Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, United States
- Departments of Gynecologic Oncology, Immunology, and Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, United States
- Penn Ovarian Cancer Research Center, University of Pennsylvania Perelman School of Medicine, United States
- Massachusetts General Hospital Cancer Center, Harvard Medical School, United States
Figures
Figure 1
The 12p13.33 amplicon in high-grade serous carcinoma (HGSC).
(A) Recurrent copy number amplifications in The Cancer Genome Atlas HGSC data (n = 579), as determined by GISTIC. Black vertical line indicates the threshold for significance, corresponding to an …
Figure 2 with 2 supplements
FOXM1/RHNO1 expression correlation in high-grade serous carcinoma (HGSC) and genomic characteristics.
(A) Hierarchical clustering dendrogram of The Cancer Genome Atlas HGSC mRNA expression correlations of the 33 genes in the 12p13.33 amplicon. FOXM1 and RHNO1 are boxed. (B) Genomic configuration and …
Figure 2—figure supplement 1
The FOXM1/RHNO1 bidirectional promoter (F/R-BDP) region is hypomethylated in normal and cancer tissues.
(A) Distribution of DNA methylation at the F/R-BDP in The Cancer Genome Atlas normal and tumor tissues and Cancer Cell Line Encyclopedia cancer cell lines. Beta values represent the level of DNA …
Figure 2—figure supplement 2
DNA sequence of the FOXM1/RHNO1 bidirectional promoter (F/R-BDP).
Transcriptional start sites predicted by NCBI are shown with broken arrows. E2F and MYC sites, known to regulate BDPs and FOXM1, are indicated.
Figure 3
FOXM1 and RHNO1 expression correlates with genomic copy number in high-grade serous carcinoma (HGSC).
(A) FOXM1 and RHNO1 mRNA expression (RNA-seq) vs. GISTIC copy number in The Cancer Genome Atlas HGSC data (N = 157). (B) FOXM1 and RHNO1 mRNA expression (microarray) vs. copy number (GISTIC) in …
Figure 4
FOXM1 and RHNO1 expression correlates in high-grade serous carcinoma (HGSC) and in HGSC precursor cells.
(A) FOXM1 vs. RHNO1 expression in primary HGSC tumors, as determined by RT-qPCR. (B) FOXM1 vs. RHNO1 expression in Fallopian tube epithelium (N = 5), ovarian surface epithelium (N = 3), and HGSC (N =…
Figure 5 with 1 supplement
Distribution of correlation coefficients for bidirectional gene pairs (n = 2172) from scRNA-seq data.
Data are shown for (A) FT282 and (B) OVCAR8 cell lines. The x-axis plots the degree of co-expression (Pearson's coefficient) between bidirectional gene pairs, and y-axis plots the frequency of …
Figure 5—figure supplement 1
Principal component analyses (PCA) of FT282 (n = 1440) and OVCAR8 (n = 1454) single cells, using scRNA-seq data.
PCA analyses were performed using Python.
Figure 6
FOXM1 and RHNO1 mRNA expression and expression ratio in normal and cancer tissues.
(A) FOXM1 and (B) RHNO1 expression (RNA-seq) in normal tissues (from Genotype-Tissue Expression and The Cancer Genome Atlas [TCGA]) vs. different types of TCGA tumor tissues (i.e., primary, …
Figure 7
FOXM1 and RHNO1 are overexpressed in high-grade serous carcinoma (HGSC).
(A) FOXM1 and RHNO1 expression in Genotype-Tissue Expression normal Fallopian tube (FT; N = 5) vs. The Cancer Genome Atlas HGSC tissues (RNA-seq) (N = 427). (B) FOXM1 and RHNO1 mRNA expression in …
Figure 8
FOXM1 and RHNO1 expression in primary and recurrent high-grade serous carcinoma (HGSC).
(A) FOXM1 vs. RHNO1 expression (RNA-seq data) in primary (left) and recurrent (right) HGSC samples from Kreuzinger et al., 2017. (B) FOXM1 vs. RHNO1 expression (RNA-seq data) in primary (left) and …
Figure 9 with 2 supplements
F/R-BDP promoter activity assays.
(A) Schematic of the F/R-BDP dual luciferase reporter construct. The FOXM1 promoter direction drives Renilla luciferase, and the RHNO1 promoter direction drives firefly luciferase. Secreted …
Figure 9—figure supplement 1
FOXM1 and RHNO1 transcriptional start sites.
