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

213 results found

Cheng JN, Frye JB, Whitman SA, Ehsani S, Ali S, Funk JLet al., 2024, Interrogating Estrogen Signaling Pathways in Human ER-Positive Breast Cancer Cells Forming Bone Metastases in Mice., Endocrinology, Vol: 165

Breast cancer bone metastases (BMET) are incurable, primarily osteolytic, and occur most commonly in estrogen receptor-α positive (ER+) breast cancer. ER+ human breast cancer BMET modeling in mice has demonstrated an estrogen (E2)-dependent increase in tumor-associated osteolysis and bone-resorbing osteoclasts, independent of estrogenic effects on tumor proliferation or bone turnover, suggesting a possible mechanistic link between tumoral ERα-driven osteolysis and ER+ bone progression. To explore this question, inducible secretion of the osteolytic factor, parathyroid hormone-related protein (PTHrP), was utilized as an in vitro screening bioassay to query the osteolytic potential of estrogen receptor- and signaling pathway-specific ligands in BMET-forming ER+ human breast cancer cells expressing ERα, ERß, and G protein-coupled ER. After identifying genomic ERα signaling, also responsibility for estrogen's proliferative effects, as necessary and sufficient for osteolytic PTHrP secretion, in vivo effects of a genomic-only ER agonist, estetrol (E4), on osteolytic ER+ BMET progression were examined. Surprisingly, while pharmacologic effects of E4 on estrogen-dependent tissues, including bone, were evident, E4 did not support osteolytic BMET progression (vs robust E2 effects), suggesting an important role for nongenomic ER signaling in ER+ metastatic progression at this site. Because bone effects of E4 did not completely recapitulate those of E2, the relative importance of nongenomic ER signaling in tumor vs bone cannot be ascertained here. Nonetheless, these intriguing findings suggest that targeted manipulation of estrogen signaling to mitigate ER+ metastatic progression in bone may require a nuanced approach, considering genomic and nongenomic effects of ER signaling on both sides of the tumor/bone interface.

Journal article

Shaw JA, Page K, Wren E, de Bruin EC, Kalashnikova E, Hastings R, McEwen R, Zhang E, Wadsley M, Acheampong E, Renner D, Gleason KLT, Ambasager B, Stetson D, Fernandez-Garcia D, Guttery D, Allsopp RC, Rodriguez A, Zimmermann B, Sethi H, Aleshin A, Liu MC, Richards C, Stebbing J, Ali S, Rehman F, Cleator S, Kenny L, Ahmed S, Armstrong AC, Coombes RCet al., 2024, Serial Postoperative Circulating Tumor DNA Assessment Has Strong Prognostic Value During Long-Term Follow-Up in Patients With Breast Cancer., JCO Precis Oncol, Vol: 8

PURPOSE: Here, we report the sensitivity of a personalized, tumor-informed circulating tumor DNA (ctDNA) assay (Signatera) for detection of molecular relapse during long-term follow-up of patients with breast cancer. METHODS: A total of 156 patients with primary breast cancer were monitored clinically for up to 12 years after surgery and adjuvant chemotherapy. Semiannual blood samples were prospectively collected, and analyzed retrospectively to detect residual disease by ultradeep sequencing using ctDNA assays, developed from primary tumor whole-exome sequencing data. RESULTS: Personalized Signatera assays detected ctDNA ahead of clinical or radiologic relapse in 30 of the 34 patients who relapsed (patient-level sensitivity of 88.2%). Relapse was predicted with a lead interval of up to 38 months (median, 10.5 months; range, 0-38 months), and ctDNA positivity was associated with shorter relapse-free survival (P < .0001) and overall survival (P < .0001). All relapsing triple-negative patients (n = 7/23) had a ctDNA-positive test within a median of 8 months (range, 0-19 months), while the 16 nonrelapsed patients with triple-negative breast cancer remained ctDNA-negative during a median follow-up of 58 months (range, 8-99 months). The four patients who had negative tests before relapse all had hormone receptor-positive (HR+) disease and conversely, five of the 122 nonrelapsed patients (all HR+) had an occasional positive test. CONCLUSION: Serial postoperative ctDNA assessment has strong prognostic value, provides a potential window for earlier therapeutic intervention, and may enable more effective monitoring than current clinical tests such as cancer antigen 15-3. Our study provides evidence that those with serially negative ctDNA tests have superior clinical outcomes, providing reassurance to patients with breast cancer. For select cases with HR+ disease, decisions about treatment management might require serial monitoring despite the ctDNA-positive result.

