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1.
J Clin Oncol ; : JCO2400942, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38976807
2.
Br J Surg ; 111(5)2024 May 03.
Article in English | MEDLINE | ID: mdl-38736137

ABSTRACT

BACKGROUND: Barrett's oesophagus surveillance places significant burden on endoscopy services yet is vital to detect early cancerous change. Oesophageal cell collection device (OCCD) testing was introduced across Scotland for Barrett's surveillance in response to the COVID-19 pandemic. This national pragmatic retrospective study presents the CytoSCOT programme results and evaluates whether OCCD testing is successfully identifying high-risk Barrett's patients requiring urgent endoscopy. METHODS: All patients undergoing OCCD testing for Barrett's surveillance across 11 Scottish health boards over a 32-month period were identified. Patients who underwent endoscopy within 12 months of OCCD test were included. Individual patient records were interrogated to record clinical information and OCCD test result to categorize patients into risk groups. Endoscopic histopathology results were analysed according to risk group and segment length. Patients were deemed high risk if the OCCD test demonstrated atypia and/or p53 positivity. RESULTS: 4204 OCCD tests were performed in 3745 patients: 608 patients underwent endoscopy within 12 months and were included in this analysis. Patients with longer Barrett's segments were significantly more likely to have an abnormal OCCD test. 50/608 patients (8.2%) had high-grade dysplasia or cancer on endoscopic biopsies: this equates to 1.3% of the total group (50/3745). 46/50 patients (92.0%) were deemed high risk, triggering urgent endoscopy: this rose to 100% with insufficient tests removed. There were no cancers diagnosed within 12 months post-OCCD in the low-risk group. CONCLUSION: OCCD testing is an effective triage tool to identify high-risk patients with Barrett's oesophagus requiring further investigation with endoscopy within the real-world setting.


Subject(s)
Barrett Esophagus , Esophageal Neoplasms , Esophagoscopy , Humans , Barrett Esophagus/pathology , Barrett Esophagus/diagnosis , Male , Female , Retrospective Studies , Middle Aged , Aged , Esophagoscopy/methods , Esophageal Neoplasms/diagnosis , Esophageal Neoplasms/pathology , COVID-19/diagnosis , Scotland/epidemiology , Biomarkers/metabolism , Risk Assessment , Esophagus/pathology , Early Detection of Cancer/methods , Adult
3.
J Clin Oncol ; 42(12): 1439-1449, 2024 Apr 20.
Article in English | MEDLINE | ID: mdl-38408285

ABSTRACT

PURPOSE: Imatinib resistance in GI stromal tumors (GISTs) is primarily caused by secondary KIT mutations, and clonal heterogeneity of these secondary mutations represents a major treatment obstacle. KIT inhibitors used after imatinib have clinical activity, albeit with limited benefit. Ripretinib is a potent inhibitor of secondary KIT mutations in the activation loop (AL). However, clinical benefit in fourth line remains limited and the molecular mechanisms of ripretinib resistance are largely unknown. PATIENTS AND METHODS: Progressing lesions of 25 patients with GISTs refractory to ripretinib were sequenced for KIT resistance mutations. Resistant genotypes were validated and characterized using novel cell line models and in silico modeling. RESULTS: GISTs progressing on ripretinib were enriched for secondary mutations in the ATP-binding pocket (AP), which frequently occur in cis with preexisting AL mutations, resulting in highly resistant AP/AL genotypes. AP/AL mutations were rarely observed in a cohort of progressing GIST samples from the preripretinib era but represented 50% of secondary KIT mutations in patients with tumors resistant to ripretinib. In GIST cell lines harboring secondary KIT AL mutations, the sole genomic escape mechanisms during ripretinib drug selection were AP/AL mutations. Ripretinib and sunitinib synergize against mixed clones with secondary AP or AL mutants but do not suppress clones with AP/AL genotypes. CONCLUSION: Our findings underscore that KIT remains the central oncogenic driver even in late lines of GIST therapy. KIT-inhibitor combinations may suppress resistance because of secondary KIT mutations. However, the emergence of KIT AP/AL mutations after ripretinib treatment calls for new strategies in the development of next-generation KIT inhibitors.


