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1.
Blood Adv ; 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38991137

ABSTRACT

Children and adults with sickle cell disease (SCD) have increases in morbidity and mortality with COVID-19 infections. The ASH Research Collaborative Sickle Cell Disease Research Network performed a prospective COVID-19 vaccine study to assess antibody responses and analyze whether mRNA vaccination precipitated any adverse effects unique to individuals with SCD. Forty-one participants received two doses of the Pfizer-BioNTech vaccine and provided baseline blood samples prior to vaccination and 2 months after the initial vaccination for analysis of IgG reactivity against the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Six month IgG reactivity against the viral RBD was also available in 37 patients. Post-vaccination reactogenicity was common and similar to the general population. There were no fevers that required inpatient admission. Vaso-occlusive pain within 2-3 days of 1st or 2nd vaccination was reported by 5 (12%) participants including 4 (10%) who sought medical care. Twenty-seven participants (66%) were seropositive at baseline, and all 14 (34%) initially seronegative participants converted to seropositive post vaccination. Overall, mRNA vaccination had a good risk benefit-profile in individuals with sickle cell disease.This mRNA vaccine study also marks the first evaluation of vaccine safety and antibody response in very young children with sickle cell disease. NCT05139992.

2.
JCO Clin Cancer Inform ; 7: e2300104, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37956387

ABSTRACT

PURPOSE: Osteosarcoma research advancement requires enhanced data integration across different modalities and sources. Current osteosarcoma research, encompassing clinical, genomic, protein, and tissue imaging data, is hindered by the siloed landscape of data generation and storage. MATERIALS AND METHODS: Clinical, molecular profiling, and tissue imaging data for 573 patients with pediatric osteosarcoma were collected from four public and institutional sources. A common data model incorporating standardized terminology was created to facilitate the transformation, integration, and load of source data into a relational database. On the basis of this database, a data commons accompanied by a user-friendly web portal was developed, enabling various data exploration and analytics functions. RESULTS: The Osteosarcoma Explorer (OSE) was released to the public in 2021. Leveraging a comprehensive and harmonized data set on the backend, the OSE offers a wide range of functions, including Cohort Discovery, Patient Dashboard, Image Visualization, and Online Analysis. Since its initial release, the OSE has experienced an increasing utilization by the osteosarcoma research community and provided solid, continuous user support. To our knowledge, the OSE is the largest (N = 573) and most comprehensive research data commons for pediatric osteosarcoma, a rare disease. This project demonstrates an effective framework for data integration and data commons development that can be readily applied to other projects sharing similar goals. CONCLUSION: The OSE offers an online exploration and analysis platform for integrated clinical, molecular profiling, and tissue imaging data of osteosarcoma. Its underlying data model, database, and web framework support continuous expansion onto new data modalities and sources.


Subject(s)
Data Management , Osteosarcoma , Child , Humans , Databases, Factual , Genomics , Osteosarcoma/diagnostic imaging , Osteosarcoma/genetics
3.
Nat Commun ; 13(1): 5773, 2022 10 01.
Article in English | MEDLINE | ID: mdl-36182931

ABSTRACT

Precise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of mutated, frameshifting cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, conservation, and local intron length. This method, which we denote splicing-linked expression design (SLED), can be combined in a Boolean manner with existing techniques such as minipromoters and viral capsids. SLED can use strong constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. AAV-packaged SLED vectors can selectively deliver fluorescent reporters and calcium indicators to various neuronal subtypes in vivo. We also demonstrate gene therapy utility by creating SLED vectors that can target PRPH2 and SF3B1 mutations. The flexibility of SLED technology enables creative avenues for basic and translational research.


