168 results on '"Jean L. Nakamura"'
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2. A pooled mutational analysis identifies ionizing radiation-associated mutational signatures conserved between mouse and human malignancies
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Philip R. Davidson, Amy L. Sherborne, Barry Taylor, Alice O. Nakamura, and Jean L. Nakamura
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Medicine ,Science - Abstract
Abstract Single nucleotide variants (SNVs) identified in cancer genomes can be de-convolved using non-negative matrix factorization (NMF) into discrete trinucleotide-based mutational signatures indicative of specific cancer-causing processes. The stability of NMF-generated mutational signatures depends upon the numbers of variants available for analysis. In this work, we sought to assess whether data from well-controlled mouse models can compensate for scarce human data for some cancer types. High quality sequencing data from radiotherapy-induced cancers is particularly scarce and the mutational processes defining ionizing radiation (IR)-induced mutagenesis in vivo are poorly defined. Here, we combine sequencing data from mouse models of IR-induced malignancies and human IR-induced malignancies. To determine whether the signatures identified from IR-exposed subjects can be differentiated from other mutagenic signatures, we included data from an ultraviolet radiation (UV)-induced human skin cancer and from a mouse model of urethane-induced cancers. NMF distinguished all three mutagens and in the pooled analysis IR was associated with mutational signatures common to both species. These findings illustrate the utility of pooled analysis of mouse and human sequencing data.
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- 2017
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3. Mutational Analysis of Ionizing Radiation Induced Neoplasms
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Amy L. Sherborne, Philip R. Davidson, Katharine Yu, Alice O. Nakamura, Mamunur Rashid, and Jean L. Nakamura
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Biology (General) ,QH301-705.5 - Abstract
Ionizing radiation (IR) is a mutagen that promotes tumorigenesis in multiple exposure contexts. One severe consequence of IR is the development of second malignant neoplasms (SMNs), a radiotherapy-associated complication in survivors of cancers, particularly pediatric cancers. SMN genomes are poorly characterized, and the influence of genetic background on genotoxin-induced mutations has not been examined. Using our mouse models of SMNs, we performed whole exome sequencing of neoplasms induced by fractionated IR in wild-type and Nf1 mutant mice. Using non-negative matrix factorization, we identified mutational signatures that did not segregate by genetic background or histology. Copy-number analysis revealed recurrent chromosomal alterations and differences in copy number that were background dependent. Pathway analysis identified enrichment of non-synonymous variants in genes responsible for cell assembly and organization, cell morphology, and cell function and maintenance. In this model system, ionizing radiation and Nf1 heterozygosity each exerted distinct influences on the mutational landscape.
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- 2015
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4. Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function.
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Neal K Bennett, Hiroki J Nakaoka, Danny Laurent, Ross A Okimoto, Yoshitaka Sei, Andrew E Horvai, Trever G Bivona, Johanna Ten Hoeve, Thomas G Graeber, Ken Nakamura, and Jean L Nakamura
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Biology (General) ,QH301-705.5 - Abstract
The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and processes such as tumor dissemination and metastatic growth remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines, we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells down-regulate glycolytic mechanisms. These studies demonstrate that discrete perturbations of mitochondrial respiratory chain function impact in vivo tumor growth in a context-specific manner with differential impacts on primary and metastatic tumors.
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- 2022
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5. Adverse radiation effect and freedom from progression following repeat stereotactic radiosurgery for brain metastases
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Penny K, Sneed, Jason W, Chan, Lijun, Ma, Steve E, Braunstein, Philip V, Theodosopoulos, Shannon E, Fogh, Jean L, Nakamura, Lauren, Boreta, David R, Raleigh, Benjamin P, Ziemer, Olivier, Morin, Shawn L, Hervey-Jumper, and Michael W, McDermott
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Treatment Outcome ,Brain Neoplasms ,Humans ,General Medicine ,Radiosurgery ,Radiation Injuries ,Melanoma ,Retrospective Studies - Abstract
OBJECTIVE The authors previously evaluated risk and time course of adverse radiation effects (AREs) following stereotactic radiosurgery (SRS) for brain metastases, excluding lesions treated after prior SRS. In the present analysis they focus specifically on single-fraction salvage SRS to brain metastases previously treated with SRS or hypofractionated SRS (HFSRS), evaluating freedom from progression (FFP) and the risk and time course of AREs. METHODS Brain metastases treated from September 1998 to May 2019 with single-fraction SRS after prior SRS or HFSRS were analyzed. Serial follow-up magnetic resonance imaging (MRI) and surgical pathology reports were reviewed to score local treatment failure and AREs. The Kaplan-Meier method was used to estimate FFP and risk of ARE measured from the date of repeat SRS with censoring at the last brain MRI. RESULTS A total of 229 retreated brain metastases in 124 patients were evaluable. The most common primary cancers were breast, lung, and melanoma. The median interval from prior SRS/HFSRS to repeat SRS was 15.4 months, the median prescription dose was 18 Gy, and the median duration of follow-up imaging was 14.5 months. At 1 year after repeat SRS, FFP was 80% and the risk of symptomatic ARE was 11%. The 1-year risk of imaging changes, including asymptomatic RE and symptomatic ARE, was 30%. Among lesions that demonstrated RE, the median time to onset was 6.7 months (IQR 4.7–9.9 months) and the median time to peak imaging changes was 10.1 months (IQR 5.6–13.6 months). Lesion size by quadratic mean diameter (QMD) showed similar results for QMDs ranging from 0.75 to 2.0 cm (1-year FFP 82%, 1-year risk of symptomatic ARE 11%). For QMD < 0.75 cm, the 1-year FFP was 86% and the 1-year risk of symptomatic ARE was only 2%. Outcomes were worse for QMDs 2.01–3.0 cm (1-year FFP 65%, 1-year risk of symptomatic ARE 24%). The risk of symptomatic ARE was not increased with tyrosine kinase inhibitors or immunotherapy before or after repeat SRS. CONCLUSIONS RE on imaging was common after repeat SRS (30% at 1 year), but the risk of a symptomatic ARE was much less (11% at 1 year). The results of repeat single-fraction SRS were good for brain metastases ≤ 2 cm. The authors recommend an interval ≥ 6 months from prior SRS and a prescription dose ≥ 18 Gy. Alternatives such as HFSRS, laser interstitial thermal therapy, or resection with adjuvant radiation should be considered for recurrent brain metastases > 2 cm.