Subject(s)
Antineoplastic Agents , Gastrointestinal Neoplasms , Gastrointestinal Stromal Tumors , Naphthyridines , Proto-Oncogene Proteins c-kit , Urea , Humans , Adenosine Triphosphate/metabolism , Antineoplastic Agents/therapeutic use , Drug Resistance, Neoplasm/genetics , Gastrointestinal Neoplasms/drug therapy , Gastrointestinal Neoplasms/genetics , Gastrointestinal Stromal Tumors/drug therapy , Gastrointestinal Stromal Tumors/genetics , Imatinib Mesylate/therapeutic use , Mutation , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins c-kit/genetics , Urea/analogs & derivatives
4.
Dis Esophagus ; 37(5)2024 Apr 27.
Article in English | MEDLINE | ID: mdl-38267082

ABSTRACT

High quality Barrett's esophagus surveillance is crucial to detect early neoplastic changes. An esophageal cell collection device (OCCD) was introduced as a triage tool for Barrett's surveillance. This study aims to evaluate whether the Scottish OCCD program (CytoSCOT) has reduced delays to Barrett's surveillance, and whether delayed surveillance negatively impacts endoscopic pathology. All patients undergoing OCCD testing for Barrett's surveillance across 11 Scottish health boards between 14/9/2020 and 13/9/2022 were identified. Patients were dichotomised into two groups (Year 1 vs. Year 2), with individual records interrogated to record demographics, recommended surveillance interval, time from last endoscopy to OCCD test, and OCCD result. Patients were deemed high-risk if the OCCD demonstrated atypia and/or p53 positivity. Further analysis was performed on patients who underwent endoscopy within 12 months of OCCD testing. A total of 3223 OCCD tests were included in the analysis (1478 in Year 1; 1745 in Year 2). In Year 1 versus Year 2, there was a longer median delay to surveillance (9 vs. 5 months; P < 0.001), increased proportion of patients with delayed surveillance (72.6% vs. 57.0%; P < 0.001), and more high-risk patients (12.0% vs. 5.3%; P < 0.001). 425/3223 patients (13.2%) were further investigated with upper gastrointestinal endoscopy, 57.9% of which were high-risk. As surveillance delay increased beyond 24 months, high-risk patients were significantly more likely to develop dysplasia or malignancy (P = 0.004). Delayed Barrett's esophagus surveillance beyond 24 months is associated with increased risk of pre-cancerous pathology. The CytoSCOT program has reduced delays in surveillance, promoting earlier detection of dysplasia and reducing burden on endoscopy services.


Subject(s)
Barrett Esophagus , Esophageal Neoplasms , Esophagoscopy , Barrett Esophagus/pathology , Humans , Male , Female , Middle Aged , Aged , Esophageal Neoplasms/pathology , Esophagoscopy/methods , Esophagoscopy/statistics & numerical data , Scotland/epidemiology , Time Factors , Early Detection of Cancer/methods , Esophagus/pathology , Delayed Diagnosis/statistics & numerical data , Precancerous Conditions/pathology , Adenocarcinoma/pathology
5.
Environ Res ; 243: 117818, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38048863

ABSTRACT

Phytoremediation using floating treatment wetlands (FTWs) is an emerging nature-based solution for freshwater restoration. However, the potential to design these systems by manipulating macrophyte community composition to provide multiple ecosystem services remains unexplored. Using a tank experiment, we simulated aquatic environments impacted by multiple pollutants and employed a comparative ecological approach to design emergent macrophyte communities using the trait of plant stature (plant height) to structure communities. Ecosystem functions were quantified, and a threshold-based method used to compute an ecosystem multifunctionality index that was weighted based on three different management-driven restoration objectives: equal importance, phytoremediation, and regulation and cultural services. Across all restoration scenarios, ecosystem multifunctionality was higher when community types performed more diverse functions. Small emergent plant communities outperformed all other community types due to their increased provision of both regulation and maintenance, cultural, and provisioning services. Conversely, large emergent communities that are more typical candidates for phytoremediation had the highest levels of multifunctionality only when function was lower. Arranging emergent macrophytes in mixed-statured communities led to intermediate or poorer performance both in terms of multifunctionality and specific functions, suggesting that diversity on the plant stature axis leads to negative plant interactions and represents a 'worst of both worlds' combination. Employing comparative ecology to generalise plant selection by stature demonstrates that large emergent macrophytes are more likely to better deliver provision-based services, while small emergent communities can provide additional benefits from cultural and regulatory services. Selecting macrophytes for FTWs employed in freshwater restoration by stature is a simple and widely applicable approach for designing plant communities with predictable outcomes in terms of (multiple) ecosystem service provision and highlights the need for environmental managers to closely align restoration objectives with potential community types.


Subject(s)
Biodiversity , Ecosystem , Wetlands , Plants , Fresh Water
6.
Cancer Treat Res ; 186: 299-312, 2023.
Article in English | MEDLINE | ID: mdl-37978142

ABSTRACT

This chapter explores the multifaceted roles of DNA-PK with particular focus on its functions in non-homologous end-joining (NHEJ) DNA repair. DNA-PK is the primary orchestrator of NHEJ but also regulates other biologic processes. The growing understanding of varied DNA-PK biologic roles highlights new avenues for cancer treatment. However, these multiple roles also imply challenges, particularly in combination therapies, with perhaps a higher risk of clinical toxicities than was previously envisioned. These considerations underscore the need for compelling and innovative strategies to accomplish effective clinical translation.


