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1.
Nat Commun ; 15(1): 3422, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38653965

ABSTRACT

Targeting Anaplastic lymphoma kinase (ALK) is a promising therapeutic strategy for aberrant ALK-expressing malignancies including neuroblastoma, but resistance to ALK tyrosine kinase inhibitors (ALK TKI) is a distinct possibility necessitating drug combination therapeutic approaches. Using high-throughput, genome-wide CRISPR-Cas9 knockout screens, we identify miR-1304-5p loss as a desensitizer to ALK TKIs in aberrant ALK-expressing neuroblastoma; inhibition of miR-1304-5p decreases, while mimics of this miRNA increase the sensitivity of neuroblastoma cells to ALK TKIs. We show that miR-1304-5p targets NRAS, decreasing cell viability via induction of apoptosis. It follows that the farnesyltransferase inhibitor (FTI) lonafarnib in addition to ALK TKIs act synergistically in neuroblastoma, inducing apoptosis in vitro. In particular, on combined treatment of neuroblastoma patient derived xenografts with an FTI and an ALK TKI complete regression of tumour growth is observed although tumours rapidly regrow on cessation of therapy. Overall, our data suggests that combined use of ALK TKIs and FTIs, constitutes a therapeutic approach to treat high risk neuroblastoma although prolonged therapy is likely required to prevent relapse.


Subject(s)
Anaplastic Lymphoma Kinase , Dibenzocycloheptenes , Farnesyltranstransferase , GTP Phosphohydrolases , MicroRNAs , Neuroblastoma , Piperidines , Protein Kinase Inhibitors , Pyridines , Animals , Female , Humans , Mice , Anaplastic Lymphoma Kinase/genetics , Anaplastic Lymphoma Kinase/metabolism , Anaplastic Lymphoma Kinase/antagonists & inhibitors , Apoptosis/drug effects , Apoptosis/genetics , Cell Line, Tumor , Drug Resistance, Neoplasm/genetics , Drug Resistance, Neoplasm/drug effects , Drug Synergism , Farnesyltranstransferase/antagonists & inhibitors , Farnesyltranstransferase/metabolism , Gene Expression Regulation, Neoplastic/drug effects , GTP Phosphohydrolases/genetics , GTP Phosphohydrolases/metabolism , Membrane Proteins/metabolism , Membrane Proteins/genetics , MicroRNAs/genetics , MicroRNAs/metabolism , Mutation , Neuroblastoma/drug therapy , Neuroblastoma/genetics , Neuroblastoma/pathology , Neuroblastoma/metabolism , Piperidines/pharmacology , Piperidines/therapeutic use , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/therapeutic use , Pyridines/pharmacology , Pyridines/therapeutic use , Xenograft Model Antitumor Assays
2.
Eur Arch Otorhinolaryngol ; 281(7): 3639-3647, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38396298

ABSTRACT

OBJECTIVES: Investigate safety perceptions, quantify hazardous events, and analyse their manifestations in individuals with olfactory dysfunction through an online cross-sectional survey. METHODS: An online survey, available from 25th February to 28th September 2022, captured data on demographics, olfactory disorder causes, safety concerns, and experienced hazardous events. Distributed via Fifth Sense channels, it targeted individuals with self-claimed olfactory dysfunction. RESULTS: Of 432 responses, the majority were female (79.6%), aged 41-70, with 20.6% non-UK residents from 21 countries. Leading causes of dysfunction were Covid-19 (22%), idiopathic (20.8%), and congenital (14.4%). Safety concerns were high (85.9%), with gas, smoke, and food as major worries. Over 5 years, 32.2% faced ≥ 1 food incident, 14.8% ≥ 1 gas incident, 34.5% ≥ 1 gas scare, and 18.5% ≥ 1 work incident. Preventative measures were taken by 60.2% at home. Key limitations of this study were self-reported data and sampling bias of charity members. CONCLUSION: This study highlights the significant impact of smell loss on personal safety and emotional well-being. There is an unmet need in mitigating safety concerns/events for individuals with olfactory dysfunction. We suggest collaborate strategies such as educating the public sector and high-risk sectors (e.g. gas companies), and introducing safety 'scratch and sniff' cards as a screening method. Regular assessment of an individual's olfactory ability, similar to routine assessments for other sensory systems (sight, hearing) may allow proactive identification of at-risk people and corrective measures to take place.


