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Mishra SK, Liu T, Wang H. Thousands of oscillating LncRNAs in the mouse testis. Comput Struct Biotechnol J 2024; 23:330-346. [PMID: 38205156 PMCID: PMC10776378 DOI: 10.1016/j.csbj.2023.11.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
The long noncoding RNAs (lncRNAs) are involved in numerous fundamental biological processes, including circadian regulation. Although recent studies have revealed insights into the functions of lncRNAs, how the lncRNAs regulate circadian rhythms still requires a deeper investigation. In this study, we generate two datasets of RNA-seq profiles of the mouse (Mus musculus) testis under light-dark (LD) cycle. The first dataset included 18,613 unannotated transcripts measured at 12 time points, each with duplicate samples, under LD conditions; while the second dataset included 21,414 unannotated transcripts measured at six time points, each with three replicates, under desynchronized and control conditions. We identified 5964 testicular lncRNAs in each dataset by BLASTing these transcripts against the known mouse lncRNAs from the NONCODE database. MetaCycle analyses were performed to identify 519, 475, and 494 rhythmically expressed mouse testicular lncRNAs in the 12-time-point dataset, the six-time-point control dataset, and the six-time-point desynchronized dataset, respectively. A comparison of the expression profiles of the lncRNAs under desynchronized and control conditions revealed that 427 rhythmically expressed lncRNAs from the control condition became arrhythmic under the desynchronized condition, suggesting a possible loss of rhythmicity. In contrast, 446 arrhythmic lncRNAs from the control condition became rhythmic under the desynchronized condition, suggesting a possible gain of rhythmicity. Interestingly, 48 lncRNAs were rhythmically expressed under both desynchronized and control conditions. These oscillating lncRNAs were divided into morning lncRNAs, evening lncRNAs, and night lncRNAs based on their time-course expression patterns. We interrogated the promoter regions of these rhythmically expressed mouse testicular lncRNAs to predict their possible regulation by the E-box, D-box, or RORE promoter motifs. GO and KEGG analyses were performed to identify the possible biological functions of these rhythmically expressed mouse testicular lncRNAs. Further, we conducted conservation analyses of the rhythmically expressed mouse testicular lncRNAs with lncRNAs from humans, rats, and zebrafish, and uncovered three mouse testicular lncRNAs conserved across these four species. Finally, we computationally predicted the conserved lncRNA-encoded peptides and their 3D structures from each of the four species. Taken together, our study revealed thousands of rhythmically expressed lncRNAs in the mouse testis, setting the stage for further computational and experimental validations.
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Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Taole Liu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
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2
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Schuster EF, Lopez-Knowles E, Alataki A, Zabaglo L, Folkerd E, Evans D, Sidhu K, Cheang MCU, Tovey H, Salto-Tellez M, Maxwell P, Robertson J, Smith I, Bliss JM, Dowsett M. Molecular profiling of aromatase inhibitor sensitive and resistant ER+HER2- postmenopausal breast cancers. Nat Commun 2023; 14:4017. [PMID: 37419892 PMCID: PMC10328947 DOI: 10.1038/s41467-023-39613-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/15/2023] [Indexed: 07/09/2023] Open
Abstract
Aromatase inhibitors (AIs) reduce recurrences and mortality in postmenopausal patients with oestrogen receptor positive (ER+) breast cancer (BC), but >20% of patients will eventually relapse. Given the limited understanding of intrinsic resistance in these tumours, here we conduct a large-scale molecular analysis to identify features that impact on the response of ER + HER2- BC to AI. We compare the 15% of poorest responders (PRs, n = 177) as measured by proportional Ki67 changes after 2 weeks of neoadjuvant AI to good responders (GRs, n = 190) selected from the top 50% responders in the POETIC trial and matched for baseline Ki67 categories. In this work, low ESR1 levels are associated with poor response, high proliferation, high expression of growth factor pathways and non-luminal subtypes. PRs having high ESR1 expression have similar proportions of luminal subtypes to GRs but lower plasma estradiol levels, lower expression of estrogen response genes, higher levels of tumor infiltrating lymphocytes and immune markers, and more TP53 mutations.
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Affiliation(s)
- Eugene F Schuster
- The Breast Cancer Now Toby Robins Research Centre at the Institute of Cancer Research, London, UK.