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- 2023
6. Resection with intraoperative cesium-131 brachytherapy as salvage therapy for recurrent brain tumors
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William C, Chen, Matthieu, Lafreniere, Christina, Phuong, S John, Liu, Joe D, Baal, Michael, Lometti, Olivier, Morin, Benjamin, Ziemer, Harish N, Vasudevan, Calixto-Hope G, Lucas, Shawn L, Hervey-Jumper, Philip V, Theodosopoulos, Stephen T, Magill, Shannon, Fogh, Jean L, Nakamura, Lauren, Boreta, Penny K, Sneed, Michael W, McDermott, David R, Raleigh, and Steve E, Braunstein
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General Medicine - Abstract
OBJECTIVE The authors’ objective was to examine the safety and efficacy of salvage intracranial cesium-131 brachytherapy in combination with resection of recurrent brain tumors. METHODS The authors conducted a retrospective chart review of consecutive patients treated with intraoperative intracranial cesium-131 brachytherapy at a single institution. Permanent suture-stranded cesium-131 seeds were implanted in the resection cavity after maximal safe tumor resection. The primary outcomes of interest were local, locoregional (within 1 cm), and intracranial control, as well as rates of overall survival (OS), neurological death, symptomatic adverse radiation effects (AREs), and surgical complication rate graded according to Common Terminology Criteria for Adverse Events version 5.0. RESULTS Between 2016 and 2020, 36 patients received 40 consecutive cesium-131 implants for 42 recurrent brain tumors and received imaging follow-up for a median (interquartile range [IQR]) of 17.0 (12.7–25.9) months. Twenty patients (55.6%) with 22 implants were treated for recurrent brain metastasis, 12 patients (33.3%) with 16 implants were treated for recurrent atypical (n = 7) or anaplastic (n = 5) meningioma, and 4 patients (11.1%) were treated for other recurrent primary brain neoplasms. All except 1 tumor (97.6%) had received prior radiotherapy, including 20 (47.6%) that underwent 2 or more prior radiotherapy treatments and 23 (54.8%) that underwent prior resection. The median (IQR) tumor size was 3.0 (2.3–3.7) cm, and 17 lesions (40.5%) had radiographic evidence of ARE prior to salvage therapy. Actuarial 1-year local/locoregional/intracranial control rates for the whole cohort and patients with metastases and meningiomas were 91.6%/83.4%/47.9%, 88.8%/84.4%/45.4%, and 100%/83.9%/46.4%, respectively. No cases of local recurrence of any histology (0 of 27) occurred after gross-total resection (p = 0.012, log-rank test). The 1-year OS rates for the whole cohort and patients with metastases and meningiomas were 82.7%, 79.1%, and 91.7%, respectively, and the median (IQR) survival of all patients was 26.7 (15.6–36.4) months. Seven patients (19.4%) experienced neurological death from progressive intracranial disease (7 of 14 total deaths [50%]), 5 (13.9%) of whom died of leptomeningeal disease. Symptomatic AREs were observed in 9.5% of resection cavities (n = 4), of which 1 (2.4%) was grade 3 in severity. The surgical complication rate was 16.7% (n = 7); 4 (9.5%) of these patients had grade 3 or higher complications, including 1 patient (2.4%) who died perioperatively. CONCLUSIONS Cesium-131 brachytherapy resulted in good local control and acceptable rates of symptomatic AREs and surgical complications in this heavily pretreated cohort, and it may be a reasonable salvage adjuvant treatment for this patient population.
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- 2022
7. Figure S2 from Radiotherapy Followed by Aurora Kinase Inhibition Targets Tumor-Propagating Cells in Human Glioblastoma
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Anders I. Persson, William A. Weiss, Kevan M. Shokat, C. David James, Mitchel S. Berger, Jean L. Nakamura, Daniel W. Sirkis, Yvan H. Chanthery, Dustin J. Maly, and Nan Li
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Figure S2. Expression of potential targets of VX680 in human GBM cultures.
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- 2023
8. Fig. S2 from Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK
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Jean L. Nakamura, Gary L. Johnson, Kevin Shannon, D. Wade Clapp, Sourav Bandyopadhyay, Ganesh Krishnamurthi, Hiroki J. Nakaoka, Chi Zhang, Benjamin Huang, Steven P. Angus, and Daniela Pucciarelli
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Supplementary Figure 2
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- 2023
9. Supplementary Table 2 from Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK
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Jean L. Nakamura, Gary L. Johnson, Kevin Shannon, D. Wade Clapp, Sourav Bandyopadhyay, Ganesh Krishnamurthi, Hiroki J. Nakaoka, Chi Zhang, Benjamin Huang, Steven P. Angus, and Daniela Pucciarelli
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Supplementary Table 2
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- 2023
10. Supplementary Materials and Methods from Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK
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Jean L. Nakamura, Gary L. Johnson, Kevin Shannon, D. Wade Clapp, Sourav Bandyopadhyay, Ganesh Krishnamurthi, Hiroki J. Nakaoka, Chi Zhang, Benjamin Huang, Steven P. Angus, and Daniela Pucciarelli
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Supplementary Materials and Methods
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- 2023
11. Data from Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK
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Jean L. Nakamura, Gary L. Johnson, Kevin Shannon, D. Wade Clapp, Sourav Bandyopadhyay, Ganesh Krishnamurthi, Hiroki J. Nakaoka, Chi Zhang, Benjamin Huang, Steven P. Angus, and Daniela Pucciarelli
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Loss of the tumor suppressor NF1 leads to activation of RAS effector pathways, which are therapeutically targeted by inhibition of mTOR (mTORi) or MEK (MEKi). However, therapeutic inhibition of RAS effectors leads to the development of drug resistance and ultimately disease progression. To investigate molecular signatures in the context of NF1 loss and subsequent acquired drug resistance, we analyzed the exomes, transcriptomes, and kinomes of Nf1-mutant mouse tumor cell lines and derivatives of these lines that acquired resistance to either MEKi or mTORi. Biochemical comparisons of this unique panel of tumor cells, all of which arose in Nf1+/− mice, indicate that loss of heterozygosity of Nf1 as an initial genetic event does not confer a common biochemical signature or response to kinase inhibition. Although acquired drug resistance by Nf1-mutant tumor cells was accompanied by altered kinomes and irreversibly altered transcriptomes, functionally in multiple Nf1-mutant tumor cell lines, MEKi resistance was a stable phenotype, in contrast to mTORi resistance, which was reversible. Collectively, these findings demonstrate that Nf1-mutant tumors represent a heterogeneous group biochemically and undergo broader remodeling of kinome activity and gene expression in response to targeted kinase inhibition.
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- 2023
12. Supplementary Table 1 from Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK
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Jean L. Nakamura, Gary L. Johnson, Kevin Shannon, D. Wade Clapp, Sourav Bandyopadhyay, Ganesh Krishnamurthi, Hiroki J. Nakaoka, Chi Zhang, Benjamin Huang, Steven P. Angus, and Daniela Pucciarelli
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Supplementary Table 1
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- 2023
13. Supplementary Figure 2 from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Supplementary Figure 2 shows the exome coverage achieved with whole exome sequencing.
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- 2023
14. Supplementary Legend from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Legend for Supplementary Figures, Table and Files
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- 2023
15. Supplementary Figure 5 from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Supplementary Figure 5:Germline TP53 variants in the validation cohort Sanger sequencing-derived electropherograms displaying the germline variant in Exon 4 are shown.