Subject(s)
Biological Products , DNA-Binding Proteins , Humans , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , DNA/genetics , DNA Repair , DNA-Activated Protein Kinase/genetics , DNA-Activated Protein Kinase/metabolism
7.
J Clin Oncol ; 41(31): 4829-4836, 2023 Nov 01.
Article in English | MEDLINE | ID: mdl-37890277

ABSTRACT

PURPOSE: Most gastrointestinal stromal tumors (GISTs) express constitutively activated mutant isoforms of KIT or kinase platelet-derived growth factor receptor alpha (PDGFRA) that are potential therapeutic targets for imatinib mesylate. The relationship between mutations in these kinases and clinical response to imatinib was examined in a group of patients with advanced GIST. PATIENTS AND METHODS: GISTs from 127 patients enrolled onto a phase II clinical study of imatinib were examined for mutations of KIT or PDGFRA. Mutation types were correlated with clinical outcome. RESULTS: Activating mutations of KIT or PDGFRA were found in 112 (88.2%) and six (4.7%) GISTs, respectively. Most KIT mutations involved exon 9 (n = 23) or exon 11 (n = 85). All KIT mutant isoforms, but only a subset of PDGFRA mutant isoforms, were sensitive to imatinib, in vitro. In patients with GISTs harboring exon 11 KIT mutations, the partial response rate (PR) was 83.5%, whereas patients with tumors containing an exon 9 KIT mutation or no detectable mutation of KIT or PDGFRA had PR rates of 47.8% (P = .0006) and 0.0% (P < .0001), respectively. Patients whose tumors contained exon 11 KIT mutations had a longer event-free and overall survival than those whose tumors expressed either exon 9 KIT mutations or had no detectable kinase mutation. CONCLUSION: Activating mutations of KIT or PDGFRA are found in the vast majority of GISTs, and the mutational status of these oncoproteins is predictive of clinical response to imatinib. PDGFRA mutations can explain response and sensitivity to imatinib in some GISTs lacking KIT mutations.

8.
Pediatr Clin North Am ; 70(5): 937-950, 2023 10.
Article in English | MEDLINE | ID: mdl-37704352

ABSTRACT

Neurofibromatosis type I (NF1) is a common dominantly inherited disorder, and one of the most common of the RASopathies. Most individuals with NF1 develop plexiform neurofibromas and cutaneous neurofibromas, nerve tumors caused by NF1 loss of function in Schwann cells. Cell culture models and mouse models of NF1 are being used to test drug efficacy in preclinical trials, which led to Food and Drug Administration approval for use of MEK inhibitors to shrink most inoperable plexiform neurofibromas. This article details methods used for testing in preclinical models, and outlines newer models that may identify additional, curative, strategies.


Subject(s)
Neurofibroma, Plexiform , Neurofibromatosis 1 , United States , Humans , Animals , Mice , Child , Neurofibromatosis 1/complications , Neurofibromatosis 1/diagnosis , Neurofibromatosis 1/drug therapy , Neurofibroma, Plexiform/complications , Neurofibroma, Plexiform/drug therapy
9.
Clin Cancer Res ; 29(24): 5128-5139, 2023 12 15.
Article in English | MEDLINE | ID: mdl-37773632

ABSTRACT

PURPOSE: Leiomyosarcoma (LMS) is an aggressive sarcoma for which standard chemotherapies achieve response rates under 30%. There are no effective targeted therapies against LMS. Most LMS are characterized by chromosomal instability (CIN), resulting in part from TP53 and RB1 co-inactivation and DNA damage repair defects. We sought to identify therapeutic targets that could exacerbate intrinsic CIN and DNA damage in LMS, inducing lethal genotoxicity. EXPERIMENTAL DESIGN: We performed clinical targeted sequencing in 287 LMS and genome-wide loss-of-function screens in 3 patient-derived LMS cell lines, to identify LMS-specific dependencies. We validated candidate targets by biochemical and cell-response assays in vitro and in seven mouse models. RESULTS: Clinical targeted sequencing revealed a high burden of somatic copy-number alterations (median fraction of the genome altered =0.62) and demonstrated homologous recombination deficiency signatures in 35% of LMS. Genome-wide short hairpin RNA screens demonstrated PRKDC (DNA-PKcs) and RPA2 essentiality, consistent with compensatory nonhomologous end joining (NHEJ) hyper-dependence. DNA-PK inhibitor combinations with unconventionally low-dose doxorubicin had synergistic activity in LMS in vitro models. Combination therapy with peposertib and low-dose doxorubicin (standard or liposomal formulations) inhibited growth of 5 of 7 LMS mouse models without toxicity. CONCLUSIONS: Combinations of DNA-PK inhibitors with unconventionally low, sensitizing, doxorubicin dosing showed synergistic effects in LMS in vitro and in vivo models, without discernable toxicity. These findings underscore the relevance of DNA damage repair alterations in LMS pathogenesis and identify dependence on NHEJ as a clinically actionable vulnerability in LMS.


