Imperial College London

ProfessorSimakAli

Faculty of MedicineDepartment of Surgery & Cancer

Professor of Molecular Endocrine Oncology
 
 
 
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Contact

 

+44 (0)20 7594 2811simak.ali

 
 
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Location

 

133ICTEM buildingHammersmith Campus

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Summary

 

Publications

Publication Type
Year
to

196 results found

Coombes RC, Howell S, Lord SR, Kenny L, Mansi J, Mitri Z, Palmieri C, Chap LI, Richards P, Gradishar W, Sardesai S, Melear J, O'Shaughnessy J, Ward P, Chalasani P, Arkenau T, Baird RD, Jeselsohn R, Ali S, Clack G, Bahl A, McIntosh S, Krebs MGet al., 2023, Author Correction: Dose escalation and expansion cohorts in patients with advanced breast cancer in a Phase I study of the CDK7-inhibitor samuraciclib., Nature Communications, Vol: 14, Pages: 1-1, ISSN: 2041-1723

Journal article

Charles Coombes R, Howell S, Lord SR, Kenny L, Mansi J, Mitri Z, Palmieri C, Chap LI, Richards P, Gradishar W, Sardesai S, Melear J, O'Shaughnessy J, Ward P, Chalasani P, Arkenau T, Baird RD, Jeselsohn R, Ali S, Clack G, Bahl A, McIntosh S, Krebs MGet al., 2023, Dose escalation and expansion cohorts in patients with advanced breast cancer in a Phase I study of the CDK7-inhibitor samuraciclib, Nature Communications, Vol: 14, ISSN: 2041-1723

Samuraciclib is a selective oral CDK7-inhibitor. A multi-modular, open-label Phase I study to evaluate safety and tolerability of samuraciclib in patients with advanced malignancies was designed (ClinicalTrials.gov: NCT03363893). Here we report results from dose escalation and 2 expansion cohorts: Module 1A dose escalation with paired biopsy cohort in advanced solid tumor patients, Module 1B-1 triple negative breast cancer (TNBC) monotherapy expansion, and Module 2A fulvestrant combination in HR+/HER2- breast cancer patients post-CDK4/6-inhibitor. Core study primary endpoints are safety and tolerability, and secondary endpoints are pharmacokinetics (PK), pharmacodynamic (PD) activity, and anti-tumor activity. Common adverse events are low grade nausea, vomiting, and diarrhea. Maximum tolerated dose is 360 mg once daily. PK demonstrates dose proportionality (120 mg-480 mg), a half-life of approximately 75 hours, and no fulvestrant interaction. In dose escalation, one partial response (PR) is identified with disease control rate of 53% (19/36) and reduction of phosphorylated RNA polymerase II, a substrate of CDK7, in circulating lymphocytes and tumor tissue. In TNBC expansion, one PR (duration 337 days) and clinical benefit rate at 24 weeks (CBR) of 20.0% (4/20) is achieved. In combination with fulvestrant, 3 patients achieve PR with CBR 36.0% (9/25); in patients without detectable TP53-mutation CBR is 47.4% (9/19). In this study, samuraciclib exhibits tolerable safety and PK is supportive of once-daily oral administration. Clinical activity in TNBC and HR+/HER2-breast cancer post-CDK4/6-inhibitor settings warrants further evaluation.

Journal article

Constantin TA, Varela-Carver A, Greenland KK, de Almeida GS, Olden E, Penfold L, Ang S, Ormrod A, Leach DA, Lai C-F, Ainscow EK, Bahl AK, Carling D, Fuchter MJ, Ali S, Bevan CLet al., 2023, The CDK7 inhibitor CT7001 (Samuraciclib) targets proliferation pathways to inhibit advanced prostate cancer, British Journal of Cancer, Vol: 128, Pages: 2326-2337, ISSN: 0007-0920

BACKGROUND: Current strategies to inhibit androgen receptor (AR) are circumvented in castration-resistant prostate cancer (CRPC). Cyclin-dependent kinase 7 (CDK7) promotes AR signalling, in addition to established roles in cell cycle and global transcription, providing a rationale for its therapeutic targeting in CRPC. METHODS: The antitumour activity of CT7001, an orally bioavailable CDK7 inhibitor, was investigated across CRPC models in vitro and in xenograft models in vivo. Cell-based assays and transcriptomic analyses of treated xenografts were employed to investigate the mechanisms driving CT7001 activity, alone and in combination with the antiandrogen enzalutamide. RESULTS: CT7001 selectively engages with CDK7 in prostate cancer cells, causing inhibition of proliferation and cell cycle arrest. Activation of p53, induction of apoptosis, and suppression of transcription mediated by full-length and constitutively active AR splice variants contribute to antitumour efficacy in vitro. Oral administration of CT7001 represses growth of CRPC xenografts and significantly augments growth inhibition achieved by enzalutamide. Transcriptome analyses of treated xenografts indicate cell cycle and AR inhibition as the mode of action of CT7001 in vivo. CONCLUSIONS: This study supports CDK7 inhibition as a strategy to target deregulated cell proliferation and demonstrates CT7001 is a promising CRPC therapeutic, alone or in combination with AR-targeting compounds.

