Abstract

MicroRNAs (miRNAs) belong to a class of noncoding, regulatory RNAs that is involved in oncogenesis and shows remarkable tissue specificity. Their potential for tumor classification suggests they may be used in identifying the tissue in which cancers of unknown primary origin arose, a major clinical problem. We measured miRNA expression levels in 400 paraffin-embedded and fresh-frozen samples from 22 different tumor tissues and metastases. We used miRNA microarray data of 253 samples to construct a transparent classifier based on 48 miRNAs. Two-thirds of samples were classified with high confidence, with accuracy >90%. In an independent blinded test-set of 83 samples, overall high-confidence accuracy reached 89%. Classification accuracy reached 100% for most tissue classes, including 131 metastatic samples. We further validated the utility of the miRNA biomarkers by quantitative RT-PCR using 65 additional blinded test samples. Our findings demonstrate the effectiveness of miRNAs as biomarkers for tracing the tissue of origin of cancers of unknown primary origin.

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Acknowledgements

We thank Jung-Hwan Yoon of Seoul National University College of Medicine, Seoul, South Korea. N.R. dedicates this work to the memory of Yasha (Yaakov) Rosenfeld.

Author information

Author notes

    • Nitzan Rosenfeld
    • , Ranit Aharonov
    • , Eti Meiri
    •  & Shai Rosenwald

    These authors contributed equally to this work.

Affiliations

  1. Rosetta Genomics Ltd., Rehovot 76706, Israel.

    • Nitzan Rosenfeld
    • , Ranit Aharonov
    • , Eti Meiri
    • , Shai Rosenwald
    • , Yael Spector
    • , Merav Zepeniuk
    • , Hila Benjamin
    • , Norberto Shabes
    • , Sarit Tabak
    • , Asaf Levy
    • , Danit Lebanony
    • , Yaron Goren
    • , Erez Silberschein
    • , Nurit Targan
    • , Alex Ben-Ari
    • , Shlomit Gilad
    • , Amir Avniel
    • , Isaac Bentwich
    • , Zvi Bentwich
    • , Dalia Cohen
    •  & Ayelet Chajut
  2. Soroka University Medical Center, Beer-Sheva 84101, Israel.

    • Netta Sion-Vardy
  3. Department of Pathology, Beilinson Hospital, Rabin Medical Center, Petah-Tikva 49100, Israel.

    • Ana Tobar
    •  & Meora Feinmesser
  4. Pathology Institute, Sourasky Medical Center, Tel Aviv 64239, Israel.

    • Oleg Kharenko
  5. Bnai-Zion Medical Center, Haifa 31048, Israel.

    • Ofer Nativ
  6. Department of Pathology, Sheba Medical Center, Tel-Hashomer 52621, Israel.

    • Dvora Nass
    • , Marina Perelman
    • , Ady Yosepovich
    • , Bruria Shalmon
    • , Sylvie Polak-Charcon
    • , Eddie Fridman
    •  & Iris Barshack
  7. Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

    • Dvora Nass
    • , Marina Perelman
    • , Ady Yosepovich
    • , Bruria Shalmon
    • , Sylvie Polak-Charcon
    • , Eddie Fridman
    •  & Iris Barshack

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Contributions

R.A., A.A., I. Bentwich, Z.B., D.C., A.C. and I. Barshack directed research; N.R., R.A., E.M., S.R., Y.S., S.G., A.C. and I. Barshack designed experiments; N.S.-V., A.T., M.F., O.K., O.N., D.N., M.P., A.Y., B.S., S.P.-C., E.F. and I. Barshack provided samples and performed pathological analysis; E.M., M.Z., N.S., S.T., D.L. and S.G. performed experiments; N.R., R.A., S.R., Y.G. and E.S. developed algorithms; N.R., S.R., H.B. and Y.G. analyzed data; Y.S., A.L., N.T. and A.B.-A. provided bioinformatic and database support; N.R., R.A., A.C. and I. Barschack wrote the paper.

Competing interests

All authors affiliated with Rosetta Genomics, except E.S., are full-time employees of Rosetta Genomics Ltd. and hold equity in the company, the value of which may be influenced by this publication. E.S. was engaged as an external consultant to Rosetta Genomics. O.N. is a paid consultant to Rosetta Genomics. All other authors declare that they have no competing interests.

Corresponding authors

Correspondence to Ranit Aharonov or Iris Barshack.

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DOI

https://doi.org/10.1038/nbt1392

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