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- 2023
16. Data from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Purpose: Second malignant neoplasms (SMNs) are severe late complications that occur in pediatric cancer survivors exposed to radiotherapy and other genotoxic treatments. To characterize the mutational landscape of treatment-induced sarcomas and to identify candidate SMN-predisposing variants, we analyzed germline and SMN samples from pediatric cancer survivors.Experimental Design: We performed whole-exome sequencing (WES) and RNA sequencing on radiation-induced sarcomas arising from two pediatric cancer survivors. To assess the frequency of germline TP53 variants in SMNs, Sanger sequencing was performed to analyze germline TP53 in 37 pediatric cancer survivors from the Childhood Cancer Survivor Study (CCSS) without any history of a familial cancer predisposition syndrome but known to have developed SMNs.Results: WES revealed TP53 mutations involving p53′s DNA-binding domain in both index cases, one of which was also present in the germline. The germline and somatic TP53-mutant variants were enriched in the transcriptomes for both sarcomas. Analysis of TP53-coding exons in germline specimens from the CCSS survivor cohort identified a G215C variant encoding an R72P amino acid substitution in 6 patients and a synonymous SNP A639G in 4 others, resulting in 10 of 37 evaluable patients (27%) harboring a germline TP53 variant.Conclusions: Currently, germline TP53 is not routinely assessed in patients with pediatric cancer. These data support the concept that identifying germline TP53 variants at the time a primary cancer is diagnosed may identify patients at high risk for SMN development, who could benefit from modified therapeutic strategies and/or intensive posttreatment monitoring. Clin Cancer Res; 23(7); 1852–61. ©2016 AACR.
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- 2023
17. Supplementary Figure 1 from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Supplementary Figure 1: Radiotherapy-induced sarcomas in pediatric cancer survivors Radiation dosimetry, imaging and histology are shown.
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- 2023
18. Supplementary Files from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Supplementary File 1. SNVs for Patient 1's SMN;Supplementary File 2. SNVs for Patient 2's SMN;Supplementary File 3. List of dinucleotide substitutions;Supplementary File 4. TP53 germline sequencing primers
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- 2023
19. Supplementary Figure 4 from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Supplementary Figure 4 displays Copy number alterations and allele frequencies across all chromosomes for SMNs.
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- 2023
20. Supplementary Table 1 from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Supplementary Table 1. Treatment exposures and TP53 Variant status in the Validation cohort Tumor, TP53 variant status (G215C, A639G), and treatment exposure details are shown for each validation sample (VS).
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- 2023
21. Supplementary Figure 3 from Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors
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Jean L. Nakamura, Smita Bhatia, Kevin M. Shannon, Alice O. Nakamura, Joseph F. Costello, Rosanna Wustrack, Leslie L. Robison, Sue Hammond, Joseph P. Neglia, Robert E. Goldsby, Steven G. DuBois, Mignon Loh, Andrew E. Horvai, Ivan V. Smirnoff, Tali Mazor, Philip R. Davidson, Leah Lee, Katharine Yu, Vincent Lavergne, and Amy L. Sherborne
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Supplementary Figure 3: Somatic variants in radiation-induced SMNs Frequencies of specific types of base substitutions in SNVs (synonymous and non-synonymous SNVs) pooled from all samples are shown.
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- 2023
22. Supplementary Figure Legends 1-3 from Genetically Mediated Nf1 Loss in Mice Promotes Diverse Radiation-Induced Tumors Modeling Second Malignant Neoplasms
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Jean L. Nakamura, Bruce Faddegon, Smita Bhatia, Scott Kogan, Andrew E. Horvai, Steve E. Braunstein, Emile Pinarbasi, Brian Huang, and Grace Choi
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PDF file - 63K
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- 2023
23. Supplementary Table 1 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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Kevin Shannon, Russell O. Pieper, Richard Chao, Benjamin T. Houseman, Kevan Shokat, Dorothea Fiedler, Bruce A. Faddegon, Andrew E. Horvai, Scott Vandenberg, Scott C. Kogan, Emile Pinarbasi, Connie Phong, and Jean L. Nakamura
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Supplementary Table 1 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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- 2023
24. Supplementary Table 1 from Genetically Mediated Nf1 Loss in Mice Promotes Diverse Radiation-Induced Tumors Modeling Second Malignant Neoplasms
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Jean L. Nakamura, Bruce Faddegon, Smita Bhatia, Scott Kogan, Andrew E. Horvai, Steve E. Braunstein, Emile Pinarbasi, Brian Huang, and Grace Choi
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PDF file - 50K, Tumor Histologies generated from the AI model
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- 2023
25. Supplementary Figure 3 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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Kevin Shannon, Russell O. Pieper, Richard Chao, Benjamin T. Houseman, Kevan Shokat, Dorothea Fiedler, Bruce A. Faddegon, Andrew E. Horvai, Scott Vandenberg, Scott C. Kogan, Emile Pinarbasi, Connie Phong, and Jean L. Nakamura
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Supplementary Figure 3 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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- 2023
26. Supplementary Figure 1 from Genetically Mediated Nf1 Loss in Mice Promotes Diverse Radiation-Induced Tumors Modeling Second Malignant Neoplasms
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Jean L. Nakamura, Bruce Faddegon, Smita Bhatia, Scott Kogan, Andrew E. Horvai, Steve E. Braunstein, Emile Pinarbasi, Brian Huang, and Grace Choi
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PDF file - 678K, Abdominal Irradiation set up
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- 2023
27. Supplementary Figure 2 from Genetically Mediated Nf1 Loss in Mice Promotes Diverse Radiation-Induced Tumors Modeling Second Malignant Neoplasms
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Jean L. Nakamura, Bruce Faddegon, Smita Bhatia, Scott Kogan, Andrew E. Horvai, Steve E. Braunstein, Emile Pinarbasi, Brian Huang, and Grace Choi
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PDF file - 329K, Hematologic Endpoints
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- 2023
28. Supplementary Table 2 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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Kevin Shannon, Russell O. Pieper, Richard Chao, Benjamin T. Houseman, Kevan Shokat, Dorothea Fiedler, Bruce A. Faddegon, Andrew E. Horvai, Scott Vandenberg, Scott C. Kogan, Emile Pinarbasi, Connie Phong, and Jean L. Nakamura
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Supplementary Table 2 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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- 2023
29. Supplementary Table 2 from Genetically Mediated Nf1 Loss in Mice Promotes Diverse Radiation-Induced Tumors Modeling Second Malignant Neoplasms
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Jean L. Nakamura, Bruce Faddegon, Smita Bhatia, Scott Kogan, Andrew E. Horvai, Steve E. Braunstein, Emile Pinarbasi, Brian Huang, and Grace Choi
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PDF file - 35K, Trp53 exon sequencing primers
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- 2023
30. Supplementary Legends for Figures 1-3, Tables 1-2 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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Kevin Shannon, Russell O. Pieper, Richard Chao, Benjamin T. Houseman, Kevan Shokat, Dorothea Fiedler, Bruce A. Faddegon, Andrew E. Horvai, Scott Vandenberg, Scott C. Kogan, Emile Pinarbasi, Connie Phong, and Jean L. Nakamura
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Supplementary Legends for Figures 1-3, Tables 1-2 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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- 2023
31. Supplementary Figure 1 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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Kevin Shannon, Russell O. Pieper, Richard Chao, Benjamin T. Houseman, Kevan Shokat, Dorothea Fiedler, Bruce A. Faddegon, Andrew E. Horvai, Scott Vandenberg, Scott C. Kogan, Emile Pinarbasi, Connie Phong, and Jean L. Nakamura
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Supplementary Figure 1 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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- 2023
32. Supplementary Figure 2 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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Kevin Shannon, Russell O. Pieper, Richard Chao, Benjamin T. Houseman, Kevan Shokat, Dorothea Fiedler, Bruce A. Faddegon, Andrew E. Horvai, Scott Vandenberg, Scott C. Kogan, Emile Pinarbasi, Connie Phong, and Jean L. Nakamura
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Supplementary Figure 2 from Dose-Dependent Effects of Focal Fractionated Irradiation on Secondary Malignant Neoplasms in Nf1 Mutant Mice