Journal article

De Marchi T, Lai C-F, Simmons GM, Goldsbrough I, Harrod A, Lam T, Buluwela L, Kjellström S, Brueffer C, Saal LH, Malmström J, Ali S, Niméus Eet al., 2024, Proteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling, Scientific Reports, Vol: 14, ISSN: 2045-2322

Three quarters of all breast cancers express the estrogen receptor (ER, ESR1 gene), which promotes tumor growth and constitutes a direct target for endocrine therapies. ESR1 mutations have been implicated in therapy resistance in metastatic breast cancer, in particular to aromatase inhibitors. ESR1 mutations promote constitutive ER activity and affect other signaling pathways, allowing cancer cells to proliferate by employing mechanisms within and without direct regulation by the ER. Although subjected to extensive genetic and transcriptomic analyses, understanding of protein alterations remains poorly investigated. Towards this, we employed an integrated mass spectrometry based proteomic approach to profile the protein and phosphoprotein differences in breast cancer cell lines expressing the frequent Y537N and Y537S ER mutations. Global proteome analysis revealed enrichment of mitotic and immune signaling pathways in ER mutant cells, while phosphoprotein analysis evidenced enriched activity of proliferation associated kinases, in particular CDKs and mTOR. Integration of protein expression and phosphorylation data revealed pathway-dependent discrepancies (motility vs proliferation) that were observed at varying degrees across mutant and wt ER cells. Additionally, protein expression and phosphorylation patterns, while under different regulation, still recapitulated the estrogen-independent phenotype of ER mutant cells. Our study is the first proteome-centric characterization of ESR1 mutant models, out of which we confirm estrogen independence of ER mutants and reveal the enrichment of immune signaling pathways at the proteomic level.

Journal article

Cushing VI, Koh AF, Feng J, Jurgaityte K, Bondke A, Kroll SHB, Barbazanges M, Scheiper B, Bahl AK, Barrett AGM, Ali S, Kotecha A, Greber BJet al., 2024, High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design, Nature Communications, Vol: 15, ISSN: 2041-1723

Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.

Journal article

Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TRet al., 2024, Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma., Res Sq

Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.

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., 2024, Correction: The CDK7 inhibitor CT7001 (Samuraciclib) targets proliferation pathways to inhibit advanced prostate cancer., Br J Cancer, Vol: 130

Journal article

Mustafa EH, Laven-Law G, Kikhtyak Z, Nguyen V, Ali S, Pace AA, Iggo R, Kebede A, Noll B, Wang S, Winter JM, Dwyer AR, Tilley WD, Hickey TEet al., 2024, Selective inhibition of CDK9 in triple negative breast cancer, Oncogene, Vol: 43, Pages: 202-215, ISSN: 0950-9232

Targeted therapy for triple-negative breast cancers (TNBC) remains a clinical challenge due to tumour heterogeneity. Since TNBC have key features of transcriptionally addicted cancers, targeting transcription via regulators such as cyclin-dependent kinase 9 (CDK9) has potential as a therapeutic strategy. Herein, we preclinically tested a new selective CDK9 inhibitor (CDDD11-8) in TNBC using cell line, patient-derived organoid, and patient-derived explant models. In vitro, CDDD11-8 dose-dependently inhibited proliferation (IC50 range: 281-734 nM), induced cell cycle arrest, and increased apoptosis of cell lines, which encompassed the three major molecular subtypes of TNBC. On target inhibition of CDK9 activity was demonstrated by reduced RNAPII phosphorylation at a CDK9 target peptide and down-regulation of the MYC and MCL1 oncogenes at the mRNA and protein levels in all cell line models. Drug induced RNAPII pausing was evident at gene promoters, with strongest pausing at MYC target genes. Growth of five distinct patient-derived organoid models was dose-dependently inhibited by CDDD11-8 (IC50 range: 272-771 nM), including three derived from MYC amplified, chemo-resistant TNBC metastatic lesions. Orally administered CDDD11-8 also inhibited growth of mammary intraductal TNBC xenograft tumours with no overt toxicity in vivo (mice) or ex vivo (human breast tissues). In conclusion, our studies indicate that CDK9 is a viable therapeutic target in TNBC and that CDDD11-8, a novel selective CDK9 inhibitor, has efficacy in TNBC without apparent toxicity to normal tissues.