Subject(s)
Leiomyosarcoma , Animals , Mice , Humans , Leiomyosarcoma/drug therapy , Leiomyosarcoma/genetics , Leiomyosarcoma/pathology , DNA Repair/genetics , DNA Damage , Doxorubicin/pharmacology , Doxorubicin/therapeutic use , DNA
10.
Br J Cancer ; 129(3): 531-540, 2023 08.
Article in English | MEDLINE | ID: mdl-37369845

ABSTRACT

BACKGROUND: Mutational inactivation of the SETDB1 histone methyltransferase is found in a subset of mesothelioma, particularly in cases with near-haploidy and TP53 mutations. However, the tumourigenic consequences of SETDB1 inactivation are poorly understood. METHODS: In this study, we investigated SETDB1 tumour suppressor functions in mesothelioma and explored biologic relationships between SETDB1 and TP53. RESULTS: Immunoblotting of early passage cultures showed that SETDB1 was undetectable in 7 of 8 near-haploid mesotheliomas whereas SETDB1 expression was retained in each of 13 near-diploid mesotheliomas. TP53 aberrations were present in 5 of 8 near-haploid mesotheliomas compared to 2 of 13 near-diploid mesotheliomas, and BAP1 inactivation was demonstrated only in near-diploid mesotheliomas, indicating that near-haploid and near-diploid mesothelioma have distinct molecular and biologic profiles. Lentiviral SETDB1 restoration in near-haploid mesotheliomas (MESO257 and MESO542) reduced cell viability, colony formation, reactive oxygen species levels, proliferative marker cyclin A expression, and inhibited growth of MESO542 xenografts. The combination of SETDB1 restoration with pemetrexed and/or cisplatin treatment additively inhibited tumour growth in vitro and in vivo. Furthermore, SETDB1 restoration upregulated TP53 expression in MESO542 and MESO257, whereas SETDB1 knockdown inhibited mutant TP53 expression in JMN1B near-haploid mesothelioma cells. Likewise, TP53 knockdown inhibited SETDB1 expression. Similarly, immunoblotting evaluations of ten near-diploid mesothelioma biopsies and analysis of TCGA expression profiles showed that SETDB1 expression levels paralleled TP53 expression. CONCLUSION: These findings demonstrate that SETDB1 inactivation in near-haploid mesothelioma is generally associated with complete loss of SETDB1 protein expression and dysregulates TP53 expression. Targeting SETDB1 pathways could be an effective therapeutic strategy in these often untreatable tumours.


Subject(s)
Biological Products , Mesothelioma, Malignant , Mesothelioma , Humans , Haploidy , Mesothelioma, Malignant/genetics , Mesothelioma/genetics , Mesothelioma/pathology , Genes, Tumor Suppressor , Chromosome Aberrations , Tumor Suppressor Protein p53/genetics , Histone-Lysine N-Methyltransferase/genetics
11.
iScience ; 26(2): 106096, 2023 Feb 17.
Article in English | MEDLINE | ID: mdl-36818284

ABSTRACT

Malignant peripheral nerve sheath tumors (MPNSTs) are soft-tissue sarcomas of the peripheral nervous system that develop either sporadically or in the context of neurofibromatosis type 1 (NF1). MPNST diagnosis can be challenging and treatment outcomes are poor. We present here a resource consisting of the genomic characterization of 9 widely used human MPNST cell lines for their use in translational research. NF1-related cell lines recapitulated primary MPNST copy number profiles, exhibited NF1, CDKN2A, and SUZ12/EED tumor suppressor gene (TSG) inactivation, and presented no gain-of-function mutations. In contrast, sporadic cell lines collectively displayed different TSG inactivation patterns and presented kinase-activating mutations, fusion genes, altered mutational frequencies and COSMIC signatures, and different methylome-based classifications. Cell lines re-classified as melanomas and other sarcomas exhibited a different drug-treatment response. Deep genomic analysis, methylome-based classification, and cell-identity marker expression, challenged the identity of common MPNST cell lines, opening an opportunity to revise MPNST differential diagnosis.