5′ RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) mapping data of the 5′ ends of FOXM1 and RHNO1 mRNA. The arrows indicate the orientation of each gene 5′ to 3′. The bars indicate …
Figure 9—figure supplement 2
Fluorescence-activated cell sorting analyses of red fluorescent protein (RFP) and green fluorescent protein (GFP) expression in 293T cells.
(A, B) Empty vector transfections. (C, D) F/R-BPD dual reporter transfections. The reporter schematic is shown in Figure 9E. (E, F) Spearman correlation analyses of Quadrant 2 (i.e., RFP + GFP + …
Figure 10
Endogenous FOXM1 and RHNO1 are co-regulated by their bidirectional promoter (F/R-BDP).
(A) Schematic of the experimental approach used in (B, C). The position of the CRISPR guide RNAs is indicated with black rectangles. (B) CRISPRa experiment in FT282 cells. Endogenous FOXM1 and RHNO1 …
Figure 11 with 2 supplements
FOXM1 and RHNO1 each promote high-grade serous carcinoma cell clonogenic growth.
(A) OVCAR8 and CAOV3 cells engineered for doxycycline (dox)-inducible FOXM1 or RHNO1 shRNA knockdown. Cells were grown in the presence of dox for 72 hr, and protein was extracted for western blot …
Figure 11—figure supplement 1
FOXM1 and RHNO1 each promote high-grade serous carcinoma cell clonogenic growth.
(A) Representative colony formation data for OVCAR8 and CAOV3 cells sustaining FOXM1 or RHNO1 knockdown. NS: nontargeting shRNA. (B) Representative colony formation data for OVCAR8 and CAOV3 cells …
Figure 11—figure supplement 2
Representative TIDE analyses data for high-grade serous carcinoma cells sustaining FOXM1 or RHNO1 CRISPR gene knockout.
OVCAR8 and CAOV3 cells engineered for FOXM1 or RHNO1 CRISPR knockout were assessed for indel frequency among a mixed pool of cells. (A–D) Indel spectra for (A) OVCAR8 LCV2 FOXM1 462 cells; (B) CAOV3 …
Figure 12 with 1 supplement
OVCAR8 cells with dual FOXM1 and RHNO1 shRNA knockdown have diminished clonogenic growth.
OVCAR8 high-grade serous carcinoma cells were engineered for doxycycline (dox)-inducible FOXM1 and/or RHNO1 shRNA knockdown. (A) OVCAR8 cells treated with dox for 72 hr followed by western blot …
Figure 12—figure supplement 1
CAOV3 cells with dual FOXM1 and RHNO1 shRNA knockdown have diminished clonogenic growth.
CAOV3 high-grade serous carcinoma cells were engineered for doxycycline (dox)-inducible FOXM1 and/or RHNO1 shRNA knockdown. CAOV3 cells treated with dox for 72 hr followed by (A) western blot …
Figure 13
RHNO1 functions in the replication stress response in high-grade serous carcinoma cells.
(A) Schematic of RHNO1 wild-type and SWV mutant. The proteins are the same molecular weight but residues 55–61 are converted to alanine in the SWV mutant, disrupting its ability to interact with …
Figure 14
Binding to the 9-1-1 complex is required for RHNO1 function in OVCAR8 cell clonogenic growth.
OVCAR8 cells were engineered for doxycycline (dox)-inducible RHNO1 knockdown and simultaneous dox-inducible expression of HA-RHNO1 WT or SWV mutant. (A, B) Cells were seeded in the presence of dox …
Figure 15
Homozygous knockout of RHNO1 in FT282 cells does not impact cell proliferation, and high-grade serous carcinoma (HGSC) cells show elevated expression of replication stress (RS) biomarkers compared to Fallopian tube epithelium (FTE) cells.
RHNO1 knockout was achieved using CRISPR-Cas9 with guide RNAs that targeted near the start and stop codon of RHNO1. (A, B) RHNO1 homozygous knockout was confirmed by (A) genomic DNA PCR and (B) RHNO1…
Figure 16
FOXM1 and RHNO1 promote homologous recombination (HR).
DR-GFP cell lines were treated with doxycycline (dox) to induce shRNA expression, and mRNA knockdowns were measured by RT-qPCR. (A, B) FOXM1, RHNO1, and RAD51 mRNA expression in U2OS-DR-GFP cells …
Figure 17 with 1 supplement
FOXM1 and RHNO1 knockdown-sensitize OVCAR8 cells to olaparib.
OVCAR8 cells engineered for doxycycline (dox)-inducible FOXM1 and/or RHNO1 shRNA knockdown were grown in dox for 72 hr prior to seeding cells for experiments. (A) Cells were seeded in 96-well plates …
Figure 17—figure supplement 1
Quantification of γ-H2AX in OVCAR8 chromatin extracts following FOXM1 and/or RHNO1 knockdown and DMSO or olaparib treatment.
