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Prognostic significance of CHCHD2P9 and ZNF204P in breast cancer: exploring their expression patterns and associations with malignancy-related genes

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Abstract

Background

Non-coding RNAs (ncRNAs) have a crucial impact on diverse cellular processes, influencing the progression of breast cancer (BC). The objective of this study was to identify novel ncRNAs in BC with potential effects on patient survival and disease progression.

Methods

We utilized the cancer genome atlas data to identify ncRNAs associated with BC pathogenesis. We explored the association between these ncRNA expressions and survival rates. A risk model was developed using candidate ncRNA expression and beta coefficients obtained from a multivariate Cox regression analysis. Co-expression networks were constructed to determine potential relationships between these ncRNAs and molecular pathways. For validation, we employed BC samples and the RT-qPCR method.

Results

Our findings revealed a noteworthy increase in the expression of AC093850.2 and CHCHD2P9 in BC, which was correlated with a poor prognosis. In contrast, ADAMTS9-AS1 and ZNF204P displayed significant downregulation and were associated with a favorable prognosis. The risk model, incorporating these four ncRNAs, robustly predicted patient survival. The co-expression network showed an effective association between levels of AC093850.2, CHCHD2P9, ADAMTS9-AS1, and ZNF204P and genes involved in pathways like metastasis, angiogenesis, metabolism, and DNA repair. The RT-qPCR results verified notable alterations in the expression of CHCHD2P9 and ZNF204P in BC samples. Pan-cancer analyses revealed alterations in the expression of these two ncRNAs across various cancer types.

Conclusion

This study presents a groundbreaking discovery, highlighting the substantial dysregulation of CHCHD2P9 and ZNF204P in BC and other cancers, with implications for patient survival.

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Data availability

No datasets were generated or analysed during the current study.

Abbreviations

ncRNAs:

non-coding RNAs

BC:

breast cancer

lncRNAs:

long non-coding RNAs

TCGA:

the cancer genome atlas

K-M:

Kaplan-Meier

ROC:

receiver operating characteristic

References

  1. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A et al (2021) Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. Cancer J Clin 71(3):209–249

    Article  Google Scholar 

  2. Guo L, Kong D, Liu J, Zhan L, Luo L, Zheng W et al (2023) Breast cancer heterogeneity and its implication in personalized precision therapy. Experimental Hematol Oncol 12(1):1–27

    Article  Google Scholar 

  3. Waks AG, Winer EP (2019) Breast cancer treatment: a review. JAMA 321(3):288–300

    Article  CAS  PubMed  Google Scholar 

  4. Hombach S, Kretz M (2016) Non-coding RNAs: classification, biology and functioning. Non-coding RNAs in colorectal cancer. 3–17

  5. Vikram R, Ramachandran R, Abdul KSM (2014) Functional significance of long non-coding RNAs in breast cancer. Breast Cancer 21:515–521

    Article  PubMed  Google Scholar 

  6. Poliseno L, Marranci A, Pandolfi PP (2015) Pseudogenes in human cancer. Front Med 2:68

    Article  Google Scholar 

  7. Mahdevar M, Vatandoost J, Forootan FS, Kiani-Esfahani A, Esmaeili M, Peymani M, et al (2021) Steroid receptor RNA activator gene footprint in the progression and drug resistance of colorectal cancer through oxidative phosphorylation pathway. Life Sci 285:119950

  8. Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D et al (2016) TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res 44(8):e71–e

    Article  PubMed  Google Scholar 

  9. Law CW, Chen Y, Shi W, Smyth GK (2014) Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 15(2):1–17

    Article  Google Scholar 

  10. Yan H, Bu P (2021) Non-coding RNA in cancer. Essays Biochem 65(4):625–639

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Sharma VK, Sharma RK, Singh SK (2014) Antisense oligonucleotides: modifications and clinical trials. MedChemComm 5(10):1454–1471

    Article  CAS  Google Scholar 

  12. Li W, Cheng Y, Cheng J, Yao J, Song M, Yan M et al (2023) Long noncoding RNA LINC01614 is a diagnostic and prognostic marker for breast Cancer. Discov Med 35(174):19–27

    Article  PubMed  Google Scholar 

  13. Vishnubalaji R, Shaath H, Elkord E, Alajez NM (2019) Long non-coding RNA (lncRNA) transcriptional landscape in breast cancer identifies LINC01614 as non-favorable prognostic biomarker regulated by TGFβ and focal adhesion kinase (FAK) signaling. Cell Death Discovery 5(1):109

    Article  PubMed  PubMed Central  Google Scholar 

  14. Dong X, ** C, Chen D, Chen Y, Ye Z-q, Zhang X et al (2021) Genomic instability-related LncRNA signature predicts the prognosis and highlights LINC01614 is a tumor microenvironment-related oncogenic lncRNA of papillary thyroid carcinoma. Front Oncol 11:737867

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Jia J, Guo P, Zhang L, Kong W, Wang F (2023) LINC01614 Promotes Colorectal Cancer Cell Growth and Migration by Regulating miR-217-5p/HMGA1 Axis. Analytical Cellular Pathology. ;2023

  16. Liu AN, Qu HJ, Yu CY, Sun P (2018) Knockdown of LINC01614 inhibits lung adenocarcinoma cell progression by up-regulating miR‐217 and down‐regulating FOXP1. J Cell Mol Med 22(9):4034–4044

