Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis
MicroRNAs (miRNAs) are small noncoding RNAs of about 19-25 nt that regulate gene expression posttranscriptionally under
various cellular conditions, including apoptosis. The miRNAs involved in modulation of apoptotic events in T cells are partially known.
However, heterogeneity associated with cell lines makes it difficult to interpret gene expression signatures, especially in cancer-related
cell lines. Treatment of the Jurkat T-cell leukemia cell line with the universal apoptotic drug, camptothecin, resulted in identification of
two Jurkat subpopulations: one that is sensitive to camptothecin and another that is rather intrinsically resistant. We sorted apoptotic
Jurkat cells from nonapoptotic ones prior to profiling miRNAs through deep sequencing. Our data showed that a total of 184 miRNAs
were dysregulated. Interestingly, the apoptotic and nonapoptotic subpopulations exhibited distinct miRNA expression profiles. In
particular, 6 miRNAs were inversely expressed in these two subpopulations. The pyrosequencing results were validated by real-time
qPCR. Altogether, these results suggest that miRNAs modulate apoptotic events in T cells and that cellular heterogeneity requires careful
interpretation of miRNA expression profiles obtained from drug-treated cell lines.
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- Akao Y, Nakagawa Y, Iio A, Naoe T (2009). Role of microRNA-143 in
Fas-mediated apoptosis in human T-cell leukemia Jurkat cells.
Leukemia Res 33: 1530-1538.
- Bartel DP (2004). MicroRNAs: genomics, biogenesis, mechanism,
and function. Cell
116: 281-297.
- Bartel DP (2009). MicroRNAs: target recognition and regulatory
functions.
Cell
136
:
215-233.
- Baumann S, Krueger A, Kirchhoff S, Krammer PH (2002). Regulation
of T cell apoptosis during the immune response. Curr Mol Med
2: 257-272.
- Benchaouir R (2004). Evidence for a resident subset of cells with
SP phenotype in the C2C12 myogenic line: a tool to explore
muscle stem cell biology
.
Exp Cell Res 294: 254-268.
- Blagosklonny MV (2000). Cell death beyond apoptosis. Leukemia
14: 1502-1508.
- Blank M, Shiloh Y (2007). Programs for cell death: apoptosis is only
one way to go. Cell Cycle 6: 686-695.
- Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM (2003).
Bantam encodes a developmentally regulated microRNA that
controls cell proliferation and regulates the proapoptotic gene
hid in
Drosophila
. Cell 113: 25-36.
- Calin GA, Croce CM (2009). Chronic lymphocytic leukemia:
interplay between noncoding RNAs and protein-coding genes.
Blood 114: 4761-4770.
- Chen J, Odenike O, Rowley JD (2010). Leukaemogenesis: more than
mutant genes. Nat Rev Cancer 10: 23-36.
- De Hoon MJL, Taft, RJ, Hasimoto T, Kanamori-Katayama M, Kawaji
H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Faulkner
GJ et al. (2010). Cross-mapping and the identification of editing
sites in mature microRNAs in high-throughput sequencing
libraries. Genome Res 20:257-264.
- Fan SJ, Li HB, Cui G, Kong XL, Sun LL, Zhao YQ, Li YH, Zhou J
(2016). miRNA-149* promotes cell proliferation and suppresses
apoptosis by mediating
JunB
in T-cell acute lymphoblastic
leukemia. Leuk Res 41: 62-70.
- Georges SA, Biery MC, Kim SY, Schelter JM, Guo J, Chang AN,
Jackson AL, Carleton MO, Linsley PS, Cleary MA et al. (2008).
Coordinated regulation of cell cycle transcripts by p53-
inducible microRNA, miR-192 and miR-215. Cancer Res 68:
10105-10112.
- Ghodgaonkar MM, Shah RG, Kandan-Kulangara F, Affar EB, Qi HH,
Wiemer E, Shah GM (2009). Abrogation of DNA vector-based
RNAi during apoptosis in mammalian cells due to caspase-
mediated cleavage and inactivation of Dicer-1. Cell Death
Differ 16: 858-868.
- He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender
L, Magnus J, Ridzon D et al. (2007). A microRNA component
of the p53 tumour suppressor network. Nature 447: 1130-1134.
- Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T (2007). Impaired
microRNA processing enhances cellular transformation and
tumorigenesis. Nat Genet 39: 673-677.
- Lawrie CH (2007). MicroRNAs and hematology: small molecules,
big function. Brit J Haematol 137: 503-512.
- Li TK, Liu LF (2001). Tumor cell death induced by topoisomerase-
targeting drugs. Annu Rev Pharmacol 41: 53-77.
- Li XJ, Luo XQ, Han BW, Duan FT, Wei PP, Chen YQ (2013).
MicroRNA-100/99a, dysregulated in acute lymphoblastic
leukaemia, suppress proliferation and promote apoptosis by
regulating the FKBP51 and IGF1R/mTOR signaling pathways.
Brit J Cancer 109: 2189-2198.
- Lodish HF, Zhou B, Liu G, Chen CZ (2008). Micromanagement of
the immune system by miRNAs. Nature Rev 8: 120-130.