Journal article

HART STEPHEN GB, ALI SIMAK GB, PUFONG BORIS T GB, PORTER ANDREW C G GB, BULUWELA LAKI GB, VAINIKKA SATU GB, JENKINSON JOHN D GB, KANDA PATRICK GBet al., 2023, Control of gene expression using a complex of an oligonucleotide and a regulatory peptide, US2005136040

Patent

Saleh L, Ottewell PD, Brown JE, Wood SL, Brown NJ, Wilson C, Park C, Ali S, Holen Iet al., 2023, The CDK4/6 inhibitor palbociclib inhibits estrogen-positive and triple negative breast cancer bone metastasis in vivo, Cancers, Vol: 15, Pages: 1-23, ISSN: 2072-6694

CDK 4/6 inhibitors have demonstrated significant improved survival for patients with estrogen receptor (ER) positive breast cancer (BC). However, the ability of these promising agents to inhibit bone metastasis from either ER+ve or triple negative BC (TNBC) remains to be established. We therefore investigated the effects of the CDK 4/6 inhibitor, palbociclib, using in vivo models of breast cancer bone metastasis. In an ER+ve T47D model of spontaneous breast cancer metastasis from the mammary fat pad to bone, primary tumour growth and the number of hind limb skeletal tumours were significantly lower in palbociclib treated animals compared to vehicle controls. In the TNBC MDA-MB-231 model of metastatic outgrowth in bone (intracardiac route), continuous palbociclib treatment significantly inhibited tumour growth in bone compared to vehicle. When a 7-day break was introduced after 28 days (mimicking the clinical schedule), tumour growth resumed and was not inhibited by a second cycle of palbociclib, either alone or when combined with the bone-targeted agent, zoledronic acid (Zol), or a CDK7 inhibitor. Downstream phosphoprotein analysis of the MAPK pathway identified a number of phosphoproteins, such as p38, that may contribute to drug-insensitive tumour growth. These data encourage further investigation of targeting alternative pathways in CDK 4/6-insensitive tumour growth.

Journal article

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Supplementary Data from Hotspot <i>ESR1</i> Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis</jats:p>

Other

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis</jats:p>

Other

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>&lt;div&gt;Abstract&lt;p&gt;Constitutively active estrogen receptor α (ER/&lt;i&gt;ESR1&lt;/i&gt;) mutations have been identified in approximately one-third of ER&lt;sup&gt;+&lt;/sup&gt; metastatic breast cancers. Although these mutations are known as mediators of endocrine resistance, their potential role in promoting metastatic disease has not yet been mechanistically addressed. In this study, we show the presence of &lt;i&gt;ESR1&lt;/i&gt; mutations exclusively in distant but not local recurrences in five independent breast cancer cohorts. In concordance with transcriptomic profiling of &lt;i&gt;ESR1-&lt;/i&gt;mutant tumors, genome-edited &lt;i&gt;ESR1&lt;/i&gt; Y537S and D538G-mutant cell models exhibited a reprogrammed cell adhesive gene network via alterations in desmosome/gap junction genes and the TIMP3/MMP axis, which functionally conferred enhanced cell–cell contacts while decreasing cell-extracellular matrix adhesion. &lt;i&gt;In vivo&lt;/i&gt; studies showed &lt;i&gt;ESR1&lt;/i&gt;-mutant cells were associated with larger multicellular circulating tumor cell (CTC) clusters with increased compactness compared with &lt;i&gt;ESR1&lt;/i&gt; wild-type CTCs. These preclinical findings translated to clinical observations, where CTC clusters were enriched in patients with &lt;i&gt;ESR1&lt;/i&gt;-mutated metastatic breast cancer. Conversely, context-dependent migratory phenotypes revealed cotargeting of Wnt and ER as a vulnerability in a D538G cell model. Mechanistically, mutant &lt;i&gt;ESR1&lt;/i&gt; exhibited noncanonical regulation of several metastatic pathways, including secondary transcriptional regulation and &lt;i&gt;de novo&lt;/i&gt; FOXA1-driven chromatin remodeling. Collectively, these data provide evidence for &lt;i&gt;ESR1&