12.
Frontline Gastroenterol ; 14(2): 97-102, 2023.
Article in English | MEDLINE | ID: mdl-36818788

ABSTRACT

Objective: Emergency interim guidance from the British Society for Gastroenterology (BSG) states that a no-biopsy strategy is possible to diagnose coeliac disease (CD) in adults with elevated transglutaminase IgA antibody (TGA-IgA) levels. We aimed to determine if the suggested TGA-IgA ≥10× ULN is safe and robust in making the diagnosis in adult patients in Scotland. We also aimed to establish if any important co-diagnoses would be missed if no biopsy was performed. Method: All positive coeliac serology results for patients aged >15 years in Scotland in 2016 (Grampian 2019) were accessed. Data were collected on demographics, TGA-IgA titres, D1 sampling, histology and macroscopic findings at upper and lower gastrointestinal (GI) endoscopy. Results: 1037/1429 patients with positive serology proceeded to biopsy, of which 796/1037 (76.8%) were diagnosed as CD. A total of 320/322 (99.37%) patients with TGA-IgA ≥10× ULN were diagnosed as CD giving the cut-off a positive predictive value of 99.38%. No significant co-pathology was found at endoscopy in these patients. Conclusion: Our results show that a no-biopsy strategy using a cut-off of TGA-IgA ≥10× ULN is safe to diagnose CD and that no important pathology would be missed. The European Society for Paediatric Gastroenterology, Hepatology and Nutrition 2020 and BSG COVID-19 interim guidelines are applicable to adult patients in Scotland.

13.
Br J Cancer ; 127(11): 1939-1953, 2022 11.
Article in English | MEDLINE | ID: mdl-36097178

ABSTRACT

BACKGROUND: Rhabdomyosarcoma (RMS) is a paediatric cancer driven either by fusion proteins (e.g., PAX3-FOXO1) or by mutations in key signalling molecules (e.g., RAS or FGFR4). Despite the latter providing opportunities for precision medicine approaches in RMS, there are currently no such treatments implemented in the clinic. METHODS: We evaluated biologic properties and targeting strategies for the FGFR4 V550L activating mutation in RMS559 cells, which have a high allelic fraction of this mutation and are oncogenically dependent on FGFR4 signalling. Signalling and trafficking of FGFR4 V550L were characterised by confocal microscopy and proteomics. Drug effects were determined by live-cell imaging, MTS assay, and in a mouse model. RESULTS: Among recently developed FGFR4-specific inhibitors, FGF401 inhibited FGFR4 V550L-dependent signalling and cell proliferation at low nanomolar concentrations. Two other FGFR4 inhibitors, BLU9931 and H3B6527, lacked potent activity against FGFR4 V550L. Alternate targeting strategies were identified by RMS559 phosphoproteomic analyses, demonstrating that RAS/MAPK and PI3K/AKT are essential druggable pathways downstream of FGFR4 V550L. Furthermore, we found that FGFR4 V550L is HSP90-dependent, and HSP90 inhibitors efficiently impeded RMS559 proliferation. In a RMS559 mouse xenograft model, the pan-FGFR inhibitor, LY2874455, did not efficiently inhibit growth, whereas FGF401 potently abrogated growth. CONCLUSIONS: Our results pave the way for precision medicine approaches against FGFR4 V550L-driven RMS.


Subject(s)
Rhabdomyosarcoma, Embryonal , Rhabdomyosarcoma , Humans , Mice , Animals , Phosphatidylinositol 3-Kinases , Receptor, Fibroblast Growth Factor, Type 4/genetics , Receptor, Fibroblast Growth Factor, Type 4/metabolism , Rhabdomyosarcoma/drug therapy , Rhabdomyosarcoma/genetics , Rhabdomyosarcoma/metabolism , Protein Kinase Inhibitors/pharmacology , Cell Proliferation , Cell Line, Tumor
14.
Br J Cancer ; 127(11): 2072-2085, 2022 11.
Article in English | MEDLINE | ID: mdl-36175617

ABSTRACT

BACKGROUND: Advanced gastrointestinal stromal tumour (GIST) is characterised by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximising response to therapeutic CDK4/6 inhibition. METHODS: Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples. The impact of inhibitors of CDK2, CDK4 and CDK2/4/6 was determined through cell proliferation and protein detection assays. CDK-inhibitor resistance mechanisms were characterised in GIST cell lines after long-term exposure. RESULTS: We identify recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways in clinical GIST samples. Therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation. Moreover, RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) are mechanisms of acquired CDK-inhibitor resistance in GIST. CONCLUSIONS: These studies establish the biological rationale for CDK2 and CDK4/6 co-inhibition as a therapeutic strategy in patients with advanced GIST, including metastatic GIST progressing on tyrosine kinase inhibitors.


