Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer

Elza Kuzņecova; Zanda Daneberga; Egija Berga-Švītiņa; Miki Nakazawa-Miklasevica; Arvīds Irmejs; Jānis Gardovskis; Edvīns Miklaševičs

doi:doi:10.2478/prolas-2023-0004

Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer

Elza Kuzņecova (Corresponding Author), Zanda Daneberga, Egija Berga-Švītiņa, Miki Nakazawa-Miklasevica, Arvīds Irmejs, Jānis Gardovskis, Edvīns Miklaševičs

Department of Surgery

Research output: Contribution to journal › Article › peer-review

Abstract

Triple negative breast cancer (TNBC) is a breast cancer subtype characterised by lack of oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor, and by worse
prognosis than other cancer types. The aim of this study was to identify hub genes and molecular
pathways for possible prognostic markers for TNBC. Nineteen breast cancer transcriptomes were
sequenced using Illumina platform and analysed to identify differentially expressed genes in the
TNBC subtype. Gene ontology enrichment analysis was conducted using the ToppGene tool.
Then, the STRING online database was used for protein-protein interaction (PPI) network construction. Cytohubba and the MCODE plug-in were used to screen functional modules and hub
genes. In total, 229 DEGs were identified by differential gene expression analysis in the TNBC
group. Eight genes were screened out from the PPI network — FOXA1, ESR1, TFF1, GATA3,
TFF3, AR, SLC39A6, COL9A1. In conclusion, this study indicates that the molecular subtype specific gene expression pattern provides useful information for targeted, biomarker-driven treatment
options.

Original language	English
Pages (from-to)	33-40
Number of pages	8
Journal	Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences.
Volume	77
Issue number	1
DOIs	https://doi.org/doi:10.2478/prolas-2023-0004
Publication status	Published - 1 Feb 2023

Field of Science*

3.2 Clinical medicine
3.1 Basic medicine

Publication Type*

1.1. Scientific article indexed in Web of Science and/or Scopus database

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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doi:10.2478/prolas-2023-0004Licence: CC BY

https://doi.org/10.2478/prolas-2023-0004Licence: CC BY

Cite this

Kuzņecova, E., Daneberga, Z., Berga-Švītiņa, E., Nakazawa-Miklasevica, M., Irmejs, A., Gardovskis, J., & Miklaševičs, E. (2023). Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer. Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences., 77(1 ), 33-40. https://doi.org/doi:10.2478/prolas-2023-0004

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title = "Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer",

abstract = "Triple negative breast cancer (TNBC) is a breast cancer subtype characterised by lack of oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor, and by worseprognosis than other cancer types. The aim of this study was to identify hub genes and molecularpathways for possible prognostic markers for TNBC. Nineteen breast cancer transcriptomes weresequenced using Illumina platform and analysed to identify differentially expressed genes in theTNBC subtype. Gene ontology enrichment analysis was conducted using the ToppGene tool.Then, the STRING online database was used for protein-protein interaction (PPI) network construction. Cytohubba and the MCODE plug-in were used to screen functional modules and hubgenes. In total, 229 DEGs were identified by differential gene expression analysis in the TNBCgroup. Eight genes were screened out from the PPI network — FOXA1, ESR1, TFF1, GATA3,TFF3, AR, SLC39A6, COL9A1. In conclusion, this study indicates that the molecular subtype specific gene expression pattern provides useful information for targeted, biomarker-driven treatmentoptions.",

author = "Elza Kuzņecova and Zanda Daneberga and Egija Berga-{\v S}vītiņa and Miki Nakazawa-Miklasevica and Arvīds Irmejs and Jānis Gardovskis and Edvīns Mikla{\v s}evi{\v c}s",

note = "Publisher Copyright: {\textcopyright} 2023 Elza Kuzņecova et al., published by Sciendo.",

year = "2023",

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doi = "doi:10.2478/prolas-2023-0004",

language = "English",

volume = "77",

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Kuzņecova, E , Daneberga, Z , Berga-Švītiņa, E , Nakazawa-Miklasevica, M , Irmejs, A , Gardovskis, J & Miklaševičs, E 2023, 'Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer', Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences., vol. 77, no. 1 , pp. 33-40. https://doi.org/doi:10.2478/prolas-2023-0004

Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer. / Kuzņecova, Elza (Corresponding Author); Daneberga, Zanda ; Berga-Švītiņa, Egija et al.
In: Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences., Vol. 77, No. 1 , 01.02.2023, p. 33-40.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer

AU - Kuzņecova, Elza

AU - Daneberga, Zanda

AU - Berga-Švītiņa, Egija

AU - Nakazawa-Miklasevica, Miki

AU - Irmejs, Arvīds

AU - Gardovskis, Jānis

AU - Miklaševičs, Edvīns

PY - 2023/2/1

Y1 - 2023/2/1

N2 - Triple negative breast cancer (TNBC) is a breast cancer subtype characterised by lack of oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor, and by worseprognosis than other cancer types. The aim of this study was to identify hub genes and molecularpathways for possible prognostic markers for TNBC. Nineteen breast cancer transcriptomes weresequenced using Illumina platform and analysed to identify differentially expressed genes in theTNBC subtype. Gene ontology enrichment analysis was conducted using the ToppGene tool.Then, the STRING online database was used for protein-protein interaction (PPI) network construction. Cytohubba and the MCODE plug-in were used to screen functional modules and hubgenes. In total, 229 DEGs were identified by differential gene expression analysis in the TNBCgroup. Eight genes were screened out from the PPI network — FOXA1, ESR1, TFF1, GATA3,TFF3, AR, SLC39A6, COL9A1. In conclusion, this study indicates that the molecular subtype specific gene expression pattern provides useful information for targeted, biomarker-driven treatmentoptions.

AB - Triple negative breast cancer (TNBC) is a breast cancer subtype characterised by lack of oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor, and by worseprognosis than other cancer types. The aim of this study was to identify hub genes and molecularpathways for possible prognostic markers for TNBC. Nineteen breast cancer transcriptomes weresequenced using Illumina platform and analysed to identify differentially expressed genes in theTNBC subtype. Gene ontology enrichment analysis was conducted using the ToppGene tool.Then, the STRING online database was used for protein-protein interaction (PPI) network construction. Cytohubba and the MCODE plug-in were used to screen functional modules and hubgenes. In total, 229 DEGs were identified by differential gene expression analysis in the TNBCgroup. Eight genes were screened out from the PPI network — FOXA1, ESR1, TFF1, GATA3,TFF3, AR, SLC39A6, COL9A1. In conclusion, this study indicates that the molecular subtype specific gene expression pattern provides useful information for targeted, biomarker-driven treatmentoptions.

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DO - doi:10.2478/prolas-2023-0004

M3 - Article

SN - 2255-890X

VL - 77

SP - 33

EP - 40

JO - Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences.

JF - Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences.

IS - 1

ER -

Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer

Abstract

Field of Science*

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UN SDGs

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