Western blots are shown in Figure 17C.
Figure 18
CRISPRi repression of the F/R-BDP sensitizes OVCAR8 cells to olaparib.
(A) OVCAR8 cells expressing the KRAB transcriptional repressor and a guide RNA targeting the F/R-BDP, and the corresponding changes in mRNA expression as measured by RT-qPCR. NT: nontargeting guide …
Figure 19
CRISPRi repression of the F/R-BDP in olaparib-resistant cells increases olaparib sensitivity.
Parental and olaparib-resistant UWB1 cells were engineered to express the KRAB transcriptional repressor and a control guide RNA or guide RNA targeting the F/R-BDP (sg130). (A) Cells were seeded and …
Figure 20
FOXM1 and RHNO1 knockdown enhances OVCAR8 cell sensitivity to carboplatin.
OVCAR8 cells were treated with doxycycline (dox) for 48 hr and seeded into triplicate wells of 6-well dishes in single-cell suspension. Cells were treated with carboplatin and dox the day after …
Figure 21
Model for FOXM1/RHNO1 bidirectional gene (BDG) function and cooperativity.
FOXM1 and RHNO1 are BDGs regulated by a bidirectional promoter (BDP) and are co-amplified and co-expressed in high-grade serous carcinoma (HGSC), including single cells. Both genes are overexpressed …
Tables
Appendix 1—key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Homo sapiens) | FOXM1 | GenBank | Gene ID: 2305 | |
| Gene (Homo sapiens) | RHNO1 | GenBank | Gene ID: 83695 | |
| Antibody | FOXM1 (rabbit monoclonal) | Cell Signaling Technology | 5436 | (1:1000) |
| Antibody | β-Actin (mouse monoclonal) | Santa Cruz | sc-47778 | (1:200) |
| Antibody | α-Tubulin (rabbit polyclonal) | Cell Signaling Technology | 2144 | (1:1000) |
| Antibody | Lamin B (goat polyclonal) | Santa Cruz | sc-6217 | Discontinued |
| Antibody | Histone H3 (goat polyclonal) | Santa Cruz | sc-8654 | Discontinued |
| Antibody | CHEK1 (mouse monoclonal) | Santa Cruz | sc-8408 | (1:200) |
| Antibody | P-CHEK1 S345 (rabbit monoclonal) | Cell Signaling Technology | 2348 | (1:1000) |
| Antibody | P-CHEK1 S317 (rabbit monoclonal) | Cell Signaling Technology | 12302 | (1:1000) |
| Antibody | RPA32/RPA2 (rabbit monoclonal) | Abcam | ab76420 | (1:1000) |
| Antibody | RPA32 (S33) (rabbit polyclonal) | Bethyl | A300-246A-M | (1:1000) |
| Antibody | H2AX (goat polyclonal) | Bethyl | A303-837A | (1:2000) |
| Antibody | P-H2AX S139 (rabbit monoclonal) | Cell Signaling Technology | 9718 | (1:1000) |
| Antibody | Flag (rabbit monoclonal) | Cell Signaling Technology | 14793 | (1:1000) |
| Antibody | HA (rabbit monoclonal) | Cell Signaling Technology | 3724 | (1:1000) |
| Antibody | RHNO1 (rabbit polyclonal) | Novus | NBP1-93694 | Discontinued |
| Antibody | RHNO1 (rabbit polyclonal) | Sigma | HPA038682 | Discontinued |
| Antibody | TOPBP1 (rabbit monoclonal) | Cell Signaling Technology | 14342 | (1:1000) |
| Antibody | RAD9 (rabbit polyclonal) | Santa Cruz | sc-8324 | Discontinued |
| Antibody | RAD1 (rabbit monoclonal) | Invitrogen | 702149 | (1–2 µg/mL) |
| Antibody | HUS1 (rabbit monoclonal) | Cell Signaling Technology | 16416 | (1:1000) |
| Antibody | Anti-HA magnetic beads (mouse monoclonal) | Pierce | 88837 | |
| Cell line (Homo sapiens) | COV362 | Sigma | 7071904 | |
| Cell line (Homo sapiens) | COV318 | Sigma | 7071903 | |
| Cell line (Homo sapiens) | KURAMOCHI | JCRB | JCRB0098 | |
| Cell line (Homo sapiens) | OVSAHO | JCRB | JCRB1046 | |