Subject(s)
COVID-19 , Olfaction Disorders , Humans , Cross-Sectional Studies , Female , Male , Olfaction Disorders/epidemiology , Middle Aged , Adult , Aged , COVID-19/epidemiology , Surveys and Questionnaires , Safety
3.
Adv Ther ; 41(2): 759-776, 2024 02.
Article in English | MEDLINE | ID: mdl-38169059

ABSTRACT

INTRODUCTION: Defects in the homologous recombination repair (HRR) pathway can include mutations in BRCA1 and BRCA2 (BRCAm) and other HRR genes (HRRm). These mutations are associated with a homologous recombination deficiency (HRD) phenotype. We evaluated testing journey and treatment patterns by BRCAm, HRRm, and HRD status in a real-world dataset. METHODS: Deidentified data for patients who had undergone comprehensive genomic profiling using FoundationOne®CDx were collected through December 31, 2020, from a real-world multi-tumor clinico-genomic database (CGDB) capturing data from clinics in the United States. Patients eligible for inclusion in this analysis had a confirmed diagnosis with advanced or metastatic disease between January 1, 2018, and December 31, 2019, for 1 of 15 solid tumor types. Objectives were to evaluate patient treatment patterns by BRCAm, HRRm, and HRD status and to describe the timing of when (throughout disease course) comprehensive genomic profiling was performed. RESULTS: Among 9457 patients included in the overall population with evaluable biomarker status, 7856 (83.1%) received ≥ 1 systemic therapy. Among the 7856 patients who received systemic therapy, 2324 (30.0%) underwent testing before first-line therapy, 4114 (52.4%) were tested after receiving first-line therapy and before receiving subsequent therapy (if any), 970 (12.3%) were tested after second-line therapy and before receiving subsequent therapy (if any), and 447 (5.7%) patients underwent testing after receiving third-line therapy. A higher proportion of patients with BRCAm, HRRm, or HRD-positive status were treated with poly(ADP-ribose) polymerase (PARP) inhibitors across all lines of therapy. There was no evidence of a meaningful difference in the proportion of patients who received other treatment (including chemotherapy and immunotherapy) by BRCAm, HRRm, or HRD status. CONCLUSION: The majority of patients from this real-world dataset underwent FoundationOne®CDx testing after initiation of first-line treatment. Testing appeared to influence treatment patterns, with a higher proportion of patients with BRCAm, HRRm, and HRD-positive disease receiving PARP inhibitors.


Subject(s)
Neoplasms , Ovarian Neoplasms , Humans , Female , Recombinational DNA Repair , Neoplasms/drug therapy , Neoplasms/genetics , Mutation , Biomarkers , Genomics , Ovarian Neoplasms/pathology
4.
J Clin Med ; 12(23)2023 Nov 29.
Article in English | MEDLINE | ID: mdl-38068438

ABSTRACT

Olfactory dysfunction affects approximately 20% of the population globally, with incidence increasing over the age of 60. The pathophysiology is complex, not yet fully understood, and depends on many factors, including the underlying cause. Despite this, the present literature on olfaction is limited due to significant heterogeneity in methodological approaches. This has resulted in limited effective treatments available for olfactory dysfunction. Medications for olfactory dysfunction can be administered locally (directly to the olfactory epithelium) or systemically (orally or intravenously). Currently, there are various methods for local drug delivery to the olfactory epithelium (nasal drops, nasal sprays, atomisers, pressured meter-dosed inhalers, rinses, and exhalation delivery systems). The aims of this review are to summarise the different methods of drug delivery to the olfactory cleft, evaluate the current literature to assess which method is the most effective in delivering drugs to the olfactory epithelium, and review the medications currently available to treat olfactory dysfunction topically. Going forward, further research is required to better establish effective methods of drug delivery to the olfactory epithelium to treat smell disorders.