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- 2023
33. A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure.
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Bryce A Mendelsohn, Neal K Bennett, Maxwell A Darch, Katharine Yu, Mai K Nguyen, Daniela Pucciarelli, Maxine Nelson, Max A Horlbeck, Luke A Gilbert, William Hyun, Martin Kampmann, Jean L Nakamura, and Ken Nakamura
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Biology (General) ,QH301-705.5 - Abstract
Insufficient or dysregulated energy metabolism may underlie diverse inherited and degenerative diseases, cancer, and even aging itself. ATP is the central energy carrier in cells, but critical pathways for regulating ATP levels are not systematically understood. We combined a pooled clustered regularly interspaced short palindromic repeats interference (CRISPRi) library enriched for mitochondrial genes, a fluorescent biosensor, and fluorescence-activated cell sorting (FACS) in a high-throughput genetic screen to assay ATP concentrations in live human cells. We identified genes not known to be involved in energy metabolism. Most mitochondrial ribosomal proteins are essential in maintaining ATP levels under respiratory conditions, and impaired respiration predicts poor growth. We also identified genes for which coenzyme Q10 (CoQ10) supplementation rescued ATP deficits caused by knockdown. These included CoQ10 biosynthetic genes associated with human disease and a subset of genes not linked to CoQ10 biosynthesis, indicating that increasing CoQ10 can preserve ATP in specific genetic contexts. This screening paradigm reveals mechanisms of metabolic control and genetic defects responsive to energy-based therapies.
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- 2018
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34. Mutational Status and Clinical Outcomes Following Systemic Therapy with or without Focal Radiation for Resected Melanoma Brain Metastases
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Harish N. Vasudevan, Matthew S. Susko, Lijun Ma, Jean L. Nakamura, David R. Raleigh, Lauren Boreta, Shannon Fogh, Philip V. Theodosopoulos, Michael W. McDermott, Katy K. Tsai, Penny K. Sneed, and Steve E. Braunstein
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Surgery ,Neurology (clinical) - Abstract
Brain metastases occur frequently in advanced melanoma and traditionally require surgery and radiation therapy. New evidence demonstrates that systemic therapies are effective for controlling metastatic melanoma brain metastases. This study evaluated outcomes after resection of melanoma brain metastases treated with systemic therapy, with or without focal radiotherapy.All patients received immunotherapy or BRAF/MEK inhibitors preoperatively or in the immediate 3 months postoperatively. Resection cavity failure, distant central nervous system progression, and adverse radiation effects were reported in the presence and absence of focal radiotherapy using the Kaplan-Meier method.Between 2011 and 2020, 37 resection cavities in 29 patients met criteria for analysis. Of lesions, 22 (59%) were treated with focal radiotherapy, and 15 (41%) were treated with targeted therapy or immunotherapy alone. The 12- and 24-month freedom from local recurrence was 64.8% (95% confidence interval [CI] 42.1%-99.8%) and 46.3% (95% CI 24.5%-87.5%), respectively, for systemic therapy alone and 93.3% (95% CI 81.5%-100%) at both time points for focal radiotherapy (P = 0.01). On univariate analysis, focal radiotherapy was the only significant factor associated with reduction of local recurrence risk (hazard ratio 0.10, 95% CI 0.01-0.85; P = 0.04). There were no significant differences in central nervous system progression-free survival or overall survival between patients who received systemic therapy plus focal radiotherapy compared with systemic therapy alone. BRAF mutation status was reviewed for either the brain metastasis (n = 9 patients, 31%) or the primary site (n = 20 patients, 69%), and patients harboring BRAFFocal radiotherapy with systemic therapy for resected melanoma brain metastases significantly decreased resection cavity recurrence compared with systemic therapy alone. BRAF mutation status correlated with poorer outcomes.
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- 2022
35. Abstract 1161: Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function
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Neal K. Bennett, Hiroki J. Nakaoka, Danny Laurent, Ross Okimoto, Yoshitaka Sei, Andrew E. Horvai, Trever G. Bivona, Georgios Batsios, Pavithra Viswanath, Johanna ten Hoeve, Thomas G. Graeber, Ken Nakamura, and Jean L. Nakamura
- Subjects
Cancer Research ,Oncology - Abstract
The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and processes such as tumor dissemination and metastatic growth remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells downregulate glycolytic mechanisms. Metabolic shifts associated with silencing mito-respiratory genes can be detected in vivo with metabolic imaging. These studies demonstrate that discrete perturbations of mitochondrial respiratory chain function impact in vivo tumor growth in a context-specific manner with differential impacts on primary and metastatic tumors. Citation Format: Neal K. Bennett, Hiroki J. Nakaoka, Danny Laurent, Ross Okimoto, Yoshitaka Sei, Andrew E. Horvai, Trever G. Bivona, Georgios Batsios, Pavithra Viswanath, Johanna ten Hoeve, Thomas G. Graeber, Ken Nakamura, Jean L. Nakamura. Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1161.