Subject(s)
Gastrointestinal Neoplasms , Gastrointestinal Stromal Tumors , Humans , Cyclin-Dependent Kinase 2 , Cyclin-Dependent Kinase 4 , Gastrointestinal Stromal Tumors/drug therapy , Gastrointestinal Stromal Tumors/genetics , Cyclin-Dependent Kinase 6 , Gastrointestinal Neoplasms/drug therapy , Gastrointestinal Neoplasms/genetics
15.
Cancer Discov ; 12(9): 2120-2139, 2022 09 02.
Article in English | MEDLINE | ID: mdl-35789380

ABSTRACT

Polycomb repressive complex 2 (PRC2) has oncogenic and tumor-suppressive roles in cancer. There is clinical success of targeting this complex in PRC2-dependent cancers, but an unmet therapeutic need exists in PRC2-loss cancer. PRC2-inactivating mutations are a hallmark feature of high-grade malignant peripheral nerve sheath tumor (MPNST), an aggressive sarcoma with poor prognosis and no effective targeted therapy. Through RNAi screening in MPNST, we found that PRC2 inactivation increases sensitivity to genetic or small-molecule inhibition of DNA methyltransferase 1 (DNMT1), which results in enhanced cytotoxicity and antitumor response. Mechanistically, PRC2 inactivation amplifies DNMT inhibitor-mediated expression of retrotransposons, subsequent viral mimicry response, and robust cell death in part through a protein kinase R (PKR)-dependent double-stranded RNA sensor. Collectively, our observations posit DNA methylation as a safeguard against antitumorigenic cell-fate decisions in PRC2-loss cancer to promote cancer pathogenesis, which can be therapeutically exploited by DNMT1-targeted therapy. SIGNIFICANCE: PRC2 inactivation drives oncogenesis in various cancers, but therapeutically targeting PRC2 loss has remained challenging. Here we show that PRC2-inactivating mutations set up a tumor context-specific liability for therapeutic intervention via DNMT1 inhibitors, which leads to innate immune signaling mediated by sensing of derepressed retrotransposons and accompanied by enhanced cytotoxicity. See related commentary by Guil and Esteller, p. 2020. This article is highlighted in the In This Issue feature, p. 2007.


Subject(s)
Antineoplastic Agents , Neoplasms , Neurofibrosarcoma , Carcinogenesis/genetics , Humans , Mutation , Neoplasms/genetics , Neurofibrosarcoma/diagnosis , Neurofibrosarcoma/genetics , Neurofibrosarcoma/pathology , Polycomb Repressive Complex 2/genetics , Retroelements
16.
Clin Cancer Res ; 28(7): 1268-1276, 2022 04 01.
Article in English | MEDLINE | ID: mdl-35091442

ABSTRACT

PURPOSE: The purpose of this study is to evaluate ponatinib for advanced gastrointestinal stromal tumors (GIST). PATIENTS AND METHODS: This single-arm phase II trial enrolled patients with metastatic and/or unresectable GIST with failure of prior tyrosine kinase inhibitor (TKI) treatment into two cohorts based on presence or absence of KIT exon 11 (ex11) primary mutations. Patients initially received ponatinib 45 mg once daily. Following a temporary clinical hold in October 2013, dose reductions were implemented to reduce risk of arterial occlusive events (AOE). Primary endpoint was 16-week clinical benefit rate (CBR) in KIT ex11-positive cohort. KIT mutations in circulating tumor DNA (ctDNA) were assessed. RESULTS: Forty-five patients enrolled (30 KIT ex11-positive and 15 KIT ex11-negative); median follow-up was 14.7 and 13.6 months, respectively, as of August 1, 2016. Sixteen-week CBR was 36% (KIT ex11-positive; primary endpoint) and 20% (KIT ex11-negative). ctDNA analyses (n = 37) demonstrated strong concordance of primary KIT mutations between plasma and tumor. At least two secondary mutations were detected in 35% of patients overall and 54% of KIT ex11-positive patients. Changes from baseline in mutated ctDNA levels were consistent with clinical activity. Ponatinib was ineffective in patients with KIT exon 9 primary mutations. Resistance was associated with emergence of V654A. AOEs and venous thromboembolic events occurred in three and two patients, respectively. Six patients died; two deaths (pneumonia and pulmonary embolism) were considered possibly ponatinib-related. CONCLUSIONS: Ponatinib demonstrated activity in advanced GIST, particularly in KIT ex11-positive disease. ctDNA analysis confirmed heterogeneous resistance mutations in TKI-pretreated advanced GIST. Safety was consistent with previous studies.