Subject(s)
Calcium , RNA Splicing , Alternative Splicing/genetics , Base Sequence , Exons/genetics , Gene Expression Regulation , Introns/genetics
4.
NPJ Precis Oncol ; 6(1): 65, 2022 Sep 17.
Article in English | MEDLINE | ID: mdl-36115869

ABSTRACT

The advent of dose intensified interval compressed therapy has improved event-free survival for patients with localized Ewing sarcoma (EwS) to 78% at 5 years. However, nearly a quarter of patients with localized tumors and 60-80% of patients with metastatic tumors suffer relapse and die of disease. In addition, those who survive are often left with debilitating late effects. Clinical features aside from stage have proven inadequate to meaningfully classify patients for risk-stratified therapy. Therefore, there is a critical need to develop approaches to risk stratify patients with EwS based on molecular features. Over the past decade, new technology has enabled the study of multiple molecular biomarkers in EwS. Preliminary evidence requiring validation supports copy number changes, and loss of function mutations in tumor suppressor genes as biomarkers of outcome in EwS. Initial studies of circulating tumor DNA demonstrated that diagnostic ctDNA burden and ctDNA clearance during induction are also associated with outcome. In addition, fusion partner should be a pre-requisite for enrollment on EwS clinical trials, and the fusion type and structure require further study to determine prognostic impact. These emerging biomarkers represent a new horizon in our understanding of disease risk and will enable future efforts to develop risk-adapted treatment.

5.
Contemp Clin Trials ; 121: 106922, 2022 10.
Article in English | MEDLINE | ID: mdl-36096281

ABSTRACT

As clinical trials have become more complex, with increasing numbers of required procedures and clinic visits, gaining access to promising new treatments has become even more challenging for many individuals. To address these barriers, we implemented a financial reimbursement and outreach program designed to increase the number and diversity of participants in cancer clinical trials at centers in Dallas, Houston, and Philadelphia. As endorsed by U.S. Food and Drug Administration (FDA) and the Texas and Pennsylvania State Legislatures, the program provides financial reimbursement for non-clinical costs (e.g., travel, lodging) to patients on cancer clinical trials with household income up to 700% the Federal poverty rate. The research study described here, centered at the Dallas site, evaluates program impact by assessing (1) numbers and diversity of patients enrolled to cancer clinical trials before and after program implementation; (2) characteristics of patients offered participation in the program who do versus do not enroll; (3) characteristics of patients enrolled in the program who do versus do not complete the reimbursement process. To evaluate perceived barriers and facilitators of program participation, we will conduct semi-structured interviews and administer the Comprehensive Score for Financial Toxicity Patient Reported Outcome Measure (COST PROM) and the Short Assessment of Health Literacy (SAHL). This program will examine how reimbursement of non-clinical costs can improve access to cancer clinical trials, with the eventual goal of increasing trial enrollment, diversity, representativeness, and generalizability.


Subject(s)
Neoplasms , Clinical Trials as Topic , Humans , Neoplasms/therapy , Philadelphia , Poverty , Texas , Travel
6.
J Clin Oncol ; 40(13): 1507-1508, 2022 05 01.
Article in English | MEDLINE | ID: mdl-35235382
7.
PLoS One ; 17(2): e0259564, 2022.
Article in English | MEDLINE | ID: mdl-35157711