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Wang Z, Yan H, Cheng D, Xu L, Shen T, Chen Y et al (2021) RETRACTED ARTICLE: Novel lncRNA LINC01614 facilitates bladder Cancer Proliferation, Migration and Invasion through the miR-217/RUNX2/Wnt/β-Catenin Axis. Cancer Manage Res. 8387–8397

  18. Lu G, Li Y, Ma Y, Lu J, Chen Y, Jiang Q et al (2018) Long noncoding RNA LINC00511 contributes to breast cancer tumourigenesis and stemness by inducing the miR-185-3p/E2F1/Nanog axis. J Experimental Clin cancer Res 37:1–11

    Article  Google Scholar 

  19. Ghafouri-Fard S, Safarzadeh A, Hussen BM, Taheri M, Ayatollahi SA (2023) A review on the role of LINC00511 in cancer. Front Genet 14:1116445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Fang S, Zhao Y, Hu X (2020) LncRNA ADAMTS9-AS1 restrains the aggressive traits of breast carcinoma cells via sponging miR-513a-5p. Cancer Manage Res. 10693–10703

  21. Li N, Li J, Mi Q, **e Y, Li P, Wang L et al (2020) Long non-coding RNA ADAMTS9‐AS1 suppresses colorectal cancer by inhibiting the Wnt/β‐catenin signalling pathway and is a potential diagnostic biomarker. J Cell Mol Med 24(19):11318–11329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Wang P, Zhang Y, Lv X, Zhou J, Cang S, Song Y (2023) LncRNA ADAMTS9-AS1 inhibits the stemness of lung adenocarcinoma cells by regulating miR-5009-3p/NPNT axis. Genomics 115(3):110596

    Article  CAS  PubMed  Google Scholar 

  23. **ao R, Yang M, Tan Y, Ding R, Li D (2021) Identification of five immune-related lncRNAs predicting survival and tumor microenvironment characteristics in breast cancer. Comput Math Methods Med 2021:1–12

    Google Scholar 

  24. Ma J, Lin X, Wang X, Min Q, Wang T, Tang C (2021) Reconstruction and analysis of the immune-related LINC00987/A2M axis in lung adenocarcinoma. Front Mol Biosci 8:644557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Li J, Kang J, Liu W, Liu J, Pan G, Mao A et al (2022) Docetaxel-resistant triple-negative breast cancer cell-derived exosomal lncRNA LINC00667 reduces the chemosensitivity of breast cancer cells to docetaxel via targeting miR-200b-3p/Bcl-2 axis. Eur J Histochemistry: EJH. ;66(4)

  26. Qin Z, Liu X, Li Z, Wang G, Feng Z, Liu Y et al (2021) LncRNA LINC00667 aggravates the progression of hepatocellular carcinoma by regulating androgen receptor expression as a miRNA-130a-3p sponge. Cell Death Discovery 7(1):387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Yang H, Yang W, Dai W, Ma Y, Zhang G (2020) LINC00667 promotes the proliferation, migration, and pathological angiogenesis in non–small cell lung cancer through stabilizing VEGFA by EIF4A3. Cell Biol Int 44(8):1671–1680

    Article  CAS  PubMed  Google Scholar 

  28. Yu J, Wang F, Zhang J, Li J, Chen X, Han G (2020) LINC00667/miR-449b-5p/YY1 axis promotes cell proliferation and migration in colorectal cancer. Cancer Cell Int 20:1–13

    Article  Google Scholar 

  29. Monaco ME (2017) Fatty acid metabolism in breast cancer subtypes. Oncotarget 8(17):29487

    Article  PubMed  PubMed Central  Google Scholar 

  30. Wu R, Yu I, Tokumaru Y, Asaoka M, Oshi M, Yan L et al (2022) Elevated bile acid metabolism and microbiome are associated with suppressed cell proliferation and better survival in breast cancer. Am J Cancer Res 12(11):5271

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Modi A, Roy D, Sharma S, Vishnoi JR, Pareek P, Elhence P et al (2022) ABC transporters in breast cancer: their roles in multidrug resistance and beyond. J Drug Target 30(9):927–947

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Thanks to Genius Gene center for assisting in laboratory work and data analysis.

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Authors and Affiliations

  1. Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran

    Mozhdeh Rastegari & Hossein Sazegar

  2. Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran

    Abbas Doosti

Authors
  1. Mozhdeh Rastegari
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  2. Hossein Sazegar
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  3. Abbas Doosti
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Contributions

The study design was performed by H.S. and A.D. Data analysis and experiments were done by M.R. Interpretations of data were performed by M.R. and A.D. Bioinformatics analysis was performed by M.R. Manuscript writing was performed by M.R. The manuscript was finally approved by M.R., H.S. and A.D.

Corresponding author

Correspondence to Hossein Sazegar.

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Ethical approval and consent to participate

Ethics approval was obtained from the Research Ethics Committees of Islamic Azad University with Ethical approval number; IR.IAU.SHK.REC.1401.091. All experiments were performed in accordance with relevant guidelines and regulations. Informed consent was obtained from all the donors prior to the collection of samples.

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All authors support the submission of the present manuscript to this journal.

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The authors declare no competing interests.

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Rastegari, M., Sazegar, H. & Doosti, A. Prognostic significance of CHCHD2P9 and ZNF204P in breast cancer: exploring their expression patterns and associations with malignancy-related genes. Mol Biol Rep 51, 707 (2024). https://doi.org/10.1007/s11033-024-09643-x

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