5.
JCO Precis Oncol ; 7: e2300195, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37972338

ABSTRACT

PURPOSE: Mutations in BRCA1 and/or BRCA2 (BRCAm), other homologous recombination repair genes (HRRm), and homologous recombination deficiency (HRD) lead to an accumulation of genomic alterations that can drive tumorigenesis. The prognostic impact of these HRR pathway defects on overall survival (OS) in patients not receiving poly (ADP-ribose) polymerase inhibitors (PARPi) or immunotherapy is unclear. We evaluated the association of HRR biomarkers with OS in patients with advanced solid tumors receiving therapy excluding PARPi and immunotherapy. METHODS: Deidentified data were collected through December 31, 2020, from a real-world clinicogenomic database (CGDB) with data originating from approximately 280 cancer clinics in the United States. Patients age 18 years and older with an advanced/metastatic diagnosis between 2018 and 2019 for 1 of 15 solid tumors and available data in the CGDB were included. The primary analysis evaluated the association between HRR pathway biomarkers and OS, using start of second-line therapy as the index date (to reduce immortal time bias). RESULTS: A total of 9,457 patients had available data for BRCA/HRR and 5,792 for HRD status; 4,890 (51.7%) were women and mean (SD) age was 65.9 (11.5) years. For the primary analysis, adjusted hazard ratios for OS were BRCAm (n = 156) versus BRCA wild-type (wt; n = 3,131; 0.83 [95% CI, 0.60 to 1.17]); for HRRm (n = 467) versus HRRwt (n = 282; 0.95 [95% CI, 0.79 to 1.14]); and for HRD-positive (n = 447) versus -negative (n = 1,687; 1.22 [95% CI, 1.02 to 1.47]). Results were similar using start of first-line and start of third-line therapy as index dates. CONCLUSION: This large, real-world study found no association between OS and either BRCA or HRR status but identified a possible linkage between HRD positivity and shorter median OS in patients with advanced solid tumors who did not receive PARPi or immunotherapy.


Subject(s)
Neoplasms , Recombinational DNA Repair , Humans , Female , Adolescent , Aged , Male , Recombinational DNA Repair/genetics , Neoplasms/genetics , Neoplasms/therapy , DNA Repair , Poly(ADP-ribose) Polymerase Inhibitors , Biomarkers, Tumor/genetics
6.
Front Digit Health ; 5: 1184919, 2023.
Article in English | MEDLINE | ID: mdl-37840686

ABSTRACT

Background: Natural language processing (NLP) has the potential to automate the reading of radiology reports, but there is a need to demonstrate that NLP methods are adaptable and reliable for use in real-world clinical applications. Methods: We tested the F1 score, precision, and recall to compare NLP tools on a cohort from a study on delirium using images and radiology reports from NHS Fife and a population-based cohort (Generation Scotland) that spans multiple National Health Service health boards. We compared four off-the-shelf rule-based and neural NLP tools (namely, EdIE-R, ALARM+, ESPRESSO, and Sem-EHR) and reported on their performance for three cerebrovascular phenotypes, namely, ischaemic stroke, small vessel disease (SVD), and atrophy. Clinical experts from the EdIE-R team defined phenotypes using labelling techniques developed in the development of EdIE-R, in conjunction with an expert researcher who read underlying images. Results: EdIE-R obtained the highest F1 score in both cohorts for ischaemic stroke, ≥93%, followed by ALARM+, ≥87%. The F1 score of ESPRESSO was ≥74%, whilst that of Sem-EHR is ≥66%, although ESPRESSO had the highest precision in both cohorts, 90% and 98%. For F1 scores for SVD, EdIE-R scored ≥98% and ALARM+ ≥90%. ESPRESSO scored lowest with ≥77% and Sem-EHR ≥81%. In NHS Fife, F1 scores for atrophy by EdIE-R and ALARM+ were 99%, dropping in Generation Scotland to 96% for EdIE-R and 91% for ALARM+. Sem-EHR performed lowest for atrophy at 89% in NHS Fife and 73% in Generation Scotland. When comparing NLP tool output with brain image reads using F1 scores, ALARM+ scored 80%, outperforming EdIE-R at 66% in ischaemic stroke. For SVD, EdIE-R performed best, scoring 84%, with Sem-EHR 82%. For atrophy, EdIE-R and both ALARM+ versions were comparable at 80%. Conclusions: The four NLP tools show varying F1 (and precision/recall) scores across all three phenotypes, although more apparent for ischaemic stroke. If NLP tools are to be used in clinical settings, this cannot be performed "out of the box." It is essential to understand the context of their development to assess whether they are suitable for the task at hand or whether further training, re-training, or modification is required to adapt tools to the target task.