Subject(s)
Antineoplastic Agents , Circulating Tumor DNA , Gastrointestinal Stromal Tumors , Pyridazines , Antineoplastic Agents/adverse effects , Biomarkers , Circulating Tumor DNA/genetics , Gastrointestinal Stromal Tumors/drug therapy , Gastrointestinal Stromal Tumors/genetics , Gastrointestinal Stromal Tumors/pathology , Humans , Imidazoles , Liquid Biopsy , Mutation , Protein Kinase Inhibitors/adverse effects , Proto-Oncogene Proteins c-kit/genetics , Pyridazines/adverse effects
17.
Oncogene ; 40(48): 6614-6626, 2021 12.
Article in English | MEDLINE | ID: mdl-34621020

ABSTRACT

KIT/PDGFRA oncogenic tyrosine kinase signaling is the central oncogenic event in most gastrointestinal stromal tumors (GIST), which are human malignant mesenchymal neoplasms that often feature myogenic differentiation. Although targeted inhibition of KIT/PDGFRA provides substantial clinical benefit, GIST cells adapt to KIT/PDGFRA driver suppression and eventually develop resistance. The specific molecular events leading to adaptive resistance in GIST remain unclear. By using clinically representative in vitro and in vivo GIST models and GIST patients' samples, we found that the E3 ubiquitin ligase Atrogin-1 (FBXO32)-the main effector of muscular atrophy in cachexia-resulted in the most critical gene derepressed in response to KIT inhibition, regardless the type of KIT primary or secondary mutation. Atrogin-1 in GISTs is transcriptionally controlled by the KIT-FOXO3a axis, thus indicating overlap with Atrogin-1 regulation mechanisms in nonneoplastic muscle cells. Further, Atrogin-1 overexpression was a GIST-cell-specific pro-survival mechanism that enabled the adaptation to KIT-targeted inhibition by apoptosis evasion through cell quiescence. Buttressed on these findings, we established in vitro and in vivo the preclinical proof-of-concept for co-targeting KIT and the ubiquitin pathway to maximize the therapeutic response to first-line imatinib treatment.


Subject(s)
Drug Resistance, Neoplasm/drug effects , Gastrointestinal Stromal Tumors/drug therapy , Gene Expression Regulation, Neoplastic/drug effects , Imatinib Mesylate/pharmacology , Muscle Proteins/antagonists & inhibitors , Proto-Oncogene Proteins c-kit/antagonists & inhibitors , Pyrazoles/pharmacology , Pyrimidines/pharmacology , SKP Cullin F-Box Protein Ligases/antagonists & inhibitors , Sulfides/pharmacology , Sulfonamides/pharmacology , Animals , Antineoplastic Agents/pharmacology , Apoptosis , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Cell Proliferation , Drug Therapy, Combination , Gastrointestinal Neoplasms/drug therapy , Gastrointestinal Neoplasms/metabolism , Gastrointestinal Neoplasms/pathology , Gastrointestinal Stromal Tumors/metabolism , Gastrointestinal Stromal Tumors/pathology , Humans , Mice , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
18.
J Exp Med ; 218(8)2021 08 02.
Article in English | MEDLINE | ID: mdl-34143182

ABSTRACT

Central precocious puberty (CPP), largely caused by germline mutations in the MKRN3 gene, has been epidemiologically linked to cancers. MKRN3 is frequently mutated in non-small cell lung cancers (NSCLCs) with five cohorts. Genomic MKRN3 aberrations are significantly enriched in NSCLC samples harboring oncogenic KRAS mutations. Low MKRN3 expression levels correlate with poor patient survival. Reconstitution of MKRN3 in MKRN3-inactivated NSCLC cells directly abrogates in vitro and in vivo tumor growth and proliferation. MKRN3 knockout mice are susceptible to urethane-induced lung cancer, and lung cell-specific knockout of endogenous MKRN3 accelerates NSCLC tumorigenesis in vivo. A mass spectrometry-based proteomics screen identified PABPC1 as a major substrate for MKRN3. The tumor suppressor function of MKRN3 is dependent on its E3 ligase activity, and MKRN3 missense mutations identified in patients substantially compromise MKRN3-mediated PABPC1 ubiquitination. Furthermore, MKRN3 modulates cell proliferation through PABPC1 nonproteolytic ubiquitination and subsequently, PABPC1-mediated global protein synthesis. Our integrated approaches demonstrate that the CPP-associated gene MKRN3 is a tumor suppressor.