Other

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis</jats:p>

Other

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>&lt;div&gt;Abstract&lt;p&gt;Constitutively active estrogen receptor α (ER/&lt;i&gt;ESR1&lt;/i&gt;) mutations have been identified in approximately one-third of ER&lt;sup&gt;+&lt;/sup&gt; metastatic breast cancers. Although these mutations are known as mediators of endocrine resistance, their potential role in promoting metastatic disease has not yet been mechanistically addressed. In this study, we show the presence of &lt;i&gt;ESR1&lt;/i&gt; mutations exclusively in distant but not local recurrences in five independent breast cancer cohorts. In concordance with transcriptomic profiling of &lt;i&gt;ESR1-&lt;/i&gt;mutant tumors, genome-edited &lt;i&gt;ESR1&lt;/i&gt; Y537S and D538G-mutant cell models exhibited a reprogrammed cell adhesive gene network via alterations in desmosome/gap junction genes and the TIMP3/MMP axis, which functionally conferred enhanced cell–cell contacts while decreasing cell-extracellular matrix adhesion. &lt;i&gt;In vivo&lt;/i&gt; studies showed &lt;i&gt;ESR1&lt;/i&gt;-mutant cells were associated with larger multicellular circulating tumor cell (CTC) clusters with increased compactness compared with &lt;i&gt;ESR1&lt;/i&gt; wild-type CTCs. These preclinical findings translated to clinical observations, where CTC clusters were enriched in patients with &lt;i&gt;ESR1&lt;/i&gt;-mutated metastatic breast cancer. Conversely, context-dependent migratory phenotypes revealed cotargeting of Wnt and ER as a vulnerability in a D538G cell model. Mechanistically, mutant &lt;i&gt;ESR1&lt;/i&gt; exhibited noncanonical regulation of several metastatic pathways, including secondary transcriptional regulation and &lt;i&gt;de novo&lt;/i&gt; FOXA1-driven chromatin remodeling. Collectively, these data provide evidence for &lt;i&gt;ESR1&

Other

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis</jats:p>

Other

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis</jats:p>

Other

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2023, Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

<jats:p>Supplementary Data from Hotspot &lt;i&gt;ESR1&lt;/i&gt; Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis</jats:p>

Other

Alexandrou G, Moser N, Ali S, Coombes C, Shaw J, Georgiou P, Toumazou C, Kalofonou Met al., 2023, Distinguishing PIK3CA p.E545K Mutational Status from Pseudogene DNA with a Next-Generation ISFET Sensor Array, ISSN: 0271-4310

PIK3CA p.E545K mutation is a well-studied breast cancer biomarker with a clinical significance as a therapeutic target, particularly with the use of the small molecule inhibitor Alpelisib. An issue with detecting this mutation and other mutations in this exon is that 98% of its sequence homology is identical to a pseudogene, a non-functional non-coding gene found in chromosome 22. This paper aims to use ISFET enabled Lab-on-Chip (LoC) technology, coupled with a well-studied isothermal amplification method (LAMP), as a means to distinguish wild-type (WT), mutant (MT) and pseudogene (PG) copies of DNA. In an age where affordability and accessibility of diagnostic tests is of crucial importance, the use of CMOS technology offers a great potential as an alternative for regular near-patient molecular testing using liquid biopsies. Bespoke primer design is tested and optimised with synthetic DNA to achieve high specificity and low sensitivity (100 copies). The primer efficiencies were also tested on our in-house LoC system showing near identical results to those obtained from a qPCR instrument. Spiking experiments were also conducted, where mixed populations of WT and MT were tested to assess the primers' abilities to estimate the variant allele frequency (VAF) of p.E545K and to mimic clinical scenarios. The results continue to depict how LoC technology in partnership with LAMP detection can be used in a liquid biopsy setting to detect blood DNA biomarkers to assist better patient stratification.

Conference paper

Harrod A, Lai C, Goldsbrough I, Simmons G, Oppermans N, Santos D, Gyorffy B, Allsopp R, Toghill B, Balachandran K, Lawson M, Morrow C, Surakala M, Carnevalli L, Zhang P, Guttery D, Shaw J, Coombes RC, Buluwela L, Ali Set al., 2022, Genome engineering for estrogen receptor mutations reveals differential responses to anti-estrogens and new prognostic gene signatures for breast cancer, Oncogene, Vol: 41, Pages: 4905-4915, ISSN: 0950-9232

Mutations in the estrogen receptor (ESR1) gene are common in ER-positive breast cancer patients who progress on endocrine therapies. Most mutations localise to just three residues at, or near, the C-terminal helix 12 of the hormone binding domain, at leucine-536, tyrosine-537 and aspartate-538. To investigate these mutations, we have used CRISPR-Cas9 mediatedgenome engineering to generate a comprehensive set of isogenic mutant breast cancer cell lines. Our results confirm that L536R, Y537C, Y537N, Y537S and D538G mutations confer estrogen-independent growth in breast cancer cells. Growth assays show mutation-specific reductions in sensitivities to drugs representing three classes of clinical anti-estrogens. These differential mutation- and drug-selectivity profiles have implications for treatment choices following clinical emergence of ER mutations. Our results further suggest that mutant expression levels may be determinants of the degree of resistance to some anti-estrogens. Differential gene expression analysis demonstrates up-regulation of estrogen-responsivegenes, as expected, but also reveals that enrichment for interferon-regulated gene expression is a common feature of all mutations. Finally, a new gene signature developed from the geneexpression profiles in ER mutant cells predicts clinical response in breast cancer patients withER mutations