- Lu J, Zhang X, Zhang R, Ge Q (2015). MicroRNA heterogeneity in
endometrial cancer cell lines revealed by deep sequencing.
Oncol Letters 10: 3457-3465.
- Marcucci G, Mrozek K, Radmacher MD, Garzon R, Bloomfield CD
(2011). The prognostic and functional role of microRNAs in
acute myeloid leukemia. Blood 117: 1121-1129.
- Miska EA (2005). How microRNAs control cell division,
differentiation and death. Curr Opinion Genet Dev 15: 563-
568.
- Mott JL, Kobayashi S, Bronk SF, Gores GJ (2007). Mir-29 regulates
Mcl-1 protein expression and apoptosis. Oncogene 26: 6133-
6140.
- O’Connell R, Kahn D, Gibson WSJ, Round JL, Schotz RL, Chadhuri
AA, Kahn ME, Rao DS, Baltimore D (2010). MicroRNA-155
promotes autoimmune inflammation by enhancing
inflammatory T cell development. Immunity 33
:
607-619.
- Paek AL, Liu JC, Loewer A, Forrester WC, Lahav G (2016). Cell-to-
cell variation in p53 dynamics leads to fractional killing. Cell
165: 631-642.
- Pekarsky Y, Santanam U, Cimmino A, Palamarchuk A, Efanov
A, Maximov V, Volinia S, Alder H, Liu CG, Rassenti L et al.
(2006). Tcl1 expression in chronic lymphocytic leukemia is
regulated by miR-29 and miR-181. Cancer Res 66: 24.
- Pommier Y, Redon C, Rao VA, Seiler JA, Sordet O, Takemura H,
Antony S, Meng L, Liao Z, Kohlhagen G et al. (2003). Repair
of and checkpoint response to topoisomerase I-mediated DNA
damage. Mutat Res 532: 173-203.
- Schopman NC, Heynen S, Haasnoot J, Berkhout, B (2010). A
miRNA-tRNA mix-up: tRNA origin of proposed miRNA. RNA
Biol 7: 573-576.
- Snow K, Judd W (2009). Heterogeneity of a human T-lymphoblastoid
cell line. Exp Cell Res 171: 389-403.
- Stefani G, Slack FJ (2008). Small non-coding RNAs in animal
development. Nature Rev 9: 219-230.
- Stockholm D, Benchaouir R, Picot J, Maneau P, Neildez T, Landini
G, Laplace-Builhe C, Paldi A (2007). The origin of phenotypic
heterogeneity in a clonal cell population in vitro. PLoS One 4:
e394.
- Su Z, Yang Z, Xu Y, Chen Y, Yu Q (2015). MicroRNAs in apoptosis,
autophagy and necroptosis. Oncotarget 6: 8474-8490.
- Subramanian S, Steer CF (2010). MicroRNAs as gatekeepers of
apoptosis. J Cell Physiol 223: 289-98.
- Vaz C, Ahmad HM, Sharma P, Gupta R, Kumar L, Kulshreshtha R,
Bhattacharya A (2010). Analysis of microRNA transcriptome
by deep sequencing of small RNA libraries of peripheral blood.
BMC Genomics 11: 288.
- Vlachos IS, Zagganas K, Parashevopoulou MD, Georgakilas G,
Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou
AG (2015). DIANA-miRPath v3.0: deciphering microRNA
function with experimental support. Nucleic Acids Res 43:
W460-W466.
- Walling MA, Shepard JRE (2012). Cellular heterogeneity and live cell
arrays. Chem Soc Rev 40: 4049-4076.
- Xiao C, Srinivasan L, Calado DP, Patterson HC, Zhang B,
Wang J, Henderson JM, Kutok JL, Rajewsky K (2008).
Lymphoproliferative disease and autoimmunity in mice with
increased miR-17-92 expression in lymphocytes. Nat Immunol
9: 405-414.
- Xu P, Vernooy SY, Guo M, Hay BA (2003). The
Drosophila
microRNA
mir-14 suppresses cell death and is required for normal fat
metabolism. Curr Biol
13: 790-795.
- Yamada N, Noquichi S, Kumazaki M, Shinohara H, Miki K, Naoe
T, Akao Y (2014). Epigenetic regulation of microRNA-128a
expression contributes to the apoptosis-resistance of human
T-cell Jurkat cells by modulating expression of fas-associated
protein with death domain (FADD). Biochim Biophys Acta
1843: 590-602.
- Zanette DL, Rivadavia F, Molfetta GA, Barbuzano FG, Proto-Siqueira
R, Falcão RP, Zago MA, Silva-Jr WA (2007). MiRNA expression
profiles in chronic lymphocytic and acute lymphocytic
leukemia. Brazilian J Med Biol Res
40
:
1435-1440.
- Zhou L, Bai H, Wang C, Wei D, Qin Y, Xu U (2014). MicroRNA-
125b promotes leukemia cell resistance to daunorubicin by
inhibiting apoptosis. Mol Med Rep 9: 1909-1916.