ABSTRACT

BACKGROUND: Osteosarcoma, which is the most common malignant pediatric bone cancer, remains dependent on an imprecise systemic treatment largely unchanged in 30 years. In this study, we correlated histopathology with magnetic resonance imaging (MRI), used the correlation to extract MRI-specific features representative of tumor necrosis, and subsequently developed a novel classification model for predicting tumor response to neoadjuvant chemotherapy in pediatric patients with osteosarcoma using multi-modal MRI. The model could ultimately serve as a testable biomarker for a high-risk malignancy without successful precision treatments. METHODS: Patients with newly diagnosed high-grade appendicular osteosarcoma were enrolled in a single-center observational study, wherein patients underwent pre-surgical evaluation using both conventional MRI (post-contrast T1-weighted with fat saturation, pre-contrast T1-weighted, and short inversion-time inversion recovery (STIR)) and advanced MRI (diffusion weighted (DW) and dynamic contrast enhanced (DCE)). A classification model was established based on a direct correlation between histopathology and MRI, which was achieved through histologic-MR image co-registration and subsequent extraction of MR image features for identifying histologic tumor necrosis. By operating on the MR image features, tumor necrosis was estimated from different combinations of MR images using a multi-feature fuzzy clustering technique together with a weighted majority ruling. Tumor necrosis calculated from MR images, for either an MRI plane of interest or whole tumor volume, was compared to pathologist-estimated necrosis and necrosis quantified from digitized histologic section images using a previously described deep learning classification method. RESULTS: 15 patients were enrolled, of whom two withdrew, one became ineligible, and two were subjected to inadequate pre-surgical imaging. MRI sequences of n = 10 patients were subsequently used for classification model development. Different MR image features, depending on the modality of MRI, were shown to be significant in distinguishing necrosis from viable tumor. The scales at which MR image features optimally signified tumor necrosis were different as well depending on the MR image type. Conventional MRI was shown capable of differentiating necrosis from viable tumor with an accuracy averaging above 90%. Conventional MRI was equally effective as DWI in distinguishing necrotic from viable tumor regions. The accuracy of tumor necrosis prediction by conventional MRI improved to above 95% when DCE-MRI was added into consideration. Volume-based tumor necrosis estimations tended to be lower than those evaluated on an MRI plane of interest. CONCLUSIONS: The study has shown a proof-of-principle model for interpreting chemotherapeutic response using multi-modal MRI for patients with high-grade osteosarcoma. The model will continue to be evaluated as MR image features indicative of tumor response are now computable for the disease prior to surgery.


Subject(s)
Bone Neoplasms/pathology , Magnetic Resonance Imaging , Osteosarcoma/pathology , Adolescent , Antineoplastic Agents/therapeutic use , Bone Neoplasms/diagnostic imaging , Bone Neoplasms/drug therapy , Child , Deep Learning , Female , Humans , Male , Necrosis , Neoplasm Grading , Osteosarcoma/diagnostic imaging , Osteosarcoma/drug therapy , Prospective Studies , Young Adult
9.
J Clin Oncol ; 39(36): 4029-4038, 2021 12 20.
Article in English | MEDLINE | ID: mdl-34652968

ABSTRACT

PURPOSE: The primary aim of this phase III randomized trial was to test whether the addition of vincristine, topotecan, and cyclophosphamide (VTC) to interval compressed chemotherapy improved survival outcomes for patients with previously untreated nonmetastatic Ewing sarcoma. METHODS: Patients were randomly assigned to receive standard five-drug interval compressed chemotherapy (regimen A) for 17 cycles or experimental therapy with five cycles of VTC within the 17 cycles (regimen B). Patients were stratified by age at diagnosis (< 18 years and ≥18 years) and tumor site (pelvic bone, nonpelvic bone, and extraosseous). Tumor volume at diagnosis was categorized as < 200 mL or ≥ 200 mL. Local control occurred following six cycles. Histologic response was categorized as no viable or any viable tumor. Event-free survival (EFS) and overall survival (OS) were compared between randomized groups with stratified log-rank tests. RESULTS: Of 642 enrolled patients, 309 eligible patients received standard and 320 received experimental therapy. The 5-year EFS and OS were 78% and 87%, respectively. There was no difference in survival outcomes between randomized groups (5-year EFS regimen A v regimen B, 78% v 79%; P = .192; 5-year OS 86% v 88%; P = .159). Age and primary site did not affect the risk of an EFS event. However, age ≥ 18 years was associated with an increased risk of death at 5 years (hazard ratio 1.84; 95% CI, 1.15 to 2.96; P = .009). The 5-year EFS rates for patients with pelvic, nonpelvic bone, and extraosseous primary tumors were 75%, 78%, and 85%, respectively. Tumor volume ≥ 200 mL was significantly associated with lower EFS. CONCLUSION: While VTC added to five-drug interval compressed chemotherapy did not improve survival, these outcomes represent the best survival estimates to date for patients with previously untreated nonmetastatic Ewing sarcoma.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Cyclophosphamide/therapeutic use , Sarcoma, Ewing/drug therapy , Topotecan/therapeutic use , Vincristine/therapeutic use , Adolescent , Antineoplastic Combined Chemotherapy Protocols/pharmacology , Child , Child, Preschool , Cyclophosphamide/pharmacology , Female , Humans , Infant , Infant, Newborn , Male , Sarcoma, Ewing/pathology , Topotecan/pharmacology , Vincristine/pharmacology
10.
Nat Commun ; 12(1): 5520, 2021 09 17.
Article in English | MEDLINE | ID: mdl-34535684