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
| | - Elena Lopez-Knowles
- The Breast Cancer Now Toby Robins Research Centre at the Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Anastasia Alataki
- The Breast Cancer Now Toby Robins Research Centre at the Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | | | - Elizabeth Folkerd
- The Breast Cancer Now Toby Robins Research Centre at the Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | | | | | - Maggie Chon U Cheang
- Clinical Trials and Statistics Unit, Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Holly Tovey
- Clinical Trials and Statistics Unit, Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Manuel Salto-Tellez
- Precision Medicine Centre of Excellence, The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Cellular Pathology, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Perry Maxwell
- Precision Medicine Centre of Excellence, The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - John Robertson
- Faculty of Medicine & Health Sciences, Queen's Medical Centre, Nottingham, UK
| | | | - Judith M Bliss
- Clinical Trials and Statistics Unit, Division of Clinical Studies, The Institute of Cancer Research, London, UK
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3
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Zhou J, Zhu M, Wang Q, Deng Y, Liu N, Liu Y, Liu Q. SERPINA3-ANKRD11-HDAC3 pathway induced aromatase inhibitor resistance in breast cancer can be reversed by HDAC3 inhibition. Commun Biol 2023; 6:695. [PMID: 37414914 PMCID: PMC10326080 DOI: 10.1038/s42003-023-05065-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
Endocrine resistance is a major challenge for breast cancer therapy. To identify the genes pivotal for endocrine-resistance progression, we screened five datasets and found 7 commonly dysregulated genes in endocrine-resistant breast cancer cells. Here we show that downregulation of serine protease inhibitor clade A member 3 (SERPINA3) which is a direct target gene of estrogen receptor α contributes to aromatase inhibitor resistance. Ankyrin repeat domain containing 11 (ANKRD11) works as a downstream effector of SERPINA3 in mediating endocrine-resistance. It induces aromatase inhibitor insensitivity by interacting with histone deacetylase 3 (HDAC3) and upregulating its activity. Our study suggests that aromatase inhibitor therapy downregulates SERPINA3 and leads to the ensuing upregulation of ANKRD11, which in turn promotes aromatase inhibitor resistance via binding to and activating HDAC3. HDAC3 inhibition may reverse the aromatase inhibitor resistance in ER-positive breast cancer with decreased SERPINA3 and increased ANKRD11 expression.
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Affiliation(s)
- Jing Zhou
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiang West Road 107#, 510120, Guangzhou, China
| | - Mengdi Zhu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiang West Road 107#, 510120, Guangzhou, China
| | - Qi Wang
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiang West Road 107#, 510120, Guangzhou, China
| | - Yiyuan Deng
- The China-Japan Union Hospital of Ji Lin University, Changchun, China
| | - Nianqiu Liu
- Kunming Medical University, Kunming, Yunnan, China
| | - Yujie Liu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiang West Road 107#, 510120, Guangzhou, China
| | - Qiang Liu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiang West Road 107#, 510120, Guangzhou, China.
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4
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Bergamino MA, Morani G, Parker J, Schuster EF, Leal MF, López-Knowles E, Tovey H, Bliss JM, Robertson JF, Smith IE, Dowsett M, Cheang MC. Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor-positive Breast Cancers. Clin Cancer Res 2022; 28:1217-1228. [PMID: 34965950 PMCID: PMC7612503 DOI: 10.1158/1078-0432.ccr-21-2718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/18/2021] [Accepted: 12/16/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Aromatase inhibitor (AI) treatment is the standard of care for postmenopausal women with primary estrogen receptor-positive breast cancer. The impact of duration of neoadjuvant endocrine therapy (NET) on molecular characteristics is still unknown. We evaluated and compared changes of gene expression profiles under short-term (2-week) versus longer-term neoadjuvant AIs. EXPERIMENTAL DESIGN Global gene expression profiles from the PeriOperative Endocrine Therapy for Individualised Care (POETIC) trial (137 received 2 weeks of AIs and 47 received no treatment) and targeted gene expression from 80 patients with breast cancer treated with NET for more than 1 month (NeoAI) were assessed. Intrinsic subtyping, module scores covering different cancer pathways and immune-related genes were calculated for pretreated and posttreated tumors. RESULTS The differences in intrinsic subtypes after NET were comparable between the two cohorts, with most Luminal B (90.0% in the POETIC trial and 76.3% in NeoAI) and 50.0% of HER2 enriched at baseline reclassified as Luminal A or normal-like after NET. Downregulation of proliferative-related pathways was observed after 2 weeks of AIs. However, more changes in genes from cancer-signaling pathways such as MAPK and PI3K/AKT/mTOR and immune response/immune-checkpoint components that were associated with AI-resistant tumors and differential outcome were observed in the NeoAI study. CONCLUSIONS Tumor transcriptional profiles undergo bigger changes in response to longer NET. Changes in HER2-enriched and Luminal B subtypes are similar between the two cohorts, thus AI-sensitive intrinsic subtype tumors associated with good survival might be identified after 2 weeks of AI. The changes of immune-checkpoint component expression in early AI resistance and its impact on survival outcome warrants careful investigation in clinical trials.
