Epigenetic Reprogramming of Lineage-Committed Human Mammary Epithelial Cells Requires DNMT3A and Loss of DOT1L

Abstract

Organogenesis and tissue development occur through sequential stepwise processes leading to increased lineage restriction and loss of pluripotency. An exception to this appears in the adult human breast, where rare variant epithelial cells exhibit pluripotency and multilineage differentiation potential when removed from the signals of their native microenvironment. This phenomenon provides a unique opportunity to study mechanisms that lead to cellular reprogramming and lineage plasticity in real time. Here, we show that primary human mammary epithelial cells (HMECs) lose expression of differentiated mammary epithelial markers in a manner dependent on paracrine factors and epigenetic regulation. Furthermore, we demonstrate that HMEC reprogramming is dependent on gene silencing by the DNA methyltransferase DNMT3A and loss of histone transcriptional marks following downregulation of the methyltransferase DOT1L. These results demonstrate that lineage commitment in adult tissues is context dependent and highlight the plasticity of somatic cells when removed from their native tissue microenvironment.

Keywords: DMNT3A; DOT1L; lineage; mammary; vHMECs.

Graphical abstract

Figure 1

HMECs Lose Lineage Commitment in the Absence of Stromal Cues (A) Growth curve showing cumulative population doublings over time in primary HMECs grown in MEGM or SCM, n = 3. (B and C) qPCR analysis of mammary lineage gene expression in HMECs grown in (B) MEGM or (C) SCM at different time points. mRNA levels are shown relative to the 9-day early culture, n = 3. (D) Gene ontology (GO) analysis of the set of genes differentially expressed between vHMECs and early-passage HMECs. (E) Growth curve showing cumulative population doublings over time in HMECs with knockdown of CDKN2a (shCDKN2a) or a firefly luciferase control (shCtrl), n = 3. (F) Representative image of an shCDKN2a culture when shCtrl cells are undergoing growth arrest (day 28). shCtrl cells adopt a senescent morphology while shCDKN2a cells remain small, refractile, and highly proliferative. Scale bars, 100 μm. (G) qPCR analysis of mammary lineage gene expression in shCtrl or shCDKN2a cultures at different time points, relative to shCtrl (p10), n = 4. In all panels, error bars indicate the mean ± SEM and replicates are individual patient samples. ^∗p < 0.05, Student's t test.

Figure 2

vHMECs Arise from HMECs Following Epigenetic Reprogramming (A) Schematic of the construct used to GFP-label primary HMECs with an exogenous NES promoter; methylation-specific PCR primers are shown in red. (B) Quantification of flow cytometry analysis of the percentage of GFP+ versus GFP⁻ cells in HMEC cultures before and after FACS purification of GFP⁺ cells, n = 3. (C) Representative images of untransduced, unsorted, and GFP⁺-sorted NES:GFP cultures at the point of growth arrest. The minority GFP⁻ cells present in the unsorted cultures are absent from the FACS-purified cultures. Scale bars, 100 μm. (D) Representative low-power (top) and high-power (bottom) images of a vHMEC colony derived from FACS-purified GFP⁺ cells showing GFP⁺ senescent cells (arrows) adjacent to GFP⁻ vHMECs. Scale bars, 100 μm. (E and F) Methylation-specific PCR of the (E) exogenous NES:GFP promoter, CDKN2a, or (F) endogenous NES promoter region, in early-passage HMECs, vHMECs, or in vHMECs treated with decitabine (DAC) from (E) NES:GFP or (F) untransduced cultures. U, unmethylated; M, methylated. (G) qPCR analysis of NES expression in HMECs, vHMECs, and vHMECs treated with DAC, n = 3. (H) Flow-cytometry analysis of high GFP expression in early-passage NES:GFP HMECs, decreased expression in NES:GFP vHMECs, and partial rescue by treatment of NES:GFP vHMECs with DAC. (I) qPCR analysis of mammary lineage gene expression in early HMECs, vHMECs, and vHMECs treated with DAC, relative to vHMEC, n = 4. In all panels, error bars indicated the mean ± SEM and replicates are individual patient samples. ^∗p < 0.05, Student's t test.

Figure 3

vHMEC Reprogramming Is Partially Controlled by DNMT3a (A) Growth curve showing cumulative population doublings over time in cultures with stable depletion of DNMT3a (shDNMT3a) by two different lentiviral short hairpins versus shCtrl. (B) Quantitative analysis of the number of vHMEC colonies formed by cultures lacking DNMT3a (shDNMT3a) versus the firefly luciferase control (shCtrl), n = 3. (C) Quantitative analysis of the number of vHMEC colonies formed by DNMT3a-overexpressing cultures versus the LacZ control, n = 4. (D) Latency of vHMEC colony formation, defined as the number of days required for vHMECs to appear, in LacZ versus DNMT3a overexpressing cultures, n = 4. (E) Growth curve showing cumulative population doublings over time in cultures with LacZ or DNMT3a overexpression, n = 3. (F) Methylation-specific PCR of gene promoters in early-passage HMECs (EP) versus vHMECs (vH) expressing LacZ or DNMT3a. (G) Representative image of qPCR analysis of expression of DNA methylation-regulated genes in early HMECs versus vHMECs expressing LacZ or DNMT3a. In all panels, error bars indicate the mean ± SEM and replicates are individual patient samples. ^∗p < 0.05, Student's t test.

Figure 4

DOT1L Loss Enhances the Efficiency of Reprogramming (A) qPCR of DOT1L mRNA levels in early-passage HMECs versus vHMECs, n = 5. (B) Western blot of DOT1L and p16/INK4a protein levels following stable knockdown of DOT1L (shDOT1L) in early-passage HMECs. (C) Number of vHMEC colonies generated by shDOT1L or shCtrl control cultures, shown relative to shCtrl, n = 3. (D and E) Growth curves showing cumulative population doublings over time in cultures with (D) DOT1L depletion (shDOT1L) or (E) chemical inhibition with FED1, n = 3. (F) Latency of vHMEC colony formation, defined as the number of days required after growth arrest for vHMECs to appear, in cells with DOT1L depletion (shDOT1L) or FED1 treatment, n = 3. In all panels, error bars indicate the mean ± SEM and replicates are individual patient samples. ^∗p < 0.05, Student's t test.

Figure 5

Histone Methylation by DOT1L Is Necessary for Maintaining HMEC Differentiation (A and B) Representative western blot (A) and densitometric quantitation (B) of H3K79me2 levels in early-passage cultures versus vHMECs, n = 3. (C) Chromatin immunoprecipitation (ChIP) of H3K79me2 levels in early-passage HMECs, growth-arrested cultures, or vHMECs (shown as the percent of input normalized to the total H3 level). SAT2 is a negative control, n = 3. (D) Western blot of H3K79me2 levels in shDOT1L cultures versus shCtrl. (E) ChIP analysis of H3K79me2 in shDOT1L versus shCtrl HMECs at early-passage (shown as the percent of input normalized to the total H3 level). (F) qPCR analysis of mammary lineage gene expression in early-passage shDOT1L versus shCtrl HMECs analyzed 1 week after DOT1L depletion by shRNA, n = 3. (G) Graphical depiction of the mechanism of HMEC reprogramming showing coordinated alterations in DNA and histone methylation to promote vHMEC formation. In all panels, error bars indicate the mean ± SEM and replicates are individual patient samples. n.d., not determined; ^∗p < 0.05, Student's t test.