| Cell line (Homo sapiens) | SNU-119 | Korean Cell Line Bank | 00119 | |
| Cell line (Homo sapiens) | OVCAR4 | NCI | ||
| Cell line (Homo sapiens) | OVCAR8 | NCI | ||
| Cell line (Homo sapiens) | OVCAR3 | ATCC | HTB-161 | |
| Cell line (Homo sapiens) | CAOV3 | Anirban Mitra | ||
| Cell line (Homo sapiens) | OVCAR5 | Anirban Mitra | ||
| Cell line (Homo sapiens) | UWB1.289 | Lee Zou | ||
| Cell line (Homo sapiens) | UWB1-SyR12 | Lee Zou | ||
| Cell line (Homo sapiens) | UWB1-SyR13 | Lee Zou | ||
| Cell line (Homo sapiens) | hOSE | ScienCell | 7310 | |
| Cell line (Homo sapiens) | FT190 | Ronny Drapkin | ||
| Cell line (Homo sapiens) | FT282-E1 | Ronny Drapkin | ||
| Cell line (Homo sapiens) | FT282 | Ronny Drapkin | ||
| Cell line (Homo sapiens) | IOSE-21 | Francis Balkwill | ||
| Cell line (Homo sapiens) | IOSE-121 | Nelly Auersperg | ||
| Cell line (Homo sapiens) | 283T | ATCC | CRL-3216 | |
| Cell line (Homo sapiens) | U2OS-DR-GFP (282C) | Jeremy Stark | ||
| Cell line (Homo sapiens) | OVCAR8-DR-GFP | Larry Karnitz and Scott Kaufmann | ||
| Chemical compound, drug | Berzosertib | SelleckChem | VE-822 | |
| Chemical compound, drug | Olaparib | SelleckChem | ABT-888 | |
| Chemical compound, drug | Hydroxyurea | Sigma | H8627 | |
| Chemical compound, drug | Carboplatin | Sigma | C2538 | |
| Chemical compound, drug | Etoposide | Sigma | E1383 | |
| Chemical compound, drug | Doxycycline | Sigma | D9891 | |
| Commercial assay or kit | Direct-zol RNA Purification Kit | Zymo Research | R2072 | |
| Commercial assay or kit | Comet Assay Kit | Trevigen | 4250-050-K | |
| Commercial assay or kit | iScript cDNA Synthesis Kit | Bio-Rad | 1708890 | |
| Commercial assay or kit | DNA-free kit | Ambion | AM1906 | |
| Commercial assay or kit | NE-PER Nuclear and Cytoplasmic Extraction Kit | Pierce | 78833 | |
| Commercial assay or kit | BCA protein assay | Pierce | 23225 | |
| Commercial assay or kit | Enhanced chemiluminescence | Pierce | 32106 | |
| Commercial assay or kit | Puregene Tissue Kit | QIAGEN | 158667 | |
| Commercial assay or kit | EZ DNA Methylation Kit | Zymo Research | D5001 | |
| Commercial assay or kit | QIAquick Gel Extraction Kit | QIAGEN | 28704 | |
| Commercial assay or kit | TOPO TA Cloning Kit | Invirogen | K457501 | |
| Commercial assay or kit | FirstChoice RLM-RACE Kit | Ambion | AM1700 | |
| Commercial assay or kit | Dual-Luciferase Reporter Assay System | Promega | E1910 | |
| Commercial assay or kit | Phospha-Light SEAP Reporter Gene Assay System | Thermo Scientific | T1015 | |
| Commercial assay or kit | TRIzol reagent | Thermo Scientific | 15596026 | |
| Commercial assay or kit | Lipofectamine 2000 reagent | Life Technologies | 11668019 | |
| Commercial assay or kit | QuickExtract | Lucigen | QE09050 | |
| Commercial assay or kit | M-PER | Pierce | 78501 | |
| Commercial assay or kit | Halt Protease and Phosphatase Cocktail | Pierce | 78440 | |
| Commercial assay or kit | Turbo Nuclease | Sigma | T4330-50KU | |
| Commercial assay or kit | AlamarBlue | Bio-Rad | BUF012A | |
| Commercial assay or kit | Vectashield with DAPI | Vector Laboratories | H-1200-10 | |
| Genetic reagent (Homo sapiens) | pCBASceI | Addgene | 26477 | Plasmid |
| Genetic reagent (Homo sapiens) | pCW57-GFP-P2A-MCS | Addgene | 71783 | Plasmid |
| Genetic reagent (Homo sapiens) | pCW57-GFP-P2A-MCS-(Neo) | Addgene | 89181 | Plasmid |