Journal article

Fernandez-Garcia D, Nteliopoulos G, Hastings RK, Rushton A, Page K, Allsopp RC, Ambasager B, Gleason K, Guttery DS, Ali S, Coombes RC, Shaw JAet al., 2022, Shallow WGS of individual CTCs identifies actionable targets for informing treatment decisions in metastatic breast cancer, British Journal of Cancer, Vol: 127, Pages: 1858-1864, ISSN: 0007-0920

BackgroundWe report copy-number profiling by low-pass WGS (LP-WGS) in individual circulating tumour cells (CTCs) for guiding treatment in patients with metastatic breast cancer (MBC), comparing CTC results with mutations detected in circulating tumour DNA (ctDNA) in the same blood samples.MethodsAcross 10 patients with MBC who were progressing at the time of blood sampling and that had >20 CTCs detected by CellSearch®, 63 single cells (50 CTCs and 13 WBCs) and 16 cell pools (8 CTC pools and 8 WBC pools) were recovered from peripheral blood by CellSearch®/DEPArray™ and sequenced with Ampli1 LowPass technology (Menarini Silicon Biosystems). Copy-number aberrations were identified using the MSBiosuite software platform, and results were compared with mutations detected in matched plasma cfDNA analysed by targeted next-generation sequencing using the Oncomine™ Breast cfDNA Assay (Thermo Fisher).ResultsLP-WGS data demonstrated copy-number gains/losses in individual CTCs in regions including FGFR1, JAK2 and CDK6 in five patients, ERBB2 amplification in two HER2-negative patients and BRCA loss in two patients. Seven of eight matched plasmas also had mutations in ctDNA in PIK3CA, TP53, ESR1 and KRAS genes with mutant allele frequencies (MAF) ranging from 0.05 to 33.11%. Combining results from paired CTCs and ctDNA, clinically actionable targets were identified in all ten patients.ConclusionThis combined analysis of CTCs and ctDNA may offer a new approach for monitoring of disease progression and to direct therapy in patients with advanced MBC, at a time when they are coming towards the end of other treatment options.

Journal article

Aouad P, Zhang Y, De Martino F, Stibolt C, Ali S, Ambrosini G, Mani SA, Maggs K, Quinn HM, Sflomos G, Brisken Cet al., 2022, Epithelial-mesenchymal plasticity determines estrogen receptor positive breast cancer dormancy and epithelial reconversion drives recurrence, Nature Communications, Vol: 13, ISSN: 2041-1723

More than 70% of human breast cancers (BCs) are estrogen receptor α-positive (ER+). A clinical challenge of ER+ BC is that they can recur decades after initial treatments. Mechanisms governing latent disease remain elusive due to lack of adequate in vivo models. We compare intraductal xenografts of ER+ and triple-negative (TN) BC cells and demonstrate that disseminated TNBC cells proliferate similarly as TNBC cells at the primary site whereas disseminated ER+ BC cells proliferate slower, they decrease CDH1 and increase ZEB1,2 expressions, and exhibit characteristics of epithelial-mesenchymal plasticity (EMP) and dormancy. Forced E-cadherin expression overcomes ER+ BC dormancy. Cytokine signalings are enriched in more active versus inactive disseminated tumour cells, suggesting microenvironmental triggers for awakening. We conclude that intraductal xenografts model ER + BC dormancy and reveal that EMP is essential for the generation of a dormant cell state and that targeting exit from EMP has therapeutic potential.

Journal article

Allsopp R, Alexandrou G, Toumazou C, Ali S, Coombes C, Kalofonou M, Shaw Jet al., 2022, A comparison between Mini-loop mediated isothermal amplification and polymerase spiral reaction for selective amplification of short template DNA, bioRxiv

Journal article

Li Z, McGinn O, Wu Y, Bahreini A, Priedigkeit NM, Ding K, Onkar S, Lampenfeld C, Sartorius CA, Miller L, Rosenzweig M, Cohen O, Wagle N, Richer JK, Muller WJ, Buluwela L, Ali S, Bruno TC, Vignali DAA, Fang Y, Zhu L, Tseng GC, Gertz J, Atkinson JM, Lee A, Oesterreich Set al., 2022, ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation, Nature Communications, Vol: 13, Pages: 1-18, ISSN: 2041-1723

