Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs

Dereje D. Jima, Jenny Zhang, Cassandra Jacobs, Kristy L. Richards, Cherie H. Dunphy, William W L Choi, Wing Yan Au, Gopesh Srivastava, Magdalena Czader, David A. Rizzieri, Anand S. Lagoo, Patricia L. Lugar, Karen P. Mann, Christopher R. Flowers, Leon Bernal-Mizrachi, Kikkeri N. Naresh, Andrew M. Evens, Leo I. Gordon, Micah Luftig, Daphne R. FriedmanJ. Brice Weinberg, Michael A. Thompson, Javed I. Gill, Qingquan Liu, Tam How, Vladimir Grubor, Yuan Gao, Amee Patel, Han Wu, Jun Zhu, Gerard C. Blobe, Peter E. Lipsky, Amy Chadburn, Sandeep S. Dave

Research output: Contribution to journalArticle

138 Citations (Scopus)

Abstract

A role for microRNA (miRNA) has been recognized in nearly every biologic system examined thus far. A complete delineation of their role must be preceded by the identification of all miRNAs present in any system. We elucidated the complete small RNA transcriptome of normal and malignant B cells through deep sequencing of 31 normal and malignant human B-cell samples that comprise the spectrum of B-cell differentiation and common malignant phenotypes. We identified the expression of 333 known miRNAs, which is more than twice the number previously recognized in any tissue type. We further identified the expression of 286 candidate novel miRNAs in normal and malignant B cells. These miRNAs were validated at a high rate (92%) using quantitative polymerase chain reaction, and we demonstrated their application in the distinction of clinically relevant subgroups of lymphoma. We further demonstrated that a novel miRNA cluster, previously annotated as a hypothetical gene LOC100130622, contains 6 novel miRNAs that regulate the transforming growth factor-β pathway. Thus, our work suggests that more than a third of the miRNAs present in most cellular types are currently unknown and that these miRNAs may regulate important cellular functions.

Original languageEnglish
JournalBlood
Volume116
Issue number23
DOIs
StatePublished - Dec 2 2010

Fingerprint

High-Throughput Nucleotide Sequencing
MicroRNAs
Transcriptome
B-Lymphocytes
Cells
RNA
Polymerase chain reaction
Transforming Growth Factors
Cell Differentiation
Lymphoma
Genes
Tissue
Phenotype
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Hematology
  • Biochemistry
  • Cell Biology
  • Immunology

Cite this

Jima, D. D., Zhang, J., Jacobs, C., Richards, K. L., Dunphy, C. H., Choi, W. W. L., ... Dave, S. S. (2010). Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood, 116(23). https://doi.org/10.1182/blood-2010-05-285403

Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. / Jima, Dereje D.; Zhang, Jenny; Jacobs, Cassandra; Richards, Kristy L.; Dunphy, Cherie H.; Choi, William W L; Au, Wing Yan; Srivastava, Gopesh; Czader, Magdalena; Rizzieri, David A.; Lagoo, Anand S.; Lugar, Patricia L.; Mann, Karen P.; Flowers, Christopher R.; Bernal-Mizrachi, Leon; Naresh, Kikkeri N.; Evens, Andrew M.; Gordon, Leo I.; Luftig, Micah; Friedman, Daphne R.; Weinberg, J. Brice; Thompson, Michael A.; Gill, Javed I.; Liu, Qingquan; How, Tam; Grubor, Vladimir; Gao, Yuan; Patel, Amee; Wu, Han; Zhu, Jun; Blobe, Gerard C.; Lipsky, Peter E.; Chadburn, Amy; Dave, Sandeep S.

In: Blood, Vol. 116, No. 23, 02.12.2010.

Research output: Contribution to journalArticle

Jima, DD, Zhang, J, Jacobs, C, Richards, KL, Dunphy, CH, Choi, WWL, Au, WY, Srivastava, G, Czader, M, Rizzieri, DA, Lagoo, AS, Lugar, PL, Mann, KP, Flowers, CR, Bernal-Mizrachi, L, Naresh, KN, Evens, AM, Gordon, LI, Luftig, M, Friedman, DR, Weinberg, JB, Thompson, MA, Gill, JI, Liu, Q, How, T, Grubor, V, Gao, Y, Patel, A, Wu, H, Zhu, J, Blobe, GC, Lipsky, PE, Chadburn, A & Dave, SS 2010, 'Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs', Blood, vol. 116, no. 23. https://doi.org/10.1182/blood-2010-05-285403
Jima, Dereje D. ; Zhang, Jenny ; Jacobs, Cassandra ; Richards, Kristy L. ; Dunphy, Cherie H. ; Choi, William W L ; Au, Wing Yan ; Srivastava, Gopesh ; Czader, Magdalena ; Rizzieri, David A. ; Lagoo, Anand S. ; Lugar, Patricia L. ; Mann, Karen P. ; Flowers, Christopher R. ; Bernal-Mizrachi, Leon ; Naresh, Kikkeri N. ; Evens, Andrew M. ; Gordon, Leo I. ; Luftig, Micah ; Friedman, Daphne R. ; Weinberg, J. Brice ; Thompson, Michael A. ; Gill, Javed I. ; Liu, Qingquan ; How, Tam ; Grubor, Vladimir ; Gao, Yuan ; Patel, Amee ; Wu, Han ; Zhu, Jun ; Blobe, Gerard C. ; Lipsky, Peter E. ; Chadburn, Amy ; Dave, Sandeep S. / Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. In: Blood. 2010 ; Vol. 116, No. 23.
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AU - Choi, William W L

AU - Au, Wing Yan

AU - Srivastava, Gopesh

AU - Czader, Magdalena

AU - Rizzieri, David A.

AU - Lagoo, Anand S.

AU - Lugar, Patricia L.

AU - Mann, Karen P.

AU - Flowers, Christopher R.

AU - Bernal-Mizrachi, Leon

AU - Naresh, Kikkeri N.

AU - Evens, Andrew M.

AU - Gordon, Leo I.

AU - Luftig, Micah

AU - Friedman, Daphne R.

AU - Weinberg, J. Brice

AU - Thompson, Michael A.

AU - Gill, Javed I.

AU - Liu, Qingquan

AU - How, Tam

AU - Grubor, Vladimir

AU - Gao, Yuan

AU - Patel, Amee

AU - Wu, Han

AU - Zhu, Jun

AU - Blobe, Gerard C.

AU - Lipsky, Peter E.

AU - Chadburn, Amy

AU - Dave, Sandeep S.

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