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Affiliation(s)
- Milana A. Bergamino
- Clinical Trials and Statistics Unit (ICR-CTSU)- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Gabriele Morani
- Clinical Trials and Statistics Unit (ICR-CTSU)- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Joel Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | | | | | - Holly Tovey
- Clinical Trials and Statistics Unit (ICR-CTSU)- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Judith M. Bliss
- Clinical Trials and Statistics Unit (ICR-CTSU)- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - John F.R. Robertson
- Faculty of Medicine & Health Sciences, Queen's Medical Centre, Nottingham, United Kingdom
| | | | - Mitch Dowsett
- Royal Marsden Hospital, London, United Kingdom.,Breast Cancer Now Research Centre, The Institute of Cancer Research, Sutton, London, United Kingdom
| | - Maggie C.U. Cheang
- Clinical Trials and Statistics Unit (ICR-CTSU)- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom.,Corresponding Author: Maggie C.U. Cheang, Clinical Trials and Statistics Unit (ICR-CTSU), The Institute of Cancer Research, 15 Cotswold Rd, Sutton SM2 5NG, United Kingdom. Phone: 4420-8722-4552; E-mail:
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5
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Hugh JC, Haddon LSJ, Githaka JM, Bigras G, Hu X, Madden B, Hanson J, Gabos Z, Giannakopoulos NV, Huang F, Hitt MM, McManus KJ, Olson D, Dabbs K, Mackey JR. DREAM, a possible answer to the estrogen paradox of the Women's Health Initiative Trial. Heliyon 2022; 8:e08666. [PMID: 35028452 PMCID: PMC8741439 DOI: 10.1016/j.heliyon.2021.e08666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/21/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
Estrogen is thought to cause proliferation of all estrogen receptor positive (ER+) breast cancers. Paradoxically, in the Women's Health Initiative Trial, estrogen-only hormone replacement therapy reduced the incidence and mortality of low grade, ER+, HER2- breast cancer. We gave estradiol to 19 post-menopausal women with newly diagnosed low-grade, ER+, HER2- breast cancer in a prospective window of opportunity clinical trial and examined the changes in proliferation and gene expression before and after estradiol treatment. Ki67 decreased in 13/19 (68%) patients and 8/13 (62%) showed a decrease in Risk of Recurrence Score. We chose three prototypical estrogen responders (greatest decrease in ROR) and non-responders (no/minimal change in ROR) and applied a differential gene expression analysis to develop pre-treatment (PRESTO-30core) and post-treatment (PRESTO-45surg) gene expression profiles. The PRESTO-30core predicted adjuvant benefit in a published series of tamoxifen, the partial estrogen agonist. Of the 45 genes in the PRESTO-45surg, thirty contain the Cell cycle genes Homology Region (CHR) motif that binds the class B multi-vulva complex (MuvB) a member of the DREAM (Dimerization partner, retinoblastoma-like proteins, E2F, MuvB) complex responsible for reversible cell cycle arrest or quiescence. There was also near uniform suppression (89%) of the remaining DREAM genes consistent with estrogen induced activation of the DREAM complex to mediate cell cycle block after a short course of estrogens. To our knowledge, this is the first report to show estrogen modulation of DREAM genes and suggest involvement of DREAM pathway associated quiescence in endocrine responsive post-menopausal ER+ breast cancers. WHI trial found that estrogen decreases some ER+ post-menopausal breast cancers. Our prospective clinical trial confirmed an anti-proliferative effect of estradiol. DREAM pathway genes were downregulated during the anti-proliferative response. This suggests that estrogen may activate DREAM quiescence of ER+ breast cancers.