Journal article

Alexandrou G, Mantikas K-T, Allsopp R, Yapeter CA, Jahin M, Melnick T, Ali S, Coombes RC, Toumazou C, Shaw JA, Kalofonou Met al., 2023, The evolution of affordable technologies in liquid biopsy diagnostics: the key to clinical implementation, Cancers, Vol: 15, ISSN: 2072-6694

Cancer remains a leading cause of death worldwide, despite many advances in diagnosis and treatment. Precision medicine has been a key area of focus, with research providing insights and progress in helping to lower cancer mortality through better patient stratification for therapies and more precise diagnostic techniques. However, unequal access to cancer care is still a global concern, with many patients having limited access to diagnostic tests and treatment regimens. Noninvasive liquid biopsy (LB) technology can determine tumour-specific molecular alterations in peripheral samples. This allows clinicians to infer knowledge at a DNA or cellular level, which can be used to screen individuals with high cancer risk, personalize treatments, monitor treatment response, and detect metastasis early. As scientific understanding of cancer pathology increases, LB technologies that utilize circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) have evolved over the course of research. These technologies incorporate tumour-specific markers into molecular testing platforms. For clinical translation and maximum patient benefit at a wider scale, the accuracy, accessibility, and affordability of LB tests need to be prioritized and compared with gold standard methodologies in current use. In this review, we highlight the range of technologies in LB diagnostics and discuss the future prospects of LB through the anticipated evolution of current technologies and the integration of emerging and novel ones. This could potentially allow a more cost-effective model of cancer care to be widely adopted.

Journal article

Wilson GA, Vuina K, Sava G, Huard C, Meneguello L, Coulombe-Huntington J, Bertomeu T, Maizels RJ, Lauring J, Kriston-Vizi J, Tyers M, Ali S, Bertoli C, de Bruin RAMet al., 2023, Active growth signaling promotes senescence and cancer cell sensitivity to CDK7 inhibition, Molecular Cell, Vol: 83, Pages: 4078-4092.e6, ISSN: 1097-2765

Tumor growth is driven by continued cellular growth and proliferation. Cyclin-dependent kinase 7's (CDK7) role in activating mitotic CDKs and global gene expression makes it therefore an attractive target for cancer therapies. However, what makes cancer cells particularly sensitive to CDK7 inhibition (CDK7i) remains unclear. Here, we address this question. We show that CDK7i, by samuraciclib, induces a permanent cell-cycle exit, known as senescence, without promoting DNA damage signaling or cell death. A chemogenetic genome-wide CRISPR knockout screen identified that active mTOR (mammalian target of rapamycin) signaling promotes samuraciclib-induced senescence. mTOR inhibition decreases samuraciclib sensitivity, and increased mTOR-dependent growth signaling correlates with sensitivity in cancer cell lines. Reverting a growth-promoting mutation in PIK3CA to wild type decreases sensitivity to CDK7i. Our work establishes that enhanced growth alone promotes CDK7i sensitivity, providing an explanation for why some cancers are more sensitive to CDK inhibition than normally growing cells.

Journal article

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

Jurgaityte K, Sava G, Lai CF, Fan H, Nguyen V, Buluwela L, Ali Set al., 2023, Defining modulators of response to samuraciclib, a CDK7 inhibitor for breast cancer, 114th Annual Meeting of the American Association for Cancer Research (AACR), Publisher: AMER ASSOC CANCER RESEARCH, ISSN: 0008-5472

Conference paper

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

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, 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

Alexandrou G, Moser N, Ali S, Coombes C, Shaw J, Georgiou P, Toumazou C, Kalofonou Met al., 2023, Distinguishing <i>PIK3CA</i> p.E545K mutational status from pseudogene DNA with a next-generation ISFET sensor array, 56th IEEE International Symposium on Circuits and Systems (ISCAS), Publisher: IEEE, ISSN: 0271-4302

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

Greber B, Cushing V, Feng J, Koh A, Kotecha A, Fuchter M, Ali Set al., 2022, Harnessing the power of cryo-EM for development of cancer therapeutics: High-resolution structures of the human CDK-activating kinase bound to inhibitors, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: A239-A239, ISSN: 2053-2733

Conference paper

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

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