Subject(s)
Carcinoma, Non-Small-Cell Lung/metabolism , Lung Neoplasms/metabolism , Poly(A)-Binding Protein I/metabolism , Tumor Suppressor Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitination , Amino Acid Sequence , Animals , Carcinogenesis/metabolism , Carcinogenesis/pathology , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Proliferation , HEK293 Cells , Humans , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mice, Inbred C57BL , Mice, Knockout , Mutation/genetics , Protein Binding , Protein Biosynthesis , Proto-Oncogene Proteins p21(ras)/genetics , Reproducibility of Results , Survival Analysis , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/deficiency , Ubiquitin-Protein Ligases/genetics , Urethane
19.
Oncogenesis ; 10(5): 37, 2021 May 04.
Article in English | MEDLINE | ID: mdl-33947829

ABSTRACT

Endometrial stromal sarcoma (ESS) is the second most common subtype of uterine mesenchymal cancer, after leiomyosarcoma, and oncogenic fusion proteins are found in many ESS. Our previous studies demonstrated transforming properties and diagnostic relevance of the fusion oncoprotein YWHAE-NUTM2 in high-grade endometrial stromal sarcoma (HG-ESS) and showed that cyclin D1 is a diagnostic biomarker in these HG-ESS. However, YWHAE-NUTM2 mechanisms of oncogenesis and roles in cyclin D1 expression have not been characterized. In the current studies, we show YWHAE-NUTM2 complexes with both BRAF/RAF1 and YAP/TAZ in HG-ESS. These interactions are functionally relevant because YWHAE-NUTM2 knockdown in HG-ESS and other models inhibits RAF/MEK/MAPK phosphorylation, cyclin D1 expression, and cell proliferation. Further, cyclin D1 knockdown in HG-ESS dephosphorylates RB1 and inhibits proliferation. In keeping with these findings, we show that MEK and CDK4/6 inhibitors have anti-proliferative effects in HG-ESS, and combinations of these inhibitors have synergistic activity. These findings establish that YWHAE-NUTM2 regulates cyclin D1 expression and cell proliferation by dysregulating RAF/MEK/MAPK and Hippo/YAP-TAZ signaling pathways. Recent studies demonstrate Hippo/YAP-TAZ pathway aberrations in many sarcomas, but this is among the first studies to demonstrate a well-defined oncogenic mechanism as the cause of Hippo pathway dysregulation.

20.
Cancer ; 127(15): 2666-2673, 2021 08 01.
Article in English | MEDLINE | ID: mdl-33788262

ABSTRACT

BACKGROUND: Leiomyosarcoma (LMS) is the most common soft tissue and uterine sarcoma, but no standard therapy is available for recurrent or metastatic LMS. TP53, p16/RB1, and PI3K/mTOR pathway dysregulations are recurrent events, and some LMS express estrogen receptor (ER) and/or progesterone receptor (PR). To characterize relationships between these pathway perturbations, the authors evaluated protein expression in soft tissue and uterine nonprimary leiomyosarcoma (np-LMS), including local recurrences and distant metastases. METHODS: TP53, RB1, p16, and PTEN expression aberrations were determined by immunohistochemistry (IHC) in tissue microarrays (TMAs) from 227 np-LMS and a comparison group of 262 primary leiomyosarcomas (p-LMS). Thirty-five of the np-LMS had a matched p-LMS specimen in the TMAs. Correlative studies included differentiation scoring, ER and PR IHC, and CDKN2A/p16 fluorescence in situ hybridization. RESULTS: Dysregulation of TP53, p16/RB1, and PTEN was demonstrated in 90%, 95%, and 41% of np-LMS, respectively. PTEN inactivation was more common in soft tissue np-LMS than uterine np-LMS (55% vs 31%; P = .0005). Moderate-strong ER expression was more common in uterine np-LMS than soft tissue np-LMS (50% vs 7%; P < .0001). Co-inactivation of TP53 and RB1 was found in 81% of np-LMS and was common in both soft tissue and uterine np-LMS (90% and 74%, respectively). RB1, p16, and PTEN aberrations were nearly always conserved in p-LMS and np-LMS from the same patients. CONCLUSIONS: These studies show that nearly all np-LMS have TP53 and/or RB1 aberrations. Therefore, therapies targeting cell cycle and DNA damage checkpoint vulnerabilities should be prioritized for evaluations in LMS.


Subject(s)
Genes, p53 , Leiomyosarcoma , Retinoblastoma Binding Proteins/genetics , Ubiquitin-Protein Ligases/genetics , Uterine Neoplasms , Female , Genes, p16 , Humans , Immunohistochemistry , In Situ Hybridization, Fluorescence , Leiomyosarcoma/genetics , Leiomyosarcoma/pathology , PTEN Phosphohydrolase/genetics , Receptors, Estrogen/genetics , Receptors, Estrogen/metabolism , Uterine Neoplasms/genetics , Uterine Neoplasms/pathology
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