ; Hancock, Bradley A. ; Baptiste, Dadrie ; Atale, Rutuja ; Hickenbotham, Matthew ; Zhu, Jin ; Glasscock, Jarret ; Storniolo, Anna Maria ; Zheng, Faye ; Doerge, RW W. ; Liu, Yunlong ; Badve, Sunil ; Radovich, Milan ; Clare, Susan E. / Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank. In: Breast Cancer Research. 2014 ; Vol. 16, No. 2.
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abstract = "Introduction: Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined.Methods: Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq).Results: In total, 255 genes representing 1.4{\%} of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87{\%}) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase.Conclusions: We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle.",
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AU - Choi, MiRan

AU - Sauder, Candice A M

AU - Doxey, Diane K.

AU - Mathieson, Theresa

AU - Hancock, Bradley A.

AU - Baptiste, Dadrie

AU - Atale, Rutuja

AU - Hickenbotham, Matthew

AU - Zhu, Jin

AU - Glasscock, Jarret

AU - Storniolo, Anna Maria

AU - Zheng, Faye

AU - Doerge, RW W.

AU - Liu, Yunlong

AU - Badve, Sunil

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AU - Clare, Susan E.

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N2 - Introduction: Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined.Methods: Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq).Results: In total, 255 genes representing 1.4% of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87%) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase.Conclusions: We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle.

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