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- 2023
36. Differentiating Radiation Necrosis from Brain Tumor Using Hyperpolarized Carbon-13 MR Metabolic Imaging
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Juhyun Song, Ilwoo Park, Yun Hyeon Kim, Kyung-Hwa Lee, Jin Myung Choi, Seul Kee Kim, Daniela Pucciarelli, Woong Yoon, Jean L. Nakamura, and Shin Jung
- Subjects
Cancer Research ,Pathology ,medicine.medical_specialty ,Necrosis ,Brain tumor ,030218 nuclear medicine & medical imaging ,Metastasis ,Lesion ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Cell Line, Tumor ,Glioma ,medicine ,Animals ,Radiology, Nuclear Medicine and imaging ,Radiation Injuries ,Carbon Isotopes ,medicine.diagnostic_test ,Brain Neoplasms ,business.industry ,Brain ,Lewis lung carcinoma ,Magnetic resonance imaging ,medicine.disease ,Magnetic Resonance Imaging ,Hyperintensity ,Disease Models, Animal ,Oncology ,medicine.symptom ,business ,Neoplasm Transplantation - Abstract
Differentiation between radiation-induced necrosis and tumor recurrence is crucial to determine proper management strategies but continues to be one of the central challenges in neuro-oncology. We hypothesized that hyperpolarized 13C MRI, a unique technique to measure real-time in vivo metabolism, would distinguish radiation necrosis from tumor on the basis of cell-intrinsic metabolic differences. The purpose of this study was to explore the feasibility of using hyperpolarized [1-13C]pyruvate for differentiating radiation necrosis from brain tumors. Radiation necrosis was initiated by employing a CT-guided 80-Gy single-dose irradiation of a half cerebrum in mice (n = 7). Intracerebral tumor was modeled with two orthotopic mouse models: GL261 glioma (n = 6) and Lewis lung carcinoma (LLC) metastasis (n = 7). 13C 3D MR spectroscopic imaging data were acquired following hyperpolarized [1-13C]pyruvate injection approximately 89 and 14 days after treatment for irradiated and tumor-bearing mice, respectively. The ratio of lactate to pyruvate (Lac/Pyr), normalized lactate, and pyruvate in contrast-enhancing lesion was compared between the radiation-induced necrosis and brain tumors. Histopathological analysis was performed from resected brains. Conventional MRI exhibited typical radiographic features of radiation necrosis and brain tumor with large areas of contrast enhancement and T2 hyperintensity in all animals. Normalized lactate in radiation necrosis (0.10) was significantly lower than that in glioma (0.26, P = .004) and LLC metastatic tissue (0.25, P = .00007). Similarly, Lac/Pyr in radiation necrosis (0.18) was significantly lower than that in glioma (0.55, P = .00008) and LLC metastasis (0.46, P = .000008). These results were consistent with histological findings where tumor-bearing brains were highly cellular, while irradiated brains exhibited pathological markers consistent with reparative changes from radiation necrosis. Hyperpolarized 13C MR metabolic imaging of pyruvate is a noninvasive imaging method that differentiates between radiation necrosis and brain tumors, providing a groundwork for further clinical investigation and translation for the improved management of patients with brain tumors.
- Published
- 2021
37. Considerations for carcinogenesis countermeasure development using mouse models
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Jean L. Nakamura
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Radiation ,Ecology ,Carcinogenesis ,Health, Toxicology and Mutagenesis ,Astronomy and Astrophysics ,Radiation Exposure ,Space Flight ,Agricultural and Biological Sciences (miscellaneous) ,Mice ,Disease Models, Animal ,Radiation, Ionizing ,Animals ,Humans ,Astronauts - Abstract
Activities in space will expose humans to profoundly new environments, challenging human performance and will require innovative supportive technologies. Among these environmental variables, exposure to ionizing radiation is a major concern for astronauts, as the long-term effects of exposure on diverse tissues are poorly understood. This need however creates opportunities for novel approaches, particularly in the development of countermeasures against the effects of ionizing radiation exposure. Carcinogenesis presents a unique challenge as a disease process, due to the inherent complexities of the process and the challenges of obtaining a large volume of clinical evidence. Thus, developing the countermeasures to address potential effects of ionizing radiation exposure will require understanding biological underpinnings to design countermeasures effectively in conjunction with highly robust modeling approaches to test and examine in vivo. This review will highlight specific considerations for accelerated development of space radiation countermeasures against carcinogenesis.
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- 2022
38. Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK
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Gary L. Johnson, Kevin Shannon, Jean L. Nakamura, Ganesh Krishnamurthi, Daniela Pucciarelli, Steven P. Angus, Sourav Bandyopadhyay, Benjamin J. Huang, Hiroki J. Nakaoka, Chi Zhang, and D. Wade Clapp
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0301 basic medicine ,Cancer Research ,Drug Resistance ,Drug resistance ,Loss of heterozygosity ,Transcriptome ,Mice ,0302 clinical medicine ,Models ,Kinome ,Cancer ,Tumor ,Neurofibromin 1 ,Effector ,High-Throughput Nucleotide Sequencing ,Pharmacology and Pharmaceutical Sciences ,Phenotype ,Oncology ,5.1 Pharmaceuticals ,030220 oncology & carcinogenesis ,Development of treatments and therapeutic interventions ,Signal Transduction ,congenital, hereditary, and neonatal diseases and abnormalities ,Neurofibromatosis 1 ,Oncology and Carcinogenesis ,Context (language use) ,Biology ,Article ,Cell Line ,Neurofibromatosis ,03 medical and health sciences ,Rare Diseases ,Genetics ,Animals ,Humans ,Oncology & Carcinogenesis ,Protein Kinase Inhibitors ,PI3K/AKT/mTOR pathway ,Animal ,Gene Expression Profiling ,Neurosciences ,Computational Biology ,Biological ,nervous system diseases ,Orphan Drug ,Good Health and Well Being ,030104 developmental biology ,Disease Models ,Mutation ,Cancer research ,Neoplasm ,Protein Kinases - Abstract
Loss of the tumor suppressor NF1 leads to activation of RAS effector pathways, which are therapeutically targeted by inhibition of mTOR (mTORi) or MEK (MEKi). However, therapeutic inhibition of RAS effectors leads to the development of drug resistance and ultimately disease progression. To investigate molecular signatures in the context of NF1 loss and subsequent acquired drug resistance, we analyzed the exomes, transcriptomes, and kinomes of Nf1-mutant mouse tumor cell lines and derivatives of these lines that acquired resistance to either MEKi or mTORi. Biochemical comparisons of this unique panel of tumor cells, all of which arose in Nf1+/− mice, indicate that loss of heterozygosity of Nf1 as an initial genetic event does not confer a common biochemical signature or response to kinase inhibition. Although acquired drug resistance by Nf1-mutant tumor cells was accompanied by altered kinomes and irreversibly altered transcriptomes, functionally in multiple Nf1-mutant tumor cell lines, MEKi resistance was a stable phenotype, in contrast to mTORi resistance, which was reversible. Collectively, these findings demonstrate that Nf1-mutant tumors represent a heterogeneous group biochemically and undergo broader remodeling of kinome activity and gene expression in response to targeted kinase inhibition.