Estrogen receptor alpha (ER/ESR1) is frequently mutated in endocrine resistant ER-positive (ER+) breast cancer and linked to ligand-independent growth and metastasis. Despite the distinct clinical features of ESR1 mutations, their role in intrinsic subtype switching remains largely unknown. Here we find that ESR1 mutant cells and clinical samples show a significant enrichment of basal subtype markers, and six basal cytokeratins (BCKs) are the most enriched genes. Induction of BCKs is independent of ER binding and instead associated with chromatin reprogramming centered around a progesterone receptor-orchestrated insulated neighborhood. BCK-high ER+ primary breast tumors exhibit a number of enriched immune pathways, shared with ESR1 mutant tumors. S100A8 and S100A9 are among the most induced immune mediators and involve in tumor-stroma paracrine crosstalk inferred by single-cell RNA-seq from metastatic tumors. Collectively, these observations demonstrate that ESR1 mutant tumors gain basal features associated with increased immune activation, encouraging additional studies of immune therapeutic vulnerabilities.

Journal article

Baker S, Mason A, Slip R, Skinner K, Macdonald A, Masood O, Harris R, Fenton T, Periyasamy M, Ali S, Southgate Jet al., 2022, BK polyomavirus (BKPyV) is a risk factor for bladder cancer through induction of APOBEC3-mediated genomic damage, Oncogene, Vol: 41, Pages: 2139-2151, ISSN: 0950-9232

Limited understanding of bladder cancer aetiopathology hampers progress in reducing incidence. BK polyomavirus (BKPyV) is a common childhood infection that can be reactivated in the adult kidney leading to viruria. Here we used a mitotically-quiescent, differentiated, normal human urothelial in vitro model to study BKPyV infection. BKPyV infection led to significantly elevated APOBEC3A and APOBEC3B protein, increased deaminase activity and greater numbers of apurinic/apyrimidinic sites in the host urothelial genome. BKPyV Large T antigen (LT-Ag) stimulated re-entry into the cell cycle via inhibition of Retinoblastoma protein and activation of EZH2, E2F1 and FOXM1, which combined to push urothelial cells from G0 into an arrested G2 cell cycle state. The single-stranded DNA displacement loops formed during BKPyV-infection, provide a substrate for APOBEC3 enzymes where they interacted with LT-Ag. These results support reactivated BKPyV infections in adults as a risk factor for bladder cancer in immune-insufficient populations, including transplant patients and the elderly.

Journal article

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee A, Oesterreich Set al., 2022, Hotspot ESR1 mutations are multimodal and contextual modulators of breast cancer metastasis, Cancer Research, Vol: 82, Pages: 1321-1339, ISSN: 0008-5472

Constitutively active estrogen receptor α (ER/ESR1) mutations have been identified in approximately one-third of ER+ metastatic breast cancers. Although these mutations are known as mediators of endocrine resistance, their potential role in promoting metastatic disease has not yet been mechanistically addressed. In this study, we show the presence of ESR1 mutations exclusively in distant but not local recurrences in five independent breast cancer cohorts. In concordance with transcriptomic profiling of ESR1-mutant tumors, genome-edited ESR1 Y537S and D538G-mutant cell models exhibited a reprogrammed cell adhesive gene network via alterations in desmosome/gap junction genes and the TIMP3/MMP axis, which functionally conferred enhanced cell–cell contacts while decreasing cell-extracellular matrix adhesion. In vivo studies showed ESR1-mutant cells were associated with larger multicellular circulating tumor cell (CTC) clusters with increased compactness compared with ESR1 wild-type CTCs. These preclinical findings translated to clinical observations, where CTC clusters were enriched in patients with ESR1-mutated metastatic breast cancer. Conversely, context-dependent migratory phenotypes revealed cotargeting of Wnt and ER as a vulnerability in a D538G cell model. Mechanistically, mutant ESR1 exhibited noncanonical regulation of several metastatic pathways, including secondary transcriptional regulation and de novo FOXA1-driven chromatin remodeling. Collectively, these data provide evidence for ESR1 mutation–modulated metastasis and suggest future therapeutic strategies for targeting ESR1-mutant breast cancer.

Journal article

Baker SC, Mason AS, Slip RG, Skinner KT, Macdonald A, Masood O, Harris RS, Fenton TR, Periyasamy M, Ali S, Southgate Jet al., 2022, Induction of APOBEC3-mediated genomic damage in urothelium implicates BK polyomavirus (BKPyV) as a hit-and-run driver for bladder cancer, Oncogene, Vol: 41, Pages: 2139-2151, ISSN: 0950-9232