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Affiliation(s)
- Judith C Hugh
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Lacey S J Haddon
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - John Maringa Githaka
- Department of Biochemistry, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Gilbert Bigras
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Xiuying Hu
- Department of Psychiatry, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Brittney Madden
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - John Hanson
- Department of Oncology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Zsolt Gabos
- Department of Oncology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Nadia V Giannakopoulos
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Fleur Huang
- Department of Oncology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Mary M Hitt
- Department of Oncology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Kirk J McManus
- Department of Oncology, University of Manitoba, 675 McDermot Avenue, Winnipeg, Manitoba R3E 0V9, Canada
| | - David Olson
- Department of Oncology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - Kelly Dabbs
- Department of Oncology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, 116 St & 85 Ave, Edmonton, Alberta T6G 2R3 Canada
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6
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Orozco JIJ, Chang SC, Matsuba C, Ensenyat-Mendez M, Grunkemeier GL, Marzese DM, Grumley JG. Is the 21-Gene Recurrence Score on Core Needle Biopsy Equivalent to Surgical Specimen in Early-Stage Breast Cancer? A Comparison of Gene Expression Between Paired Core Needle Biopsy and Surgical Specimens. Ann Surg Oncol 2021; 28:5588-5596. [PMID: 34244898 DOI: 10.1245/s10434-021-10457-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/08/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Molecular testing on surgical specimens predicts disease recurrence and benefit of adjuvant chemotherapy in hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) early-stage breast cancer (EBC). Testing on core biopsies has become common practice despite limited evidence of concordance between core/surgical samples. In this study, we compared the gene expression of the 21 genes and the recurrence score (RS) between paired core/surgical specimens. METHODS Eighty patients with HR+/HER2- EBC were evaluated from two publicly available gene expression datasets (GSE73235, GSE76728) with paired core/surgical specimens without neoadjuvant systemic therapy. The expression of the 21 genes was compared in paired samples. A microarray-based RS was calculated and a value ≥ 26 was defined as high-RS. The concordance rate and kappa statistic were used to evaluate the agreement between the RS of paired samples. RESULTS Overall, there was no significant difference and a high correlation in the gene expression levels of the 21 genes between paired samples. However, CD68 and RPLP0 in GSE73235, AURKA, BAG1, and TFRC in GSE76728, and MYLBL2 and ACTB in both datasets exhibited weak to moderate correlation (r < 0.5). There was a high correlation of the microarray-based RS between paired samples in GSE76728 (r = 0.91, 95% confidence interval [CI] 0.81-0.96) and GSE73235 (r = 0.82, 95% CI 0.71-0.89). There were no changes in RS category in GSE76728, whereas 82% of patients remained in the same RS category in GSE73235 (κ = 0.64). CONCLUSIONS Gene expression levels of the 21-gene RS showed a high correlation between paired specimens. Potential sampling and biological variability on a set of genes need to be considered to better estimate the RS from core needle biopsy.
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Affiliation(s)
- Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Shu-Ching Chang
- Center for Cardiovascular Analytics, Research and Data Science (CARDS), Providence Saint Joseph Health, Portland, OR, USA
| | - Chikako Matsuba
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory, Balearic Islands Health Research Institute (IdISBa), Palma, Spain
| | - Gary L Grunkemeier
- Center for Cardiovascular Analytics, Research and Data Science (CARDS), Providence Saint Joseph Health, Portland, OR, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory, Balearic Islands Health Research Institute (IdISBa), Palma, Spain
| | - Janie G Grumley
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.
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7
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Gao Q, López-Knowles E, Cheang MCU, Morden J, Ribas R, Sidhu K, Evans D, Martins V, Dodson A, Skene A, Holcombe C, Mallon E, Evans A, Bliss JM, Robertson J, Smith I, Martin LA, Dowsett M. Impact of aromatase inhibitor treatment on global gene expression and its association with antiproliferative response in ER+ breast cancer in postmenopausal patients. Breast Cancer Res 2019; 22:2. [PMID: 31892336 PMCID: PMC6938628 DOI: 10.1186/s13058-019-1223-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
Background Endocrine therapy reduces breast cancer mortality by 40%, but resistance remains a major clinical problem. In this study, we sought to investigate the impact of aromatase inhibitor (AI) therapy on gene expression and identify gene modules representing key biological pathways that relate to early AI therapy resistance. Methods Global gene expression was measured on pairs of core-cut biopsies taken at baseline and at surgery from 254 patients with ER-positive primary breast cancer randomised to receive 2-week presurgical AI (n = 198) or no presurgical treatment (control n = 56) from the POETIC trial. Data from the AI group was adjusted to eliminate artefactual process-related changes identified in the control group. The response was assessed by changes in the proliferation marker, Ki67. Results High baseline ESR1 expression associated with better AI response in HER2+ tumours but not HER2− tumours. In HER2− tumours, baseline expression of 48 genes associated with poor antiproliferative response (p < 0.005) including PERP and YWHAQ, the two most significant, and the transcription co-regulators (SAP130, HDAC4, and NCOA7) which were among the top 16 most significant. Baseline gene signature scores measuring cell proliferation, growth factor signalling (ERBB2-GS, RET/GDNF-GS, and IGF-1-GS), and immune activity (STAT1-GS) were significantly higher in poor AI responders. Two weeks of AI caused downregulation of genes involved in cell proliferation and ER signalling, as expected. Signature scores of E2F activation and TP53 dysfunction after 2-week AI were associated with poor AI response in both HER2− and HER2+ patients. Conclusions There is a high degree of heterogeneity in adaptive mechanisms after as little as 2-week AI therapy; however, all appear to converge on cell cycle regulation. Our data support the evaluation of whether an E2F signatures after short-term exposure to AI may identify those patients most likely to benefit from the early addition of CDK4/6 inhibitors. Trial registration ISRCTN, ISRCTN63882543, registered on 18 December 2007.
