Oncology Letters (2018)
PMID: 30675199
DOI: 10.3892/ol.2018.9745
AUTHORS
Jue Liu1,Xiaobo Zhang2,Yuliang Huang1,Qunfeng Zhang1,Jianbin Zhou1,Xiaodi Zhang1,Xiaoxu Wang3AFFILIATIONS
1Department of Obstetrics and Gynecology, The Second Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China
2Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
3Department of Joint Surgery, The Second Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China
#1Actinopolyspora Biskrensis
1 month ago
Concerning flow cytometry plot similarities across at least 4 papers.
Figure 4A, Cancer Letters (2013), doi: 10.1016/j.canlet.2013.06.027, discussed here: https://pubpeer.com/publications/C1AD6E1FE5D8C6686DC934F31F913C
Figure 3C, Oncotarget (2015), doi: 10.18632/oncotarget.4039, discussed here: https://pubpeer.com/publications/B7BFB40425F2C63B9FC1E61E9E9451
Figure 2D, Oncology Letters (2018), doi: 10.3892/ol.2018.9745, discussed here: https://pubpeer.com/publications/B34BAF6DDD57B1D9C9416B5AD34D36
Figure 3A, Frontiers in Pharmacology (2018) doi: 10.3389/fphar.2018.01248, discussed here: https://pubpeer.com/publications/6851ED170164F13D1F64FE236E4EA6
#2Aphilanthops Foxi
1 month ago
miR-200b-3p and miR-200c-3p (or "miR-200b" and "miR-200c") appear to be confused in this paper with miR-200b-5p and miR-200b-5p. Mature microRNAs are processed from a precursor hairpin molecule, and mature microRNAs are typically designated by a "-5p" or "-3p" suffix based on the originating arm of the precursor. Sometimes, this suffix is omitted when referring to the predominant or exclusive arm, that is, if one arm is mostly or exclusively retained. In this paper, the 5p arms of miR-200b and miR-200c are incorrectly and presumably mistakenly presented as "miR-200b" and "miR-200c" when they should be referred to as "miR-200b-5p" and "miR-200c-5p". These sequences are in the minority and may not be represented at all in some samples (see below, images from miRBase.org, miR-200b and miR-200c). Also below, the sequences presented in the methods for the two miRNAs are identical to the 5p arms, not, as one would assume, the 3p arms.
#3Aphilanthops Foxi
1 month ago
As is also clear from the illustration in #2, the FISH probe sequences from the Methods section are identical to the mature miRNAs (and the listed miRNA mimics). To function as a hybridization probe, the sequence would instead need to be the reverse complement of the target.
#4Aphilanthops Foxi
1 month ago
The PCR primers for the mature miRNAs are provided as: "The primer sequence for miR-200b was as follows: Forward, 5′-CACACTGAAATCCTGTCAGCTTC-3′ and reverse, 5-CTA ACT. The primer sequence for miR-200b mimics was sense, 5′-UUCUCCGAACGUGUCACGUTT-3′ and anti-sense, 5′-ACGUGACACGUUCGGAGAATT-3′."
This raises several questions:
Why are two sets of "miR-200b" primers given? Should the second set be "miR-200c"?
How does the first forward primer, 5′-CACACTGAAATCCTGTCAGCTTC-3′, relate to miR-200b-5p (or -3p)?
The first reverse primer, CTAACT, is only six nucleotides long. How would this primer function?
How does the second forward primer relate to any miRNA in the miR-200 family?
Why are the primers in the second set presented as RNA/DNA hybrids?
#5Aphilanthops Foxi
1 month ago
The rationale for studying miR-200b-5p or miR-200c-5p is presented in two sentences in the introduction, supported by three references:
One particular miRNA family, the miRNA-200 family, regulates DNA methylation in a number of types of cancer (12,17). Ectopic overexpression of the two miRNAs increased the sensitivity of the resistant ovarian cancer cells to cisplatin by promoting apoptosis by directly suppressing DNMT3A and DNMT3B, and also indirectly decreasing the expression of DNMT1 via the downregulation of specificity protein (Sp)1, a transactivating factor of the DNMT1 gene (12,18).
Of these three references, Reference 12, Lin et al, 2010, contains no information on microRNAs. Reference 18, Liu et al, 2008, contains no information on microRNAs. Reference 17, Lynch et al, 2016, does not appear to offer support, as it covers miR-200c-3p, not miR-200c-5p. What was the rationale for studying these miRNAs?
#6Aphilanthops Foxi
1 month ago
According to the methods, qPCR data were analyzed by the delta-delta Ct method. However, no reference RNA is mentioned (the first "delta" in "delta-delta"). Could the authors please share the reference RNA and the primers used to measure it?