ABSTRACT

PTEN promoter hypermethylation is nearly universal and PTEN copy number loss occurs in ~25% of fusion-negative rhabdomyosarcoma (FN-RMS). Here we show Pten deletion in a mouse model of FN-RMS results in less differentiated tumors more closely resembling human embryonal RMS. PTEN loss activated the PI3K pathway but did not increase mTOR activity. In wild-type tumors, PTEN was expressed in the nucleus suggesting loss of nuclear PTEN functions could account for these phenotypes. Pten deleted tumors had increased expression of transcription factors important in neural and skeletal muscle development including Dbx1 and Pax7. Pax7 deletion completely rescued the effects of Pten loss. Strikingly, these Pten;Pax7 deleted tumors were no longer FN-RMS but displayed smooth muscle differentiation similar to leiomyosarcoma. These data highlight how Pten loss in FN-RMS is connected to a PAX7 lineage-specific transcriptional output that creates a dependency or synthetic essentiality on the transcription factor PAX7 to maintain tumor identity.


Subject(s)
PAX7 Transcription Factor/metabolism , PTEN Phosphohydrolase/metabolism , Rhabdomyosarcoma/metabolism , Rhabdomyosarcoma/pathology , Animals , Breeding , Cell Differentiation , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Homeodomain Proteins/metabolism , Humans , Integrases/metabolism , Mechanistic Target of Rapamycin Complex 1/metabolism , Mice, Knockout , Muscle Development , PTEN Phosphohydrolase/deficiency , Phosphoproteins/metabolism , Proto-Oncogene Proteins c-akt/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Rhabdomyosarcoma/genetics
11.
Clin Cancer Res ; 26(12): 2882-2890, 2020 06 15.
Article in English | MEDLINE | ID: mdl-32122923

ABSTRACT

PURPOSE: Several aggressive pediatric cancers harbor alterations in SMARCB1, including rhabdoid tumors, epithelioid sarcoma, and chordoma. As tumor profiling has become more routine in clinical care, we investigated the relationship between SMARCB1 genetic variants identified by next-generation sequencing (NGS) and INI1 protein expression. Therapeutic approaches for INI1-deficient tumors are limited. Early reports suggest a potential role for immune checkpoint inhibition in these patients. Thus, we also investigated PD-L1 and CD8 expression in INI1-negative pediatric brain and solid tumors. EXPERIMENTAL DESIGN: We performed immunohistochemistry (IHC) for INI1 and immune markers (PD-L1, CD8, and CD163) and NGS on tumor samples from 43 pediatric patients who had tumors with INI1 loss on previous IHC or SMARCB1 genomic alterations on prior somatic sequencing. RESULTS: SMARCB1 two-copy deletions and inactivating mutations on NGS were associated with loss of INI1 protein expression. Single-copy deletion of SMARCB1 was not predictive of INI1 loss in tumor histologies not known to be INI1-deficient. In the 27 cases with INI1 loss and successful tumor sequencing, 24 (89%) had a SMARCB1 alteration detected. In addition, 47% (14/30) of the patients with INI1-negative tumors had a tumor specimen that was PD-L1 positive and 60% (18/30) had positive or rare CD8 staining. We report on 3 patients with INI1-negative tumors with evidence of disease control on immune checkpoint inhibitors. CONCLUSIONS: A significant proportion of the INI1-negative tumors express PD-L1, and PD-L1 positivity was associated with extracranial tumor site. These results suggest that clinical trials of immune checkpoint inhibitors are warranted in INI1-negative pediatric cancers.