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Affiliation(s)
- Qiong Gao
- Breast Cancer Now Research Centre, ICR, London, UK
| | - Elena López-Knowles
- Breast Cancer Now Research Centre, ICR, London, UK.,Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Maggie Chon U Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - James Morden
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | | | - Kally Sidhu
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - David Evans
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Vera Martins
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Andrew Dodson
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Anthony Skene
- Royal Bournemouth Hospital, Castle Lane East, Bournemouth, UK
| | - Chris Holcombe
- Royal Liverpool University Hospital, 200 London Road, Liverpool, UK
| | | | | | - Judith M Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | | | - Ian Smith
- Breast Unit, Royal Marsden Hospital, London, UK
| | | | - Mitch Dowsett
- Breast Cancer Now Research Centre, ICR, London, UK. .,Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
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8
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Haynes BP, Ginsburg O, Gao Q, Folkerd E, Afentakis M, Buus R, Quang LH, Thi Han P, Khoa PH, Dinh NV, To TV, Clemons M, Holcombe C, Osborne C, Evans A, Skene A, Sibbering M, Rogers C, Laws S, Noor L, Smith IE, Dowsett M. Menstrual cycle associated changes in hormone-related gene expression in oestrogen receptor positive breast cancer. NPJ Breast Cancer 2019; 5:42. [PMID: 31754627 PMCID: PMC6858333 DOI: 10.1038/s41523-019-0138-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/24/2019] [Indexed: 01/25/2023] Open
Abstract
The major changes in hormone levels that occur through the menstrual cycle have been postulated to affect the expression of hormone-regulated and proliferation-associated genes (PAGs) in premenopausal ER+ breast cancer. Whilst previous studies have demonstrated differences in gene expression, here, we investigated if there are within patient changes in the expression of oestrogen- and progesterone-regulated genes (ERGs and PRGs) and PAGs in ER+ breast cancer during the menstrual cycle. Samples from 96 patients in two independent prospective studies of the effect of menstrual cycle on ER+ breast cancer were used. Plasma hormone measurements were used to assign tumours to one of three pre-defined menstrual cycle windows: W1 (days 27-35 and 1-6; low oestradiol and low progesterone), W2 (days 7-16; high oestradiol and low progesterone) and W3 (days 17-26; intermediate oestradiol and high progesterone). RNA expression of 50 genes, including 27 ERGs, 11 putative PRGs and seven PAGs was measured. The AvERG (geomean of PGR, GREB1, TFF1 and PDZK1) was used as a composite measure of ERG expression and showed significant changes between the three windows of the menstrual cycle increasing over 2.2-fold between W1 and W2 and decreasing between W2 and W3 and between W3 and W1. Proliferation gene expression also varied significantly, following the same pattern of changes as ERG expression, but the changes were of lower magnitude (1.4-fold increase between W1 and W2). Significant changes in the expression of eight individual ERGs, including GREB1, PGR and TFF1, and two PAGs were observed between W1 and either W2 or W3 with all genes showing higher levels in W2 or W3 (1.3-2.4-fold; FDR 0.016-0.05). The AvProg, a composite measure of PRG expression, increased significantly (1.5-fold) in W3 compared to W1 or W2 but no significant changes were observed for individual PRGs. In conclusion, we observed significant changes in ERG, PRG and PAG expression in ER+ breast tumours during the menstrual cycle that may affect the assessment and interpretation of prominent biomarkers (e.g. PgR) and commonly used multigene prognostic signatures in premenopausal ER+ breast cancer.