Limited understanding of bladder cancer aetiopathology hampers progress in reducing incidence. Mutational signatures show the anti-viral apolipoprotein B mRNA editing enzyme catalytic polypeptide (APOBEC) enzymes are responsible for the preponderance of mutations in bladder tumour genomes, but no causative viral agent has been identified. BK polyomavirus (BKPyV) is a common childhood infection that remains latent in the adult kidney, where reactivation leads to viruria. This study provides missing mechanistic evidence linking reactivated BKPyV-infection to bladder cancer risk. We used a mitotically-quiescent, functionally-differentiated model of normal human urothelium to examine BKPyV-infection. BKPyV-infection led to significantly elevated APOBEC3A and APOBEC3B protein, increased deaminase activity and greater numbers of apurinic/apyrimidinic sites in the host urothelial genome. BKPyV Large T antigen (LT-Ag) stimulated re-entry from G0 into the cell cycle through inhibition of retinoblastoma protein and activation of EZH2, E2F1 and FOXM1, with cells arresting in G2. The single-stranded DNA displacement loops formed in urothelial cells during BKPyV-infection interacted with LT-Ag to provide a substrate for APOBEC3-activity. Addition of interferon gamma (IFNγ) to infected urothelium suppressed expression of the viral genome. These results support reactivated BKPyV infections in adults as a risk factor for bladder cancer in immune-insufficient populations.

Journal article

Howell SJ, Kenny LM, Lord S, Krebs MG, Arkenau T, Baird R, MacPherson IR, Bahl A, Clack G, Ainscow E, Barrett AGM, Dickinson PA, Fuchter MJ, Lehnert M, Ali S, McIntosh S, Coombes Cet al., 2022, A clinical study of samuraciclib (CT7001), a first-in-class, oral, selective inhibitor of CDK7, in patients with advanced triple negative breast cancer (TNBC), San Antonio Breast Cancer Symposium, Publisher: AMER ASSOC CANCER RESEARCH, ISSN: 0008-5472

Conference paper

Mayayo-Peralta I, Faggion B, Hoekman L, Morris B, Lieftink C, Goldsbrough I, Buluwela L, Siefert JC, Post H, Altelaar M, Beijersbergen R, Ali S, Zwart W, Prekovic Set al., 2021, Ribociclib induces broad chemotherapy resistance and EGFR dependency in ESR1 wildtype and mutant breast cancer, Cancers, Vol: 13, ISSN: 2072-6694

While endocrine therapy is highly effective for the treatment of oestrogen receptor-α (ERα)-positive breast cancer, a significant number of patients will eventually experience disease progression and develop treatment-resistant, metastatic cancer. The majority of resistant tumours remain dependent on ERα-action, with activating ESR1 gene mutations occurring in 15–40% of advanced cancers. Therefore, there is an urgent need to discover novel effective therapies that can eradicate cancer cells with aberrant ERα and to understand the cellular response underlying their action. Here, we evaluate the response of MCF7-derived, CRISPR-Cas9-generated cell lines expressing mutant ERα (Y537S) to a large number of drugs. We report sensitivity to numerous clinically approved inhibitors, including CDK4/6 inhibitor ribociclib, which is a standard-of-care therapy in the treatment of metastatic ERα-positive breast cancer and currently under evaluation in the neoadjuvant setting. Ribociclib treatment induces senescence in both wildtype and mutant ERα breast cancer models and leads to a broad-range drug tolerance. Strikingly, viability of cells undergoing ribociclib-induced cellular senescence is maintained via engagement of EGFR signalling, which may be therapeutically exploited in both wildtype and mutant ERα-positive breast cancer. Our study highlights a wide-spread reduction in sensitivity to anti-cancer drugs accompanied with an acquired vulnerability to EGFR inhibitors following CDK4/6 inhibitor treatment

Journal article

Page K, Martinson LJ, Fernandez-Garcia D, Hills A, Gleason KLT, Gray MC, Rushton AJ, Nteliopoulos G, Hastings RK, Goddard K, Ions C, Parmar V, Primrose L, Openshaw MR, Guttery DS, Palmieri C, Ali S, Stebbing J, Coombes RC, Shaw JAet al., 2021, Circulating tumor DNA profiling from breast cancer screening through to metastatic disease, JCO Precision Oncology, Vol: 5, Pages: 1768-1776, ISSN: 2473-4284

PURPOSE: We investigated the utility of the Oncomine Breast cfDNA Assay for detecting circulating tumor DNA (ctDNA) in women from a breast screening population, including healthy women with no abnormality detected by mammogram, and women on follow-up through to advanced breast cancer. MATERIALS AND METHODS: Blood samples were taken from 373 women (127 healthy controls recruited through breast screening, 28 ductal carcinoma in situ, 60 primary breast cancers, 47 primary breast cancer on follow-up, and 111 metastatic breast cancers [MBC]) to recover plasma and germline DNA for analysis with the Oncomine Breast cfDNA Assay on the Ion S5 platform. RESULTS: One hundred sixteen of 373 plasma samples had one or more somatic variants detected across eight of the 10 genes and were called ctDNA-positive; MBC had the highest proportion of ctDNA-positive samples (61; 55%) and healthy controls the lowest (20; 15.7%). ESR1, TP53, and PIK3CA mutations account for 93% of all variants detected and predict poor overall survival in MBC (hazard ratio = 3.461; 95% CI, 1.866 to 6.42; P = .001). Patients with MBC had higher plasma cell-free DNA levels, higher variant allele frequencies, and more polyclonal variants, notably in ESR1 than in all other groups. Only 15 individuals had evidence of potential clonal hematopoiesis of indeterminate potential mutations. CONCLUSION: We were able detect ctDNA across the breast cancer spectrum, notably in MBC where variants in ESR1, TP53, and PIK3CA predicted poor overall survival. The assay could be used to monitor emergence of resistance mutations such as in ESR1 that herald resistance to aromatase inhibitors to tailor adjuvant therapies. However, we suggest caution is needed when interpreting results from a single plasma sample as variants were also detected in a small proportion of HCs.