Subject(s)
B7-H1 Antigen/metabolism , Biomarkers, Tumor/genetics , Immune Checkpoint Inhibitors/therapeutic use , Mutation , Neoplasms/pathology , SMARCB1 Protein/deficiency , Adolescent , B7-H1 Antigen/antagonists & inhibitors , B7-H1 Antigen/genetics , Child , Child, Preschool , Female , Follow-Up Studies , Gene Expression Regulation, Neoplastic , High-Throughput Nucleotide Sequencing , Humans , Infant , Male , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/immunology , Prognosis , SMARCB1 Protein/genetics
12.
Nat Commun ; 11(1): 137, 2020 01 09.
Article in English | MEDLINE | ID: mdl-31919425

ABSTRACT

Public archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize splice variants across tens of thousands of bulk and single-cell data sets in the public archive. To demonstrate the utility of ASCOT, we identify novel cell type-specific alternative exons across the nervous system and leverage ENCODE and GTEx data sets to study the unique splicing of photoreceptors. We find that PTBP1 knockdown and MSI1 and PCBP2 overexpression are sufficient to activate many photoreceptor-specific exons in HepG2 liver cancer cells. This work demonstrates how large-scale analysis of public RNA-Seq data sets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.


Subject(s)
Alternative Splicing/genetics , Computational Biology/methods , Data Analysis , Photoreceptor Cells/cytology , RNA Splice Sites/genetics , Animals , Cell Line, Tumor , Gene Expression/genetics , Hep G2 Cells , Heterogeneous-Nuclear Ribonucleoproteins/genetics , High-Throughput Nucleotide Sequencing , Humans , Liver Neoplasms/genetics , Mice , Nerve Tissue Proteins/biosynthesis , Nerve Tissue Proteins/genetics , Neurons/cytology , Polypyrimidine Tract-Binding Protein/genetics , RNA-Binding Proteins/biosynthesis , RNA-Binding Proteins/genetics , Retina/cytology , Sequence Analysis, RNA/methods
13.
Article in English | MEDLINE | ID: mdl-31645346

ABSTRACT

Infantile myofibromatosis (IM) is an aggressive neoplasm composed of myofibroblast-like cells in children. Although typically localized, it can also present as multifocal disease, which represents a challenge for effective treatment. IM has previously been linked to activating somatic and germline point mutations in the PDGFRß tyrosine kinase encoded by the PDGFRB gene. Clinical panel-based targeted tumor sequencing of a tumor from a newborn with multifocal IM revealed a novel PDGFRB rearrangement, which was reported as being of unclear significance. Additional sequencing of cDNA from tumor and germline DNA confirmed a complex somatic/mosaic PDGFRB rearrangement with an apparent partial tandem duplication disrupting the juxtamembrane domain. Ectopic expression of cDNA encoding the mutant form of PDGFRB markedly enhanced cell proliferation of mouse embryo fibroblasts (MEFs) compared to wild-type PDGFRB and conferred tumor-forming capacity on nontumorigenic 10T1/2 fibroblasts. The mutated protein enhanced MAPK activation and retained sensitivity to the PDGFRß inhibitor imatinib. Our findings reveal a new mechanism by which PDGFRB can be activated in IM, suggest that therapy with tyrosine kinase inhibitors including imatinib may be beneficial, and raise the possibility that this receptor tyrosine kinase might be altered in a similar fashion in additional cases that would similarly present annotation challenges in clinical DNA sequencing analysis pipelines.


Subject(s)
Imatinib Mesylate/pharmacology , Myofibromatosis/congenital , Receptor, Platelet-Derived Growth Factor beta/genetics , Animals , Cell Line , Extracellular Signal-Regulated MAP Kinases/metabolism , Female , Fibroblasts/metabolism , Germ-Line Mutation/genetics , Humans , Infant, Newborn , Mice , Myofibromatosis/genetics , Myofibromatosis/metabolism , Protein Kinase Inhibitors/therapeutic use , Receptor, Platelet-Derived Growth Factor beta/metabolism
14.
Br J Cancer ; 120(8): 869, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30880335