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Affiliation(s)
- Ben P. Haynes
- The Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, UK
| | - Ophira Ginsburg
- Perlmutter Cancer Center and the Department of Population Health, NYU Langone Health, New York, USA
| | - Qiong Gao
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London, UK
| | - Elizabeth Folkerd
- The Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, UK
| | - Maria Afentakis
- The Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, UK
| | - Richard Buus
- The Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London, UK
| | - Le Hong Quang
- Department of Breast Surgery, National Cancer Hospital, Hanoi, Vietnam
| | - Pham Thi Han
- Department of Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Pham Hong Khoa
- Department of Breast Surgery, National Cancer Hospital, Hanoi, Vietnam
| | - Nguyen Van Dinh
- Department of Breast Surgery, National Cancer Hospital, Hanoi, Vietnam
| | - Ta Van To
- Department of Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Mark Clemons
- Department of Medicine, Division of Medical Oncology, The Ottawa Hospital and University of Ottawa, Ottawa, Canada
| | - Chris Holcombe
- Royal Liverpool University Hospital, Prescott Street, Liverpool, UK
| | | | | | - Anthony Skene
- Royal Bournemouth Hospital, Castle Lane East, Bournemouth, Dorset UK
| | | | - Clare Rogers
- Doncaster Royal Infirmary, Armthorpe Road, Doncaster, South Yorkshire UK
| | - Siobhan Laws
- Royal Hampshire County Hospital, Winchester Hampshire, UK
| | - Lubna Noor
- University Hospital North Tees, Hardwick Road, Stockton-on-Tees, UK
| | - Ian E. Smith
- The Breast Unit, Department of Medicine, Royal Marsden Hospital, Fulham Road, London, UK
| | - Mitch Dowsett
- The Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London, UK
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Leal MF, Haynes BP, MacNeill FA, Dodson A, Dowsett M. Comparison of protein expression between formalin-fixed core-cut biopsies and surgical excision specimens using a novel multiplex approach. Breast Cancer Res Treat 2019; 175:317-326. [PMID: 30796652 PMCID: PMC6533418 DOI: 10.1007/s10549-019-05163-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 01/03/2023]
Abstract
PURPOSE We evaluated whether multiplex protein quantification using antibody bar-coding with photocleavable oligonucleotides (NanoString) can be applied to evaluate protein expression in breast cancer FFPE specimens. We also assessed whether diagnostic core-cuts fixed immediately at time of procedures and surgical excision sections from routinely fixed breast cancers are affected by the same fixation related differences noted using immunohistochemistry (IHC). METHODS The expression of 26 proteins was analysed using NanoString technology in 16 pairs of FFPE breast cancer core-cuts and surgical excisions. The measurements yielded were compared with those by IHC on Ki67, PgR and HER2 biomarkers and pAKT and pERK1/2 phosphorylated proteins. RESULTS When considered irrespective of sample type, expression measured by the two methods was strongly correlated for all markers (p < 0.001; ρ = 0.69-0.88). When core-cuts and excisions were evaluated separately, the correlations between NanoString and IHC were weaker but significant except for pAKT in excisions. Surgical excisions showed lower levels of 8/12 phosphoproteins and higher levels of 4/13 non-phosphorylated proteins in comparison to core-cuts (p < 0.01). Reduced p4EBP1, pAMPKa, pRPS6 and pRAF1 immunogenicity in excisions was correlated with tumour size and mastectomy specimens showed lower p4EBP1 and pRPS6 expression than lumpectomy (p < 0.05). CONCLUSIONS Our study supports the validity of the new multiplex approach to protein analysis but indicates that, as with IHC, caution is necessary for the analysis in excisions particularly of phosphoproteins. The specimen type, tumour size and surgery type may lead to biases in the quantitative analysis of many proteins of biologic and clinical interest in excision specimens.
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Affiliation(s)
- Mariana Ferreira Leal
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 4th Floor Wallace Wing, 203 Fulham Road, London, SW3 6JJ, UK.
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK.
| | - Ben P Haynes
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 4th Floor Wallace Wing, 203 Fulham Road, London, SW3 6JJ, UK
| | - Fiona A MacNeill
- Breast Unit, The Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Andrew Dodson
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 4th Floor Wallace Wing, 203 Fulham Road, London, SW3 6JJ, UK
| | - Mitch Dowsett
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 4th Floor Wallace Wing, 203 Fulham Road, London, SW3 6JJ, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
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