7.
J Pers Med ; 13(8)2023 Aug 03.
Article in English | MEDLINE | ID: mdl-37623478

ABSTRACT

Despite the OlympiA trial demonstrating that early-stage, high-risk, HER2- germline BRCA1 and BRCA2 mutation (gBRCAm) positive breast cancer patients can benefit from PARPi in the adjuvant setting, the gBRCA testing rate in early-stage HR+/HER2- patients remains suboptimal compared to that in early-stage TNBC patients. To better understand the perceived barriers associated with gBRCA testing in HR+/HER2- disease, a quantitative survey was conducted across stakeholders (n = 430) including medical oncologists, surgeons, nurses, physician assistants, payers, and patients. This study revealed that while payers claim to cover gBRCA testing, poor clinician documentation and overutilization are key challenges. Therefore, payers place utilization management controls on gBRCA testing due to their impression that clinicians overtest. These controls have led to healthcare professionals experiencing payer pushback in the form of reimbursement limitations and denials. The perceived challenges to gBRCA testing stem from the lack of consensus dictating which patients are high risk and should be tested. While payers define high risk based on the CPS + EG score from the OlympiA trial, HCPs adopt a broader definition including genomic risk scores, lymph node involvement, and tumor grade and size. A dialogue to harmonize risk classification and testing eligibility across stakeholders is critical to address this disconnect and increase gBRCA testing in appropriate patients.

8.
J Clin Med ; 12(16)2023 Aug 18.
Article in English | MEDLINE | ID: mdl-37629408

ABSTRACT

The aim is to understand the patient experience of living with chronic rhinosinusitis with nasal polyposis (CRSwNP), clinician interactions and how symptoms, smell and taste disturbance are managed. An anonymized, online survey was distributed through a UK charity, Fifth Sense, a UK otolaryngology clinic and online support groups to capture qualitative and quantitative data. Data were collected from 1st December 2022 to 1st February 2023. A total of 124 individuals participated. The majority were female (66%) and in the age range of 41-70 years; 74.2% of participants were from the UK with the rest from North America, Europe and Asia. A total of 107 participants declared they had CRSwNP. Rhinologists and general otolaryngology clinicians scored the highest for patient satisfaction whilst general practitioners scored the lowest. Satisfaction with the management of smell and taste disturbance was lower amongst all clinicians compared to overall satisfaction. Ratings correlated with response to therapy and clinician interactions. Respondents reported hyposmia/anosmia to be the most debilitating symptom. Surgery and oral steroids were considered to be effective; however, the benefit lasted less than six months (62%). Hyposmia/anosmia is a key CRSwNP symptom that has limited treatment options and is frequently undervalued by clinicians. There is a need for more effective management options, education and patient support.

9.
Curr Otorhinolaryngol Rep ; 10(4): 377-384, 2022.
Article in English | MEDLINE | ID: mdl-36465666

ABSTRACT

Purpose of Review: To provide a detailed overview of the investigations and core outcome measures for olfactory disorders. Recent Findings: Olfactory disorders can have a detrimental impact to the quality of life of patients. There are a wide range of causes of olfactory loss including sinonasal conditions, idiopathic, post-head trauma or infection. This review highlights the key investigations and reasoning for their use to clinically assess and research patients with olfactory disorders. In addition, this review outlines the core outcome measures for olfaction that will help inform future research in olfactory disorders. Summary: A systematic approach with history taking and examination particularly with nasal endoscopy can determine the cause of the olfactory disorder in most cases. Specific olfactory disorder questionnaires can demonstrate the impact on quality of life, while psychophysical testing can objectively assess and monitor olfaction over time. Olfactory-evoked potentials and functional MRI are reserved for research, whereas CT and MRI imaging are used depending on history and examination. A core outcome set for olfaction has been developed that will help standardise the outcome measures used in olfaction and olfactory disorders research.

10.
Cell Rep ; 37(4): 109899, 2021 10 26.
Article in English | MEDLINE | ID: mdl-34706226

ABSTRACT

Although commonly associated with autophagosomes, LC3 can also be recruited to membranes by covalent lipidation in a variety of non-canonical contexts. These include responses to ionophores such as the M2 proton channel of influenza A virus. We report a subtractive CRISPR screen that identifies factors required for non-canonical LC3 lipidation. As well as the enzyme complexes directly responsible for LC3 lipidation in all contexts, we show the RALGAP complex is important for M2-induced, but not ionophore drug-induced, LC3 lipidation. In contrast, ATG4D is responsible for LC3 recycling in M2-induced and basal LC3 lipidation. Identification of a vacuolar ATPase subunit in the screen suggests a common mechanism for non-canonical LC3 recruitment. Influenza-induced and ionophore drug-induced LC3 lipidation lead to association of the vacuolar ATPase and ATG16L1 and can be antagonized by Salmonella SopF. LC3 recruitment to erroneously neutral compartments may therefore represent a response to damage caused by diverse invasive pathogens.