| Genetic reagent (Homo sapiens) | pCW57-MCS1-P2A-MCS2-(Hygro) | Addgene | 80922 | Plasmid |
| Genetic reagent (Homo sapiens) | pCW57-MCS1-P2A-MCS2-(Blast) | Addgene | 80921 | Plasmid |
| Genetic reagent (Homo sapiens) | pCW57-RFP-P2A-MCS | Addgene | 78933 | Plasmid |
| Genetic reagent (Homo sapiens) | pCW57-RFP-P2A-MCS-(Neo) | Addgene | 89182 | Plasmid |
| Genetic reagent (Homo sapiens) | pTRIPZ Non-silencing | Dharmacon | NC0257175 | Plasmid |
| Genetic reagent (Homo sapiens) | pGL4 Luc Rluc Empty | Addgene | 64034 | Plasmid |
| Genetic reagent (Homo sapiens) | pCMV6-SEAP | Addgene | 24595 | Plasmid |
| Genetic reagent (Homo sapiens) | pTurbo-GFP-RFP-empty | Custom | Plasmid | |
| Genetic reagent (Homo sapiens) | pTurbo-GFP-PGK | Custom | Plasmid | |
| Genetic reagent (Homo sapiens) | pTurbo-RFP-PGK | Custom | Plasmid | |
| Genetic reagent (Homo sapiens) | pTurboGFP-RFP-FOXM1-RHNO1 | Custom | Plasmid | |
| Genetic reagent (Homo sapiens) | pLentiCRISPRv2 | Addgene | 52961 | Plasmid |
| Genetic reagent (Homo sapiens) | PX458-WT-Cas9-empty | Addgene | 48138 | Plasmid |
| Genetic reagent (Homo sapiens) | lenti-SAMv2-Puro | Addgene | 92062 | Plasmid |
| Genetic reagent (Homo sapiens) | lenti-MPHv2-Neo | Addgene | 92065 | Plasmid |
| Genetic reagent (Homo sapiens) | pLV hU6-sgRNA hUbC-dCas9-KRAB-T2A-Puro (KRAB) | Addgene | 71236 | Plasmid |
| Genetic reagent (Homo sapiens) | psPAX2 | Addgene | 12260 | Plasmid |
| Genetic reagent (Homo sapiens) | pMD2.G | Addgene | 12259 | Plasmid |
| Genetic reagent (Homo sapiens) | pOTB7-RHNO1 | Harvard PlasmID Repository | HsCD00326310 | Plasmid |
| Genetic reagent (Homo sapiens) | pENTR-MGC RHNO1 siR | Stephen Elledge | Plasmid | |
| Genetic reagent (Homo sapiens) | pENTR-MGC RHNO1 SWV | Stephen Elledge | Plasmid | |
| Genetic reagent (Homo sapiens) | pCMV6 AN-HA empty | Origene | PS100013 | Plasmid |
| Genetic reagent (Homo sapiens) | AdNGUS24i | Frank Graham and Phillip Ng | Adenovirus | |
| Software, algorithm | Prism 8 statistical software | GraphPad | ||
| Software, algorithm | Lasergene SeqMan Pro | DNASTAR | ||
| Software, algorithm | Comet Analysis Software | Trevigen | ||
| Software, algorithm | R package | R Project | ||
| Software, algorithm | Cell Ranger Single Cell Software | 10X Genomics | ||
| Software, algorithm | GSEA software version 3 | Broad Institute | ||
| Software, algorithm | Cufflinks (v2.1.1) | https://doi.org/10.1038/nbt.1621 | ||
| Software, algorithm | Trim Galore software package | The Babraham Institute | ||
| Software, algorithm | TopHat (v2.0.8) | https://doi.org/10.1186/gb-2013-14-4-r36 | ||
| Software, algorithm | Cuffdiff (v2.1.1) | https://doi.org/10.1038/nbt.2450 | ||
| Software, algorithm | Perl | The Perl Foundation | ||
| Software, algorithm | scImpute | https://doi.org/10.1038/s41467-018-03405-7 |
Additional files
-
Supplementary file 1
FOXM1 vs. RHNO1 mRNA expression correlations.
- https://cdn.elifesciences.org/articles/55070/elife-55070-supp1-v2.docx
-
Supplementary file 2
Oligonucleotide sequences.
- https://cdn.elifesciences.org/articles/55070/elife-55070-supp2-v2.xlsx
-
Supplementary file 3
List of bidirectional gene pairs to support Figure 5 (Excel file).
- https://cdn.elifesciences.org/articles/55070/elife-55070-supp3-v2.xlsx
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/55070/elife-55070-transrepform-v2.docx