ABSTRACT

The authors have noticed that the final paragraph of the Results section contains errors in the number of patients involved. The correct number of patients is included in the text below. These errors do not affect the Figure referenced.In osteosarcoma, we focused on 8q gain as a specific biological feature of interest. Among the 41 patients with detectable ctDNA in the osteosarcoma cohort, 8q gain was detected in 73.2% (30/41). The 3-year EFS for patients with 8q gain (n = 30) in ctDNA was 60.0% (95% CI 40.5-75.0) compared to 80.8 (95% CI 42.4-94.9) in patients without 8q gain (n = 11) in ctDNA (p = 0.18; Fig. 3).

15.
Eur J Cancer ; 109: 36-50, 2019 03.
Article in English | MEDLINE | ID: mdl-30685685

ABSTRACT

BACKGROUND: High-grade osteosarcoma is a primary malignant bone tumour mainly affecting children and young adults. The European and American Osteosarcoma Study (EURAMOS)-1 is a collaboration of four study groups aiming to improve outcomes of this rare disease by facilitating randomised controlled trials. METHODS: Patients eligible for EURAMOS-1 were aged ≤40 years with M0 or M1 skeletal high-grade osteosarcoma in which case complete surgical resection at all sites was deemed to be possible. A three-drug combination with methotrexate, doxorubicin and cisplatin was defined as standard chemotherapy, and between April 2005 and June 2011, 2260 patients were registered. We report survival outcomes and prognostic factors in the full cohort of registered patients. RESULTS: For all registered patients at a median follow-up of 54 months (interquartile range: 38-73) from biopsy, 3-year and 5-year event-free survival were 59% (95% confidence interval [CI]: 57-61%) and 54% (95% CI: 52-56%), respectively. Multivariate analyses showed that the most adverse factors at diagnosis were pulmonary metastases (hazard ratio [HR] = 2.34, 95% CI: 1.95-2.81), non-pulmonary metastases (HR = 1.94, 95% CI: 1.38-2.73) or an axial skeleton tumour site (HR = 1.53, 95% CI: 1.10-2.13). The histological subtypes telangiectatic (HR = 0.52, 95% CI: 0.33-0.80) and unspecified conventional (HR = 0.67, 95% CI: 0.52-0.88) were associated with a favourable prognosis compared with chondroblastic subtype. The 3-year and 5-year overall survival from biopsy were 79% (95% CI: 77-81%) and 71% (95% CI: 68-73%), respectively. For patients with localised disease at presentation and in complete remission after surgery, having a poor histological response was associated with worse outcome after surgery (HR = 2.13, 95% CI: 1.76-2.58). In radically operated patients, there was no good evidence that axial tumour site was associated with worse outcome. CONCLUSIONS: In conclusion, data from >2000 patients registered to EURAMOS-1 demonstrated survival rates in concordance with institution- or group-level osteosarcoma trials. Further efforts are required to drive improvements for patients who can be identified to be at higher risk of adverse outcome. This trial reaffirms known prognostic factors, and owing to the large numbers of patients registered, it sheds light on some additional factors to consider.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Bone Neoplasms/mortality , Osteosarcoma/mortality , Adolescent , Adult , Bone Neoplasms/drug therapy , Bone Neoplasms/secondary , Child , Cisplatin/administration & dosage , Cohort Studies , Doxorubicin/administration & dosage , Female , Follow-Up Studies , Humans , Male , Methotrexate/administration & dosage , Neoplasm Metastasis , Osteosarcoma/drug therapy , Osteosarcoma/pathology , Prognosis , Survival Rate
16.
Pediatr Blood Cancer ; 66(1): e27493, 2019 01.
Article in English | MEDLINE | ID: mdl-30318721

ABSTRACT

Outcome for patients with metastatic or recurrent/refractory osteosarcoma remains poor. Responses to sorafenib, a multikinase inhibitor, have been seen in recurrent/refractory osteosarcoma, although specific biomarkers of response have not been described. We report a partial response in a 7-year-old with refractory osteosarcoma treated with sorafenib 200 mg twice daily. Toxicities included Common Terminology Criteria for Adverse Events Grade 2 skin toxicities and growth suppression. After 51 months of therapy, he suffered a recurrence. Tumor sequencing later revealed a PDGFRA D846V mutation that was not identified in the relapse specimen. This case demonstrates prolonged partial response to sorafenib and provides a potential biomarker for response.