- Published
- 2020
39. Stereotactic Radiosurgery to More Than 10 Brain Metastases: Evidence to Support the Role of Radiosurgery for Ideal Hippocampal Sparing in the Treatment of Multiple Brain Metastases
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Steve Braunstein, Philip V. Theodosopoulos, Jean L. Nakamura, Michael W. McDermott, Shannon Fogh, Penny K. Sneed, David R. Raleigh, Matthew S. Susko, Michael Garcia, and Lijun Ma
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Male ,medicine.medical_treatment ,Salvage therapy ,Hippocampal formation ,Hippocampus ,0302 clinical medicine ,7.1 Individual care needs ,Interquartile range ,Cancer ,Brain Neoplasms ,Middle Aged ,Treatment Outcome ,Local ,030220 oncology & carcinogenesis ,Female ,Radiology ,medicine.symptom ,medicine.medical_specialty ,Clinical Sciences ,Radiosurgery ,Article ,SRS ,Lesion ,03 medical and health sciences ,Rare Diseases ,parasitic diseases ,Hippocampal sparing ,medicine ,Humans ,In patient ,Aged ,Retrospective Studies ,Salvage Therapy ,business.industry ,Brain metastasis ,Neurosciences ,medicine.disease ,Confidence interval ,Brain Disorders ,Neoplasm Recurrence ,Surgery ,Management of diseases and conditions ,Neurology (clinical) ,Cranial Irradiation ,Neoplasm Recurrence, Local ,business ,030217 neurology & neurosurgery - Abstract
BACKGROUND: Brain metastases are a common occurrence, with literature supporting the treatment of a limited number of brain metastases with stereotactic radiosurgery (SRS), as opposed to whole brain radiotherapy (WBRT). Less well understood is the role of SRS in patients with ≥10 brain metastases. METHODS: Patients treated with SRS to ≥10 brain metastases without concurrent WBRT between March 1999 and December 2016 were reviewed. Analysis was performed for overall survival, treated lesion freedom from progression (FFP), freedom from new metastases (FFNMs), and adverse radiation effect. Hippocampal volumes were retrospectively generated in patients treated with up-front SRS for evaluation of dose volume metrics. RESULTS: A total of 143 patients were identified with 75 patients having up-front SRS and 68 patients being treated as salvage therapy after prior WBRT. The median number of lesions per patient was 13 (interquartile range [IQR], 11–17). Median total volume of treatment was 4.1 cm(3) (IQR, 2.0–9.9 cm(3)). The median 12-month FFP for up-front and salvage treatment was 96.8% (95% confidence interval [CI], 95.5–98.1) and 83.6% (95% CI, 79.9–87.5), respectively (P < 0.001). Twelve-month FFNMs for up-front and salvage SRS was 18.8% (95% CI, 10.9–32.3) versus 19.2% (95% CI, 9.7–37.8), respectively (P = 0.90). The mean hippocampal dose was 150 cGy (IQR, 100–202 cGy). CONCLUSIONS: Excellent rates of local control can be achieved when treating patients with >10 intracranial metastases either in the up-front or salvage setting. Hippocampal sparing is readily achievable with expected high rates of new metastatic lesions in treated patients.
- Published
- 2020
40. Estimating the Risk of Radiation-Induced Malignancy Following Radiotherapy for Benign Disease
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Jean L. Nakamura, Steve E. Braunstein, and Stephanie R. McKeown
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- 2022
41. Letter: Patterns of Intermediate- and High-Risk Meningioma Recurrence After Treatment With Postoperative External Beam Radiotherapy
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Matthew S. Susko, Philip V. Theodosopoulos, Stephen T. Magill, Javier Villanueva-Meyer, Nancy Ann Oberheim Bush, David R. Raleigh, William C. Chen, Calixto-Hope G Lucas, Harish N. Vasudevan, Steve Braunstein, Lauren Boreta, David A. Solomon, Michael W. McDermott, Jean L. Nakamura, and Penny K. Sneed
- Subjects
medicine.medical_specialty ,business.industry ,medicine.medical_treatment ,MEDLINE ,medicine.disease ,CORRESPONDENCE ,Meningioma ,Text mining ,medicine ,Surgery ,Neurology (clinical) ,Radiology ,External beam radiotherapy ,business ,After treatment - Published
- 2021
42. In vivo CRISPRi screen reveals the differential requirement for mitochondrial respiratory chain function between in vivo and in vitro tumor growth
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Johanna ten Hoeve, Neal Bennett, Danny Laurent, Jean L. Nakamura, Trever G. Bivona, Thomas G. Graeber, Hiroki Nakaoka, Ken Nakamura, Ross A. Okimoto, and Yoshitaka Sei
- Subjects
Mitochondrial respiratory chain ,Anaerobic glycolysis ,In vivo ,Cell culture ,Cancer cell ,Respiratory chain ,Respiratory function ,Biology ,Warburg effect ,Cell biology - Abstract
The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and significant processes such as tumor dissemination and metastases remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells downregulate glycolytic mechanisms. These studies demonstrate that discrete perturbations of mitochondrial metabolism impact in vivo tumor growth in a context-specific manner and provides systems-level evidence that respiratory function modulates tumor growth in vivo, suggesting that ATP limits growth and metastatic potential.
- Published
- 2021
43. Irradiation of
- Author
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Danny, Laurent, Abbi E, Smith, Waylan K, Bessler, Marc, Mendonca, Helen, Chin-Sinex, Martina, Descovich, Andrew E, Horvai, D Wade, Clapp, and Jean L, Nakamura
- Subjects
radiation ,malignant transformation ,plexiform neurofibromas ,Basic and Translational Investigations ,AcademicSubjects/MED00300 ,heterozygosity ,AcademicSubjects/MED00310 ,Neurofibromatosis I - Abstract
Background Genetically susceptible individuals can develop malignancies after irradiation of normal tissues. In the context of therapeutic irradiation, it is not known whether irradiating benign neoplasms in susceptible individuals promotes neoplastic transformation and worse clinical outcomes. Individuals with Neurofibromatosis 1 (NF1) are susceptible to both radiation-induced second malignancies and spontaneous progression of plexiform neurofibromas (PNs) to malignant peripheral nerve sheath tumors (MPNSTs). The role of radiotherapy in the treatment of benign neoplasms such as PNs is unclear. Methods To test whether radiotherapy promotes neoplastic progression of PNs and reduces overall survival, we administered spinal irradiation (SI) to conditional knockout mouse models of NF1-associated PNs in 2 germline contexts: Nf1fllfl; PostnCre+ and Nf1fl/-; PostnCre+. Both genotypes develop extensive Nf1 null spinal PNs, modeling PNs in NF1 patients. A total of 101 mice were randomized to 0 Gy, 15 Gy (3 Gy × 5), or 30 Gy (3 Gy × 10) of spine-focused, fractionated SI and aged until signs of illness. Results SI decreased survival in both Nf1fllfl mice and Nf1fl/- mice, with the worst overall survival occurring in Nf1fl/- mice receiving 30 Gy. SI was also associated with increasing worrisome histologic features along the PN-MPNST continuum in PNs irradiated to higher radiation doses. Conclusions This preclinical study provides experimental evidence that irradiation of pre-existing PNs reduces survival and may shift PNs to higher grade neoplasms.