Subject(s)
Autophagy-Related Proteins , Lipoylation , Microtubule-Associated Proteins , Autophagosomes/genetics , Autophagosomes/metabolism , Autophagy-Related Proteins/genetics , Autophagy-Related Proteins/metabolism , CRISPR-Cas Systems , HCT116 Cells , HEK293 Cells , Humans , Influenza A virus/genetics , Influenza A virus/metabolism , Microtubule-Associated Proteins/genetics , Microtubule-Associated Proteins/metabolism , Salmonella/genetics , Salmonella/metabolism , Viral Matrix Proteins/genetics , Viral Matrix Proteins/metabolism , Viroporin Proteins/genetics , Viroporin Proteins/metabolism
11.
Br J Haematol ; 192(2): 354-365, 2021 01.
Article in English | MEDLINE | ID: mdl-32880915

ABSTRACT

Burkitt lymphoma (BL) accounts for almost two-thirds of all B-cell non-Hodgkin lymphoma (B-NHL) in children and adolescents and is characterised by a MYC translocation and rapid cell turnover. Intensive chemotherapeutic regimens have been developed in recent decades, including the lymphomes malins B (LMB) protocol, which have resulted in a survival rate in excess of 90%. Recent clinical trials have focused on immunochemotherapy, with the addition of rituximab to chemotherapeutic backbones, showing encouraging results. Despite these advances, relapse and refractory disease occurs in up to 10% of patients and salvage options for these carry a dismal prognosis. Efforts to better understand the molecular and functional characteristics driving relapse and refractory disease may help improve this prognosis. This study has established a paediatric BL patient-derived xenograft (PDX) resource which captures and maintains tumour heterogeneity, may be used to better characterise tumours and identify cell populations responsible for therapy resistance.


Subject(s)
Burkitt Lymphoma/pathology , Animals , Burkitt Lymphoma/genetics , Burkitt Lymphoma/therapy , Child , Disease Models, Animal , Female , Gene Expression Regulation, Neoplastic , Heterografts/pathology , Humans , Male , Mice , Neoplasm Transplantation , Tumor Cells, Cultured
12.
Blood ; 136(14): 1657-1669, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32573700

ABSTRACT

Anaplastic large cell lymphoma (ALCL) is a T-cell malignancy predominantly driven by a hyperactive anaplastic lymphoma kinase (ALK) fusion protein. ALK inhibitors, such as crizotinib, provide alternatives to standard chemotherapy with reduced toxicity and side effects. Children with lymphomas driven by nucleophosmin 1 (NPM1)-ALK fusion proteins achieved an objective response rate to ALK inhibition therapy of 54% to 90% in clinical trials; however, a subset of patients progressed within the first 3 months of treatment. The mechanism for the development of ALK inhibitor resistance is unknown. Through genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) activation and knockout screens in ALCL cell lines, combined with RNA sequencing data derived from ALK inhibitor-relapsed patient tumors, we show that resistance to ALK inhibition by crizotinib in ALCL can be driven by aberrant upregulation of interleukin 10 receptor subunit alpha (IL10RA). Elevated IL10RA expression rewires the STAT3 signaling pathway, bypassing otherwise critical phosphorylation by NPM1-ALK. IL-10RA expression does not correlate with response to standard chemotherapy in pediatric patients, suggesting that a combination of crizotinib and chemotherapy could prevent ALK inhibitor resistance-specific relapse.


Subject(s)
Antineoplastic Agents/pharmacology , Crizotinib/pharmacology , Drug Resistance, Neoplasm/genetics , Interleukin-10 Receptor alpha Subunit/genetics , Lymphoma, Large-Cell, Anaplastic/genetics , Protein Kinase Inhibitors/pharmacology , Protein-Tyrosine Kinases/genetics , Antineoplastic Agents/therapeutic use , CRISPR-Cas Systems , Cell Line , Crizotinib/therapeutic use , Dose-Response Relationship, Drug , Gene Editing , Gene Expression , Humans , Immunohistochemistry , Interleukin-10 Receptor alpha Subunit/metabolism , Lymphoma, Large-Cell, Anaplastic/drug therapy , Lymphoma, Large-Cell, Anaplastic/metabolism , Lymphoma, Large-Cell, Anaplastic/pathology , Models, Biological , Nucleophosmin , Protein Kinase Inhibitors/therapeutic use , Protein-Tyrosine Kinases/metabolism , STAT3 Transcription Factor/metabolism , Signal Transduction/drug effects
13.
Nat Commun ; 10(1): 5428, 2019 11 28.
Article in English | MEDLINE | ID: mdl-31780656

