Fig. 2: ERα-LBD is encoded by an ESR1 transcript variant.

a Heat map showing ESR1 exon expression in BC cell lines, calculated by using DEXSeq-count tool (log2, mean-centered). Exons encoding ERα-FL protein are indicated in black (CDS). BC cell lines were grouped as ERα-FL(+), including T-47D, MCF-7, PDX-ERα(+) (in purple), and ERα-FL(−), including MDA-MB-453, MDA-MB-231, PDX-ERα(−) (in teal). b Differential ESR1 exon expression between ERα-FL(+) and ERα-FL(−) groups was calculated using DEXSeq and plotted using plotDEXSeq tools. Exons associated with two different ESR1 transcript variants were taken under consideration for the analysis: ESR1-FL (main variant encoding ERα-FL) and ESR1-LBD (predicted, encoding ERα-LBD). Expression values for ERα-FL(+) and ERα-FL(−) groups are plotted in purple and in teal, respectively. BH adjusted P-values (FDR test): *P < 0.05, **P < 0.01 (n = 6/group). c Heat map showing ESR1 transcript (ESR1-FL and ESR1-LBD) expression among BC cell lines, grouped as ERα-FL(+) (purple) and ERα-FL(−) (teal). Transcript expression was calculated by using Kallisto tool and quantified as counts/transcript length. d ESR1-LBD transcript expression plotted as log2 fold change, relative to ESR1-FL. ESR1-FL, empty circles; ESR1-LBD, solid circles. Mean ± s.e.m. is shown (n = 6); **P < 0.01, ratio paired t test, two-sided. e ESR1-FL transcript expression was calculated in BC samples by using Kallisto and plotted as Transcripts Per Kilobase Million (TPM). ERα(+) BC primary tumors (n = 42); uninvolved breast tissue adjacent to ERα(+) primary tumors (n = 30); TNBC primary tumors (n = 42); uninvolved breast tissue adjacent to TNBC primary tumors (n = 21); metaplastic BC primary tumors (MpBC, n = 17). f Heat map showing ESR1 exon expression in BC patient groups. Exon expression was calculated by using DEXSeq-count tool [# of read counts/exon length] and scaled by column. g Dispersion plot for ESR1 transcript variants expression (ESR1-FL vs. ESR1-LBD), calculated as TPM. Dashed lines corresponding to ESR1-LBD expression median and Q1-Q3 quartiles are shown. Color code as in e. h Box and whiskers plot representing the distribution of ESR1-LBD expression values (TPM) from BC samples. Median, Q1/Q3 and Min/Max values are shown. Color code as in e. Percentage of samples from each group is also shown, distributed into quartiles. Source data are provided as Supplementary Data 2 file.