- Published
- 2021
44. Subsequent Neoplasms After a Primary Tumor in Individuals With Neurofibromatosis Type 1
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Lindsey Hageman, Michael Fisher, Michael Arnold, Peter de Blank, Bruce R. Korf, Lucie M. Turcotte, Gregory K. Friedman, Gregory T. Armstrong, Smita Bhatia, Joseph P. Neglia, Katie Metrock, Yanjun Chen, Kevin Shannon, F. Lennie Wong, Ashley Cannon, Daniel J Leidy, Wendy M. Leisenring, Kandice Smith, Jean L. Nakamura, Joseph E Andress, Leslie L. Robison, Alejandro Paz, and D. Wade Clapp
- Subjects
Adult ,Male ,Risk ,Oncology ,congenital, hereditary, and neonatal diseases and abnormalities ,Cancer Research ,medicine.medical_specialty ,Neurofibromatosis 1 ,Adolescent ,Cohort Studies ,Young Adult ,Cancer Survivors ,Biology of Neoplasia ,Neoplasms ,Internal medicine ,Humans ,Medicine ,Longitudinal Studies ,Neurofibromatosis ,Young adult ,Child ,Proportional Hazards Models ,Retrospective Studies ,business.industry ,Proportional hazards model ,Extramural ,Incidence ,Retrospective cohort study ,medicine.disease ,Primary tumor ,United States ,nervous system diseases ,Child, Preschool ,Female ,business - Abstract
PURPOSE Fundamental gaps in knowledge regarding the risk of subsequent neoplasms (SNs) in children with pathogenic neurofibromatosis type 1 (NF1) variants exposed to radiation and/or alkylator chemotherapy have limited the use of these agents. METHODS We addressed these gaps by determining the SN risk in 167 NF1-affected versus 1,541 non–NF1-affected 5-year childhood cancer survivors from the Childhood Cancer Survivor Study and 176 nonoverlapping NF1-affected individuals with primary tumors from University of Alabama at Birmingham and Children’s Hospital of Philadelphia exposed to radiation and/or chemotherapy. Proportional subdistribution hazards multivariable regression analysis was used to examine risk factors, adjusting for type and age at primary tumor diagnosis and therapeutic exposures. RESULTS In the Childhood Cancer Survivor Study cohort, the 20-year cumulative incidence of SNs in NF1 childhood cancer survivors was 7.3%, compared with 2.9% in the non-NF1 childhood cancer survivors ( P = .003), yielding a 2.4-fold higher risk of SN (95% CI, 1.3 to 4.3; P = .005) in the NF1-affected individuals. In the University of Alabama at Birmingham and Children’s Hospital of Philadelphia cohort, among NF1-affected individuals with a primary tumor, the risk of SNs was 2.8-fold higher in patients with irradiated NF1 (95% CI, 1.3 to 6.0; P = .009). In contrast, the risk of SNs was not significantly elevated after exposure to alkylating agents (hazard ratio, 1.27; 95% CI, 0.3 to 3.0; P = .9). CONCLUSION Children with NF1 who develop a primary tumor are at increased risk of SN when compared with non-NF1 childhood cancer survivors. Among NF1-affected children with a primary tumor, therapeutic radiation, but not alkylating agents, confer an increased risk of SNs. These findings can inform evidence-based clinical management of primary tumors in NF1-affected children.
- Published
- 2019
45. Multiplatform Molecular Profiling of Vestibular Schwannoma Reveals 2 Subgroups of Tumors With Distinct Radiographic Features and a Methylation-Based Predictor of Local Recurrence
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Jean L. Nakamura, Penny K. Sneed, Ursula E. Lang, Harish N. Vasudevan, Abrar Choudhury, Javier Villanueva-Meyer, William C. Chen, Stephen T. Magill, Chetna Gopinath, S. John Liu, Philip V. Theodosopoulos, Jonathan D. Breshears, Melike Pekmezci, Steve Braunstein, David R. Raleigh, Arie Perry, Michael W. McDermott, and Maria R H Castro
- Subjects
Vestibular system ,Pathology ,medicine.medical_specialty ,medicine.diagnostic_test ,business.industry ,Radiography ,Estrogen receptor ,Magnetic resonance imaging ,Methylation ,Schwannoma ,medicine.disease ,Preoperative care ,medicine ,Cranial nerve disease ,Surgery ,Neurology (clinical) ,medicine.symptom ,business - Published
- 2019
46. Reirradiation of recurrent high-grade glioma and development of prognostic scores for progression and survival
- Author
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David R. Raleigh, Jennie Taylor, Jennifer Clarke, Shannon Fogh, Jared Hara, Christopher H. Chapman, Jean L. Nakamura, Susan M. Chang, Steve Braunstein, Penny K. Sneed, Nicholas Butowski, Annette M. Molinaro, and Nancy Ann Oberheim Bush
- Subjects
Re-Irradiation ,medicine.medical_specialty ,recurrence ,medicine.medical_treatment ,Medicine (miscellaneous) ,Effective dose (radiation) ,Radiosurgery ,Rare Diseases ,glioma ,Glioma ,reirradiation ,Medicine ,Cancer ,Performance status ,Receiver operating characteristic ,business.industry ,glioblastoma ,Neurosciences ,Area under the curve ,Original Articles ,medicine.disease ,Brain Disorders ,Brain Cancer ,prognosis ,Fresh frozen plasma ,Radiology ,business - Abstract
Background Optimal techniques and patient selection for salvage reirradiation of high-grade glioma (HGG) are unclear. In this study, we identify prognostic factors for freedom from progression (FFP) and overall survival (OS) after reirradiation, risk factors for high-grade toxicity, and validate clinical prognostic scores. Methods A total of 116 patients evaluated between 2000 and 2018 received reirradiation for HGG (99 WHO grade IV, 17 WHO grade III). Median time to first progression after initial therapy was 10.6 months. Salvage therapies before reirradiation included surgery (31%) and systemic therapy (41%). Sixty-five patients (56%) received single-fraction stereotactic radiosurgery (SRS) as reirradiation. The median biologically effective dose (BED) was 47.25 Gy, and the median planning target volume (PTV) was 4.8 cc for SRS and 95.0 cc for non-SRS treatments. Systemic therapy was given concurrently to 52% and adjuvantly to 74% of patients. Results Median FFP was 4.9 months, and median OS was 11.0 months. Significant multivariable prognostic factors for FFP were performance status, time to initial progression, and BED; for OS they were age, time to initial progression, and PTV volume at recurrence. High-grade toxicity was correlated to PTV size at recurrence. Three-level prognostic scores were generated for FFP and OS, with cross-validated receiver operating characteristic area under the curve (AUC) of 0.640 and 0.687, respectively. Conclusions Clinical variables at the time of reirradiation for HGG can be used to prognosticate FFP and OS.