ABSTRACT

Resistance to anaplastic lymphoma kinase (ALK)-targeted therapy in ALK-positive non-small cell lung cancer has been reported, with the majority of acquired resistance mechanisms relying on bypass signaling. To proactively identify resistance mechanisms in ALK-positive neuroblastoma (NB), we herein employ genome-wide CRISPR activation screens of NB cell lines treated with brigatinib or ceritinib, identifying PIM1 as a putative resistance gene, whose high expression is associated with high-risk disease and poor survival. Knockdown of PIM1 sensitizes cells of differing MYCN status to ALK inhibitors, and in patient-derived xenografts of high-risk NB harboring ALK mutations, the combination of the ALK inhibitor ceritinib and PIM1 inhibitor AZD1208 shows significantly enhanced anti-tumor efficacy relative to single agents. These data confirm that PIM1 overexpression decreases sensitivity to ALK inhibitors in NB, and suggests that combined front-line inhibition of ALK and PIM1 is a viable strategy for the treatment of ALK-positive NB independent of MYCN status.


Subject(s)
Anaplastic Lymphoma Kinase/antagonists & inhibitors , Drug Resistance, Neoplasm/genetics , Neuroblastoma/genetics , Proto-Oncogene Proteins c-pim-1/genetics , Anaplastic Lymphoma Kinase/genetics , Animals , Apoptosis/drug effects , Biphenyl Compounds/pharmacology , Cell Line, Tumor , Gene Knockdown Techniques , Humans , Mice , N-Myc Proto-Oncogene Protein/genetics , Neuroblastoma/drug therapy , Organophosphorus Compounds/therapeutic use , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins c-pim-1/antagonists & inhibitors , Pyrimidines/pharmacology , Pyrimidines/therapeutic use , Sulfones/pharmacology , Sulfones/therapeutic use , Thiazolidines/pharmacology , Xenograft Model Antitumor Assays
14.
Proc Natl Acad Sci U S A ; 116(10): 4508-4517, 2019 03 05.
Article in English | MEDLINE | ID: mdl-30709910

ABSTRACT

Oncogenic mutations in the small GTPase KRAS are frequently found in human cancers, and, currently, there are no effective targeted therapies for these tumors. Using a combinatorial siRNA approach, we analyzed a panel of KRAS mutant colorectal and pancreatic cancer cell lines for their dependency on 28 gene nodes that represent canonical RAS effector pathways and selected stress response pathways. We found that RAF node knockdown best differentiated KRAS mutant and KRAS WT cancer cells, suggesting RAF kinases are key oncoeffectors for KRAS addiction. By analyzing all 376 pairwise combination of these gene nodes, we found that cotargeting the RAF, RAC, and autophagy pathways can improve the capture of KRAS dependency better than targeting RAF alone. In particular, codepletion of the oncoeffector kinases BRAF and CRAF, together with the autophagy E1 ligase ATG7, gives the best therapeutic window between KRAS mutant cells and normal, untransformed cells. Distinct patterns of RAS effector dependency were observed across KRAS mutant cell lines, indicative of heterogeneous utilization of effector and stress response pathways in supporting KRAS addiction. Our findings revealed previously unappreciated complexity in the signaling network downstream of the KRAS oncogene and suggest rational target combinations for more effective therapeutic intervention.


Subject(s)
Autophagic Cell Death , Colorectal Neoplasms/metabolism , Extracellular Signal-Regulated MAP Kinases/metabolism , MAP Kinase Signaling System , Pancreatic Neoplasms/metabolism , Proto-Oncogene Proteins p21(ras)/metabolism , Caco-2 Cells , Cell Survival/genetics , Colorectal Neoplasms/genetics , Extracellular Signal-Regulated MAP Kinases/genetics , HCT116 Cells , Humans , Pancreatic Neoplasms/genetics , Proto-Oncogene Proteins p21(ras)/genetics
15.
Cell Rep ; 22(7): 1889-1902, 2018 02 13.
Article in English | MEDLINE | ID: mdl-29444439

ABSTRACT

KRAS can bind numerous effector proteins, which activate different downstream signaling events. The best known are RAF, phosphatidylinositide (PI)-3' kinase, and RalGDS families, but many additional direct and indirect effectors have been reported. We have assessed how these effectors contribute to several major phenotypes in a quantitative way, using an arrayed combinatorial siRNA screen in which we knocked down 41 KRAS effectors nodes in 92 cell lines. We show that every cell line has a unique combination of effector dependencies, but in spite of this heterogeneity, we were able to identify two major subtypes of KRAS mutant cancers of the lung, pancreas, and large intestine, which reflect different KRAS effector engagement and opportunities for therapeutic intervention.