Subject(s)
Biomarkers, Tumor/genetics , Bone Neoplasms/drug therapy , Drug Resistance, Neoplasm , Mutation , Osteosarcoma/drug therapy , Receptor, Platelet-Derived Growth Factor alpha/genetics , Sorafenib/therapeutic use , Antineoplastic Agents/therapeutic use , Bone Neoplasms/genetics , Bone Neoplasms/secondary , Child , Humans , Male , Osteosarcoma/genetics , Osteosarcoma/pathology , Prognosis , Salvage Therapy
17.
J Thorac Oncol ; 13(12): 1818-1831, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30268698

ABSTRACT

This Review Article provides a multi-stakeholder view on the current status of neoadjuvant therapy in lung cancer. Given the success of oncogene-targeted therapy and immunotherapy for patients with advanced lung cancer, there is a renewed interest in studying these agents in earlier disease settings with the opportunity to have an even greater impact on patient outcomes. There are unique opportunities and challenges with the neoadjuvant approach to drug development. To achieve more rapid knowledge turns, study designs, endpoints, and definitions of pathologic response should be standardized and harmonized. Continued dialogue with all stakeholders will be critical to design and test novel induction strategies, which could expedite drug development for patients with early lung cancer who are at high risk for metastatic recurrence.


Subject(s)
Antineoplastic Agents/therapeutic use , Lung Neoplasms/drug therapy , Neoadjuvant Therapy , Humans , Prognosis
18.
Br J Cancer ; 119(5): 615-621, 2018 08.
Article in English | MEDLINE | ID: mdl-30131550

ABSTRACT

BACKGROUND: New prognostic markers are needed to identify patients with Ewing sarcoma (EWS) and osteosarcoma unlikely to benefit from standard therapy. We describe the incidence and association with outcome of circulating tumour DNA (ctDNA) using next-generation sequencing (NGS) assays. METHODS: A NGS hybrid capture assay and an ultra-low-pass whole-genome sequencing assay were used to detect ctDNA in banked plasma from patients with EWS and osteosarcoma, respectively. Patients were coded as positive or negative for ctDNA and tested for association with clinical features and outcome. RESULTS: The analytic cohort included 94 patients with EWS (82% from initial diagnosis) and 72 patients with primary localised osteosarcoma (100% from initial diagnosis). ctDNA was detectable in 53% and 57% of newly diagnosed patients with EWS and osteosarcoma, respectively. Among patients with newly diagnosed localised EWS, detectable ctDNA was associated with inferior 3-year event-free survival (48.6% vs. 82.1%; p = 0.006) and overall survival (79.8% vs. 92.6%; p = 0.01). In both EWS and osteosarcoma, risk of event and death increased with ctDNA levels. CONCLUSIONS: NGS assays agnostic of primary tumour sequencing results detect ctDNA in half of the plasma samples from patients with newly diagnosed EWS and osteosarcoma. Detectable ctDNA is associated with inferior outcomes.


Subject(s)
Biomarkers, Tumor/genetics , Bone Neoplasms/genetics , Circulating Tumor DNA/analysis , High-Throughput Nucleotide Sequencing/methods , Osteosarcoma/genetics , Adolescent , Biomarkers, Tumor/blood , Bone Neoplasms/blood , Child , Child, Preschool , Cohort Studies , Female , Humans , Male , Osteosarcoma/blood , Prognosis , Retrospective Studies , Sarcoma, Ewing/blood , Sarcoma, Ewing/genetics , Sequence Analysis, DNA/methods , Survival Analysis
19.
Oncogene ; 37(15): 1991-2007, 2018 04.
Article in English | MEDLINE | ID: mdl-29367756