Journal article

Kumar U, Hu Y, Masrour N, Castellanos-Uribe M, Harrod A, May ST, Ali S, Speirs V, Charles Coombes R, Yag├╝e Eet al., 2021, MicroRNA-495/TGF-β/FOXC1 axis regulates multidrug resistance in metaplastic breast cancer cells, Biochemical Pharmacology, Vol: 192, Pages: 1-15, ISSN: 0006-2952

Triple-negative metaplastic breast carcinoma (MBC) poses a significant treatment challenge due to lack of targeted therapies and chemotherapy resistance. We isolated a novel MBC cell line, BAS, which showed a molecular and phenotypic profile different from the only other metaplastic cell model, HS578T cells. To gain insight behind chemotherapeutic resistance, we generated doxorubicin (HS-DOX, BAS-DOX) and paclitaxel (HS-TX, BAS-TX) resistant derivatives of both cell lines. Drug sensitivity assays indicated a truly multidrug resistant (MDR) phenotype. Both BAS-DOX and BAS-TX showed up-regulation of FOXC1 and its experimental down-regulation re-sensitized cells to doxorubicin and paclitaxel. Experimental modulation of FOXC1 expression in MCF-7 and MDA-MB-231 cells corroborated its role in MDR. Genome-wide expression analyses identified gene expression signatures characterized by up-regulation of TGFB2, which encodes cytokine TGF-β2, in both BAS-DOX and BAS-TX cells. Pharmacological inhibition of the TGF-β pathway with galunisertib led to down-regulation of FOXC1 and increase in drug sensitivity in both BAS-DOX and BAS-TX cells. MicroRNA (miR) expression analyses identified high endogenous miR-495-3p levels in BAS cells that were downregulated in both BAS MDR cells. Transient expression of miR-495-3p mimic in BAS-DOX and BAS-TX cells caused downregulation of TGFB2 and FOXC1 and re-sensitized cells to doxorubicin and paclitaxel, whereas miR-495-3p inhibition in BAS cells led to increase in resistance to both drugs and up-regulation of TGFB2 and FOXC1. Together, these data suggest interplay between miR-495-3p, TGF-β2 and FOXC1 regulating MDR in MBC and open the exploration of novel therapeutic strategies.

Journal article

Alexandrou G, Moser N, Mantikas K-T, Rodriguez-Manzano J, Ali S, Coombes RC, Shaw J, Georgiou P, Toumazou C, Kalofonou Met al., 2021, Detection of Multiple Breast Cancer ESR1 mutations on an ISFET based Lab-on-Chip Platform., IEEE Trans Biomed Circuits Syst, Vol: PP

ESR1 mutations are important biomarkers in metastatic breast cancer. Specifically, p.E380Q and p.Y537S mu- tations arise in response to hormonal therapies given to patients with hormone receptor positive (HR+) breast cancer (BC). This paper demonstrates the efficacy of an ISFET based CMOS integrated Lab-on-Chip (LoC) system, coupled with variant- specific isothermal amplification chemistries, for detection and discrimination of wild type (WT) from mutant (MT) copies of the ESR1 gene. Hormonal resistant cancers often lead to increased chances of metastatic disease which leads to high mortality rates, especially in low-income regions and areas with low healthcare coverage. Design and optimization of bespoke primers was carried out and tested on a qPCR instrument and then benchmarked versus the LoC platform. Assays for detection of p.Y537S and p.E380Q were developed and tested on the LoC platform, achieving amplification in under 25 minutes and sensitivity of down to 1000 copies of DNA per reaction for both target assays. The LoC system hereby presented, is cheaper and smaller than other standard industry equivalent technologies such as qPCR and sequencing. The LoC platform proposed, has the potential to be used at a breast cancer point-of-care testing setting, offering mutational tracking of circulating tumour DNA in liquid biopsies to assist patient stratification and metastatic monitoring.