Subject(s)
Oncogenes , Proto-Oncogene Proteins p21(ras)/metabolism , AMP-Activated Protein Kinase Kinases , Adenylate Kinase/metabolism , Cell Line, Tumor , Drug Evaluation, Preclinical , Gene Expression Regulation, Neoplastic/drug effects , Humans , Metabolic Networks and Pathways/drug effects , Models, Biological , Mutation/genetics , Protein Serine-Threonine Kinases/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , RNA Interference , RNA, Small Interfering/metabolism , Small Molecule Libraries/pharmacology
16.
Cell Biosci ; 6: 57, 2016.
Article in English | MEDLINE | ID: mdl-27891214

ABSTRACT

BACKGROUND: The ability to transform normal human cells into cancer cells with the introduction of defined genetic alterations is a valuable method for understanding the mechanisms of oncogenesis. Easy establishment of immortalized but non-transformed human cells from various tissues would facilitate these genetic analyses. RESULTS: We report here a simple, one-step immortalization method that involves retroviral vector mediated co-expression of the human telomerase protein and a shRNA targeting the CDKN2A gene locus. We demonstrate that this method could successfully immortalize human small airway epithelial cells while maintaining their chromosomal stability. We further showed that these cells retain p53 activity and can be transformed by the KRAS oncogene. CONCLUSIONS: Our method simplifies the immortalization process and is broadly applicable for establishing immortalized epithelial cell lines from primary human tissues for cancer research.

17.
Proc Natl Acad Sci U S A ; 112(14): E1724-33, 2015 Apr 07.
Article in English | MEDLINE | ID: mdl-25805818

ABSTRACT

The small GTPase KRAS is frequently mutated in human cancer and currently there are no targeted therapies for KRAS mutant tumors. Here, we show that the small ubiquitin-like modifier (SUMO) pathway is required for KRAS-driven transformation. RNAi depletion of the SUMO E2 ligase Ubc9 suppresses 3D growth of KRAS mutant colorectal cancer cells in vitro and attenuates tumor growth in vivo. In KRAS mutant cells, a subset of proteins exhibit elevated levels of SUMOylation. Among these proteins, KAP1, CHD1, and EIF3L collectively support anchorage-independent growth, and the SUMOylation of KAP1 is necessary for its activity in this context. Thus, the SUMO pathway critically contributes to the transformed phenotype of KRAS mutant cells and Ubc9 presents a potential target for the treatment of KRAS mutant colorectal cancer.


Subject(s)
Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Gene Expression Regulation, Neoplastic , Ubiquitin-Conjugating Enzymes/metabolism , raf Kinases/metabolism , ras Proteins/metabolism , Animals , Caco-2 Cells , Carcinogenesis , Cell Line, Tumor , Cell Transformation, Neoplastic , Genes, ras , HCT116 Cells , Humans , Mice , Mice, Inbred NOD , Mice, SCID , Mutation , Neoplasm Transplantation , RNA Interference , RNA, Small Interfering/metabolism
18.
Cancer Discov ; 4(10): 1182-1197, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25100204

ABSTRACT

UNLABELLED: RNAi is a powerful tool for target identification and can lead to novel therapies for pharmacologically intractable targets such as KRAS. RNAi therapy must combine potent siRNA payloads with reliable in vivo delivery for efficient target inhibition. We used a functional "Sensor" assay to establish a library of potent siRNAs against RAS pathway genes and to show that they efficiently suppress their targets at low dose. This reduces off-target effects and enables combination gene knockdown. We administered Sensor siRNAs in vitro and in vivo and validated the delivery of KRAS siRNA alone and siRNA targeting the complete RAF effector node (A/B/CRAF) as promising strategies to treat KRAS-mutant colorectal cancer. We further demonstrate that improved therapeutic efficacy is achieved by formulating siRNA payloads that combine both single-gene siRNA and node-targeted siRNAs (KRAS + PIK3CA/B). The customizable nature of Sensor siRNA payloads offers a universal platform for the combination target identification and development of RNAi therapeutics. SIGNIFICANCE: To advance RNAi therapy for KRAS-mutant cancer, we developed a validated siRNA library against RAS pathway genes that enables combination gene silencing. Using an in vivo model for real-time siRNA delivery tracking, we show that siRNA-mediated inhibition of KRAS as well as RAF or PI3K combinations can impair KRAS-mutant colorectal cancer in xenograft models.