ABSTRACT

Rhabdomyosarcoma is the most common soft-tissue sarcoma in childhood and histologically resembles developing skeletal muscle. Alveolar rhabdomyosarcoma (ARMS) is an aggressive subtype with a higher rate of metastasis and poorer prognosis. The majority of ARMS tumors (80%) harbor a PAX3-FOXO1 or less commonly a PAX7-FOXO1 fusion gene. The presence of either the PAX3-FOXO1 or PAX7-FOXO1 fusion gene foretells a poorer prognosis resulting in clinical re-classification as either fusion-positive (FP-RMS) or fusion-negative RMS (FN-RMS). The PAX3/7-FOXO1 fusion genes result in the production of a rogue transcription factors that drive FP-RMS pathogenesis and block myogenic differentiation. Despite knowing the molecular driver of FP-RMS, targeted therapies have yet to make an impact for patients, highlighting the need for a greater understanding of the molecular consequences of PAX3-FOXO1 and its target genes including microRNAs. Here we show FP-RMS patient-derived xenografts and cell lines display a distinct microRNA expression pattern. We utilized both loss- and gain-of function approaches in human cell lines with knockdown of PAX3-FOXO1 in FP-RMS cell lines and expression of PAX3-FOXO1 in human myoblasts and identified microRNAs both positively and negatively regulated by the PAX3-FOXO1 fusion protein. We demonstrate PAX3-FOXO1 represses miR-221/222 that functions as a tumor suppressing microRNA through the negative regulation of CCND2, CDK6, and ERBB3. In contrast, miR-486-5p is transcriptionally activated by PAX3-FOXO1 and promotes FP-RMS proliferation, invasion, and clonogenic growth. Inhibition of miR-486-5p in FP-RMS xenografts decreased tumor growth, illustrating a proof of principle for future therapeutic intervention. Therefore, PAX3-FOXO1 regulates key microRNAs that may represent novel therapeutic vulnerabilities in FP-RMS.


Subject(s)
MicroRNAs/genetics , Muscle Neoplasms/genetics , Oncogene Proteins, Fusion/physiology , Paired Box Transcription Factors/physiology , Rhabdomyosarcoma, Alveolar/genetics , Animals , Cell Proliferation/genetics , Cell Transformation, Neoplastic/genetics , Cells, Cultured , Child , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Gene Knockdown Techniques , HEK293 Cells , Humans , Mice , Mice, SCID , Microarray Analysis , Muscle Neoplasms/pathology , Oncogene Proteins, Fusion/genetics , Paired Box Transcription Factors/genetics , Rhabdomyosarcoma, Alveolar/pathology
20.
J Pediatr Psychol ; 43(2): 152-161, 2018 03 01.
Article in English | MEDLINE | ID: mdl-29049751

ABSTRACT

Objective: To examine hope and its components of agency and pathways as predictors of anxiety and depressive symptoms in children receiving cancer treatment. Methods: Sixty patients (mean standard deviation age = 13.3 (2.7); 57% male) completed Snyder's Hope Scales, the Children's Depression Inventory, and the State-Trait Anxiety Inventory at diagnosis and 3 month intervals for 1 year following pediatric cancer diagnosis. Parents also completed Snyder's Hope Scales. Linear mixed-effect regression was used to assess hope's role in longitudinal models of symptoms of depression and anxiety. Results: Agency was a significant predictor of between-patient differences and within-patient changes in symptoms of depression and anxiety. Neither patient pathways nor either component of parent hope was predictive of symptoms of depression or anxiety. Patients who were more likely to have depressive symptoms at baseline were older, diagnosed with leukemia, and non-Hispanic White as opposed to Hispanic. Patient demographics were not predictive of anxiety. Conclusions: Patient agency is a potential target for intervention to prevent or reduce anxiety and depressive symptoms following pediatric cancer diagnosis.


Subject(s)
Anxiety/psychology , Depression/psychology , Hope , Neoplasms/psychology , Adolescent , Child , Female , Humans , Longitudinal Studies , Male , Neoplasms/diagnosis
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