Journal article

Greber BJ, Remis J, Ali S, Nogales Eet al., 2021, 2.5 angstrom-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942, Biophysical Journal, Vol: 120, Pages: 677-686, ISSN: 0006-3495

The human CDK-activating kinase (CAK), composed of CDK7, cyclin H, and MAT1, is involved in the control of transcription initiation and the cell cycle. Because of these activities, it has been identified as a promising target for cancer chemotherapy. A number of CDK7 inhibitors have entered clinical trials, among them ICEC0942 (also known as CT7001). Structural information can aid in improving the affinity and specificity of such drugs or drug candidates, reducing side effects in patients. Here, we have determined the structure of the human CAK in complex with ICEC0942 at 2.5 Å-resolution using cryogenic electron microscopy. Our structure reveals conformational differences of ICEC0942 compared with previous X-ray crystal structures of the CDK2-bound complex, and highlights the critical ability of cryogenic electron microscopy to resolve structures of drug-bound protein complexes without the need to crystalize the protein target

Journal article

Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer J-U, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich Set al., 2021, Hotspot <i>ESR1</i> mutations are multimodal and contextual drivers of breast cancer metastasis

<jats:title>Abstract</jats:title><jats:p>Constitutively active estrogen receptor-α (ER/<jats:italic>ESR1</jats:italic>) mutations have been identified in approximately one third of ER+ metastatic breast cancer. Although these mutations are known mediators of endocrine resistance, their potential role in promoting metastatic disease has not yet been mechanistically addressed. In this study, we show the presence of <jats:italic>ESR1</jats:italic> mutations exclusively in distant, but not local recurrences. In concordance with transcriptomic profiling of <jats:italic>ESR1</jats:italic> mutant tumors, genome-edited Y537S and D538G cell models have a reprogrammed cell adhesive gene network via alterations in desmosome/gap junction genes and the <jats:italic>TIMP3/MMP</jats:italic> axis, which functionally confers enhanced cell-cell contacts while decreased cell-ECM adhesion. Context-dependent migratory phenotypes revealed co-targeting of Wnt and ER as vulnerability. Mutant ESR1 exhibits non-canonical regulation of several metastatic pathways including secondary transactivation and <jats:italic>de novo</jats:italic> FOXA1-driven chromatin remodeling. Collectively, our data supports evidence for <jats:italic>ESR1</jats:italic> mutation-driven metastases and provides insight for future preclinical therapeutic strategies.</jats:p><jats:sec><jats:title>Significance</jats:title><jats:p>Context and allele-dependent transcriptome and cistrome reprogramming in genome-edited <jats:italic>ESR1</jats:italic> mutation cell models elicit diverse metastatic phenotypes, including but not limited to alterations in cell adhesion and migration. The gain-of-function mutations can be pharmacologically targeted, and thus may be key components of novel therapeutic treatment strategies for ER-mutant metastatic breast cancer.</jats:p></jats:sec>

Journal article

Li Z, Wu Y, Bahreini A, Priedigkeit NM, Ding K, Sartorius CA, Miller L, Rosenzweig M, Wagle N, Richer JK, Muller WJ, Buluwela L, Ali S, Fang Y, Zhu L, Tseng GC, Gertz J, Atkinson JM, Lee AV, Oesterreich Set al., 2020, <i>ESR1</i>mutant breast cancers show elevated basal cytokeratins and immune activation

<jats:title>Abstract</jats:title><jats:p>Estrogen receptor alpha (ER/<jats:italic>ESR1</jats:italic>) is mutated in 30-40% of endocrine resistant ER-positive (ER+) breast cancer.<jats:italic>ESR1</jats:italic>mutations cause ligand-independent growth and increased metastasis<jats:italic>in vivo</jats:italic>and<jats:italic>in vitro</jats:italic>. Despite the distinct clinical features and changes in therapeutic response associated with<jats:italic>ESR1</jats:italic>mutations, there are no data about their potential role in intrinsic subtype switching. Applying four luminal and basal gene set pairs,<jats:italic>ESR1</jats:italic>mutant cell models and clinical samples showed a significant enrichment of basal subtype markers. Among them, the six basal cytokeratins (BCKs) were the most enriched genes. Induction of BCKs was independent of ER binding and instead associated with chromatin reprogramming centered around a progesterone receptor-orchestrated topological associated domain at the<jats:italic>KRT14/16/17</jats:italic>genomic region. Unexpectedly, high<jats:italic>BCK</jats:italic>expression in ER+ primary breast cancer is associated with good prognosis, and these tumors show enriched activation of a number of immune pathways, a distinctive feature shared with<jats:italic>ESR1</jats:italic>mutant tumors. S100A8 and S100A9 were among the most highly induced immune mediators shared between high-<jats:italic>BCK</jats:italic>s ER+ and<jats:italic>ESR1</jats:italic>mutant tumors, and single-cell RNA-seq analysis inferred their involvement in paracrine crosstalk between epithelial and stromal cells. Collectively, these observations demonstrate that<jats:italic>ESR1</jats:italic>mutant tumors gain basal features with induction of basal cytokeratins via epigenetic mechanisms in rare subpopulation of cells. This

Working paper

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