Subject(s)
Genes, ras , Mutation , Neoplasms/genetics , RNA Interference , RNA, Small Interfering/genetics , Animals , Cell Line, Tumor , Cluster Analysis , Disease Models, Animal , Drug Delivery Systems , Gene Expression Profiling , Gene Knockdown Techniques , Gene Library , Gene Transfer Techniques , Humans , Mice , Nanoparticles , Neoplasms/metabolism , Neoplasms/pathology , Phosphatidylinositol 3-Kinases/genetics , Phosphatidylinositol 3-Kinases/metabolism , RNA, Small Interfering/administration & dosage , Reproducibility of Results , Signal Transduction , Tumor Burden/genetics , Xenograft Model Antitumor Assays
19.
Methods Mol Biol ; 1176: 45-58, 2014.
Article in English | MEDLINE | ID: mdl-25030918

ABSTRACT

Pooled shRNA library is a powerful, rapid, and cost-effective technology to carry out functional genomic screens in mammalian cells. This approach has been applied extensively to identify genetic dependencies in cancer cells that might be exploited for therapeutic purposes. In this chapter we provide a detailed protocol for using the Hannon-Elledge miR30-based library to conduct dropout screens in cancer cell lines. This protocol is readily adaptable to other pooled shRNA libraries and should facilitate the functional annotation of the human genome.


Subject(s)
Gene Library , Genes, Lethal , MicroRNAs/genetics , Mutation , Neoplasms/genetics , RNA, Small Interfering/genetics , Animals , Cell Line , Cell Line, Tumor , Computational Biology/methods , Gene Expression Profiling/methods , High-Throughput Nucleotide Sequencing , Humans
20.
J Clin Invest ; 124(7): 3003-15, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24911146

ABSTRACT

The majority of non-small cell lung cancer (NSCLC) patients harbor EGFR-activating mutations that can be therapeutically targeted by EGFR tyrosine kinase inhibitors (EGFR-TKI), such as erlotinib and gefitinib. Unfortunately, a subset of patients with EGFR mutations are refractory to EGFR-TKIs. Resistance to EGFR inhibitors reportedly involves SRC activation and induction of epithelial-to-mesenchymal transition (EMT). Here, we have demonstrated that overexpression of CRIPTO1, an EGF-CFC protein family member, renders EGFR-TKI-sensitive and EGFR-mutated NSCLC cells resistant to erlotinib in culture and in murine xenograft models. Furthermore, tumors from NSCLC patients with EGFR-activating mutations that were intrinsically resistant to EGFR-TKIs expressed higher levels of CRIPTO1 compared with tumors from patients that were sensitive to EGFR-TKIs. Primary NSCLC cells derived from a patient with EGFR-mutated NSCLC that was intrinsically erlotinib resistant were CRIPTO1 positive, but gained erlotinib sensitivity upon loss of CRIPTO1 expression during culture. CRIPTO1 activated SRC and ZEB1 to promote EMT via microRNA-205 (miR-205) downregulation. While miR-205 depletion induced erlotinib resistance, miR-205 overexpression inhibited CRIPTO1-dependent ZEB1 and SRC activation, restoring erlotinib sensitivity. CRIPTO1-induced erlotinib resistance was directly mediated through SRC but not ZEB1; therefore, cotargeting EGFR and SRC synergistically attenuated growth of erlotinib-resistant, CRIPTO1-positive, EGFR-mutated NSCLC cells in vitro and in vivo, suggesting that this combination may overcome intrinsic EGFR-inhibitor resistance in patients with CRIPTO1-positive, EGFR-mutated NSCLC.


Subject(s)
Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/genetics , GPI-Linked Proteins/genetics , Intercellular Signaling Peptides and Proteins/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Mutation , Neoplasm Proteins/genetics , Animals , Antineoplastic Agents/pharmacology , Carcinoma, Non-Small-Cell Lung/metabolism , Cell Line, Tumor , Drug Resistance, Neoplasm/genetics , Epithelial-Mesenchymal Transition , Erlotinib Hydrochloride , GPI-Linked Proteins/metabolism , Gefitinib , Genes, erbB-1 , Homeodomain Proteins/metabolism , Humans , Intercellular Signaling Peptides and Proteins/metabolism , Lung Neoplasms/metabolism , Mice , Mice, Nude , MicroRNAs/genetics , MicroRNAs/metabolism , Neoplasm Proteins/metabolism , Protein Kinase Inhibitors/pharmacology , Quinazolines/pharmacology , Transcription Factors/metabolism , Xenograft Model Antitumor Assays , Zinc Finger E-box-Binding Homeobox 1 , src-Family Kinases/metabolism
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