Table Info

Table 2.

In silico prediction of miRNAs differentially expressed in TAMr MCF-7:5C vs. TAMs MCF-7:WS8 that are predicted to interact with 3’UTR of major HPGD transcripts

miRNA	Fold change	Ensembl id^a	Binding probability^b	Longest consecutive pairings^b
hsa-miR-432-5p	105.24	ENST00000504433	0.85	7
hsa-miR-382-5p	54.71	ENST00000296521, ENST00000542498	0.85	9
hsa-miR-487a-3p^c	42.78	ENST00000296522.6	-	-
hsa-miR-31-5p	28.67	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000510901, ENST00000541923, ENST00000542498	1.0	14
hsa-miR-543	19.49	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000541923, ENST00000542498/ENST00000510901	0.85/0.92	17
hsa-miR-493-3p	13.35	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000541923, ENST00000542498/ENST00000510901	0.85/0.88	19
hsa-miR-376c-3p^c	10.65	ENST00000296522.6	-	-
hsa-miR-337-5p	6.46	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000541923, ENST00000542498/ENST00000510901	0.85/0.92	7
hsa-miR-505-5p	6.32	ENST00000296522, ENST00000422112, ENST00000504433, ENST00000510901/ENST00000541923	1.0/0.85	6
hsa-miR-1972	5.64	ENST00000504433	0.92	7
hsa-miR-410-3p^c	4.00	ENST00000296522.6	-	-
hsa-miR-154-5p	3.39	ENST00000504433	0.85	5
hsa-miR-485-5p	3.08	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000510901, ENST00000541923, ENST00000542498	1.0	7
hsa-miR-199a-3p^c	2.91	ENST00000296522.6	-	-
hsa-miR-654-3p^c	2.89	ENST00000296522.6	-	-
hsa-miR-493-5p	2.68	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000542498	0.85	10
hsa-miR-381-3p	2.66	ENST00000510901	0.85	8
hsa-miR-330-3p	2.54	ENST00000504433/ENST00000510901/ENST00000542498	0.92/0.85/1	9/7/7
hsa-miR-154-3p^c	2.35	ENST00000296522.6	-	-
hsa-miR-30a-3p	1.88	ENST00000504433	0.92/0.85	10/8
hsa-miR-4298	1.83	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000510901, ENST00000541923, ENST00000542498	1.0	8
hsa-miR-3200-3p^c	1.82	ENST00000296522.6	-	-
hsa-miR-106a-5p^c	1.75	ENST00000296522.6	-	-
hsa-miR-20b-5p^c	1.74	ENST00000296522.6	-	-
hsa-miR-425-5p^c	1.71	ENST00000296522.6	-	-
hsa-miR-17-5p	1.69	ENST00000504433	0.85	10
hsa-miR-500a-5p	1.66	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000541923, ENST00000542498, ENST00000510901	0.92	8
hsa-miR-1293	1.60	ENST00000296522, ENST00000296521, ENST00000422112, ENST00000541923, ENST00000542498, ENST00000510901	1.0	9
hsa-miR-20a-5p	1.56	ENST00000504433	0.92	10

Listed are miRNAs with fold change > 1.5; miRNAs underlined refer to the DLK-DIO3 locus on chromosome 14; miRWalk 3.0 [31] and TargetScan 7.2 [32] tools have been used to identify miRNA-target interactions; ^a major targeted transcripts are listed with respective Ensembl id; ^b binding probability and longest consecutive pairings are listed according to miRWalk 3.0 predictions; ^c additional miRNAs predicted only with TargetScan 7.2 tool (on most prevalent ENST00000296522.6 transcript)

Declarations

Acknowledgments

We thank Werbena Hamilton-Burke, Loaie Maraqa and Mark Peter for providing clinical data on the breast tumours which populated the TMAs used in this study.

Author contributions

Conception and design: MAH, VS. Acquisition of data: AMS, BA, PYM, BMB, RH, PF, HB, MV, MC, VCJ, VS. Analysis and interpretation of data: AMS, BA, PYM, BMB, RH, PF, HB, MV, MC, VCJ, VS. Writing and/or revision of the manuscript: MV, MC, MAH, VS. All authors read and approved the manuscript before submission.

Conflicts of interest

The authors declare that they have no conflicts of interest.

Ethical approval

Access to histopathology archives for TMA construction and immunohistochemistry was approved by the Leeds (East) Research Ethics (06/Q1206/180).

Consent to participate

The informed consent to participate in the study was obtained from all participants.

Consent to publication

The informed consent to publication was obtained from relevant participants.

Availability of data and materials

Part of the results described is based upon data generated by the TCGA Research Network (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga), the online resources of KMplot (https://kmplot.com/analysis/) and OncoLnc (http://www.oncolnc.org/).

Funding

This work was supported in part by Cancer Research UK grant C13432/A9047; Yorkshire Cancer Research grant L314; the Robert Bosch Foundation, Stuttgart, Germany; the NIH; MD Anderson’s Cancer Center support grant CA016672; the George and Barbara Bush Foundation for Innovative Cancer Research; and the Dallas/Fort Worth Living Legend Chair of Cancer Research. The study sponsor(s) played no part in the study design; in the collection, analysis and interpretation of the data; in the writing of the report; and in the decision to submit the paper for publication.

Copyright

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