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- 2019
47. Salvage Resection and Intracranial Cesium-131 Brachytherapy for Brain Tumors
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Michael McDermott, M Lafreniere, Olivier Morin, Shannon Fogh, David R. Raleigh, B. P. Ziemer, M Lometti, C. Phuong, Philip V. Theodosopoulos, Lauren Boreta, Harish N. Vasudevan, William C. Chen, Patricia Sneed, Shawn L. Hervey-Jumper, Jean L. Nakamura, Steve Braunstein, and Stephen Magill
- Subjects
Hemangiopericytoma ,Cancer Research ,education.field_of_study ,medicine.medical_specialty ,Radiation ,business.industry ,medicine.medical_treatment ,Population ,Brachytherapy ,Salvage therapy ,medicine.disease ,Radiosurgery ,Surgery ,Radiation therapy ,Oncology ,Interquartile range ,medicine ,Radiology, Nuclear Medicine and imaging ,education ,business ,Brain metastasis - Abstract
Purpose/objective(s) Management of progressive brain tumors following high dose radiotherapy is controversial. In select cases, surgical resection can provide rapid relief of regional mass effect and edema, and highly focal adjuvant re-irradiation can be administered in the form of brachytherapy. Permanent low-dose rate cesium-131 brachytherapy may offer dosimetric and radiobiologic advantages over other isotopes. The purpose of this study was to examine the safety and efficacy of intracranial cesium-131 brachytherapy after surgical resection in a heavily pre-treated patient cohort. Materials/methods A retrospective chart review was conducted of all patients treated with intraoperative intracranial cesium-131 brachytherapy from an institutional database. Treatment consisted of maximal safe resection followed by implantation of suture-stranded cesium-131 seeds, maintaining approximately 10mm spacing between seeds, with a planned target dose of 80 Gy to 5mm depth. Local failure was defined as recurrence in or contacting the resection cavity after salvage resection and brachytherapy. Regional failure was defined as recurrence within 10mm of the resection cavity. Recurrence was defined as a new lesion or growth of ≥25% in any axial dimension on interval MRI. Toxicity was collected based on CTCAE 4.0. Results A total of 35 patients with a median imaging follow up of 17.0 months (interquartile range [IQR] 9.7-25.9) underwent 41 consecutive cesium-131 implants between 2016 and 2020. 20 patients (59%; N = 22 implants) were treated for recurrent brain metastasis, 12 patients (34%; N = 16 implants) were treated for recurrent atypical (N = 8) or anaplastic meningioma (N = 4), and 3 patients (9%) were treated for recurrent glioma (N = 2) or hemangiopericytoma (N = 1). A majority of lesions had received prior surgery (N = 28, 66.7%, range 0-3 prior surgeries) and 34 patients had received prior high dose radiation. 34 of 41 (82.9%) tumors had received prior radiosurgery, and 12 (29.2%) had undergone prior external beam radiation (range 50-60 Gy). 17 of 41 lesions (41.5%) had radiologic evidence of adverse radiation/treatment effect (ARE) prior to salvage therapy. Median tumor size was 3.0cm (IQR 2.3-3.7). Overall actuarial local/loco-regional control at 1-year was 91.6%/84.7% (89.8%/88.9% for metastases and 100%/82.5% for meningiomas). Crude loco-regional control was 86.3% for metastases, 75% for meningiomas, and 66.7% for other lesions. Symptomatic ARE following treatment was observed in 9.8% (N = 4) resection cavities. The surgical complication rate was 14.6% (N = 6 total, N = 3 [7.3%] grade 3-5) including 1 peri-operative death. Conclusion Cesium-131 brachytherapy in this heavily pre-treated cohort resulted in good local control and an acceptable rate of symptomatic adverse radiation effect and toxicity and may be a reasonable treatment option for this select population. Author disclosure W.C. Chen: None. M. Lafreniere: None. C. Phuong: None. M. Lometti: None. O. Morin: None. B.P. Ziemer: None. H. Vasudevan: Research Grant; Children's Tumor Foundation. Patent/License Fees/Copyright; Genentech, Eli Lilly. S. Hervey-Jumper: None. P.V. Theodosopoulos: None. S. Magill: None. S.E. Fogh: Independent Contractor; Accuray. J.L. Nakamura: None. L. Boreta: None. P.K. Sneed: None. M.W. McDermott: Chair; Miami Baptist. D. Raleigh: None. S.E. Braunstein: Advisory Board; Radiation Oncology Questions, LLC.
- Published
- 2021
48. A New Benchmark of the Sharpest Dose Fall-Off for Hypo-Fractionated Radiosurgery of Large Single Target Brain Lesions
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Lin Ma, Shawn L. Hervey-Jumper, Philip V. Theodosopoulos, Steve Braunstein, Jean L. Nakamura, Lauren Boreta, B. P. Ziemer, T. Nano, David R. Raleigh, Shannon Fogh, Patricia Sneed, and Olivier Morin
- Subjects
Cancer Research ,Radiation ,business.industry ,medicine.medical_treatment ,Planning target volume ,Treatment parameters ,Radiosurgery ,Conformity index ,Target dose ,Oncology ,Radiation oncology ,Brain lesions ,Medicine ,Radiology, Nuclear Medicine and imaging ,Radiation treatment planning ,business ,Nuclear medicine - Abstract
PURPOSE/OBJECTIVE(S) Previous studies have characterized dose gradient patterns for various hypo-fractionated brain radiosurgery (hSRS) treatment platforms. The Gamma Knife Icon (GKI) has consistently exhibited either superior or non-inferior peripheral dose fall-off and normal brain sparing characteristics when compared to other Linac-based hSRS treatment platforms. Given the prevalence of Linac-based treatments, identifying planning techniques to optimize treatment parameters is desirable. In this study, we investigated a novel Linac-based treatment approach that aimed to create the sharpest dose fall-off for hSRS of large brain lesions. MATERIALS/METHODS A cohort of patient cases (n = 10) with single brain lesions (volume 27.6+/-8.1 mL, range 20.-42.1 mL) treated with GKI at our institution were selected as sample test cases for our study. A non-coplanar unconstrained VMAT (NCU-VMAT) treatment planning approach was developed, and its script was implemented on a commercial treatment planning system for clinical Linac treatment equipped with the latest high-definition multi-leaf collimators (MLCs). Treatment plans produced via the NCU-VMAT approach were then compared against further optimized treatment plans from GKI, as well as conventional coplanar and non-coplanar VMAT treatment planning approaches. The comparison was carried out using DVH-derived parameters including target volume coverage, target dose conformity, modified dose fall-off index defined as the volume of 50% prescribed target dose divided by the target volume (PIV50). RESULTS For each case studied, NCU-VMAT achieved practically identical target coverage (0.98 ± 0.01) and Paddick dose conformity index (0.87 ± 0.02) compared to optimized GKI treatments. The mean PIV50 values were 2.99 ± 0.14, 3.77 ± 0.22, and 3.36 ± 0.19 for optimized GKI, conventional coplanar, and non-coplanar VMAT treatment plans, respectively. These results were in excellent agreement with previously published studies. However, the NCU-VMAT technique yielded a mean PIV50 of 2.41 ± 0.07. This represents an improvement of approximately 40% (P < 0.001, paired two-tailed Student t-test) over all existing approaches including GKI. Further analyses revealed that PIV50 of NCU-VMAT approached the theoretical minimum for all the studied cases. CONCLUSION Our results demonstrate that in treatment of large brain tumors, a treatment planning approach using Bremsstrahlung x-ray based Linacs can achieve superior dose fall-off for intracranial hSRS compared to GKI. We dispel the myth that physical characteristics of Cobalt γ-rays are needed to create the sharpest dose fall-off. Given the prevalence of Linac-based treatments compared to GKI, we present a novel optimized planning technique that achieves a new benchmark of sharpest dose fall-off. AUTHOR DISCLOSURE T. Nano: None. O. Morin: None. B.P. Ziemer: None. D. Raleigh: None. L. Boreta: None. J.L. Nakamura: None. S.E. Fogh: Independent Contractor; Accuray. P.K. Sneed: None. S. Hervey-Jumper: None. P.V. Theodosopoulos: None. S.E. Braunstein: Advisory Board; Radiation Oncology Questions, LLC.L. Ma: Patent/License Fees/Copyright; University of California Regents.
- Published
- 2021
49. Redistributing Central Target Dose Hot Spots for Hypofractionated Radiosurgery of Large Brain Tumors: A Proof-of-Principle Study
- Author
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Lijun Ma, Steve Braunstein, Encouse Golden, Jean L. Nakamura, Penny K. Sneed, Michael W. McDermott, and Shannon Fogh
- Subjects
medicine.medical_specialty ,business.industry ,Biological modeling ,medicine.medical_treatment ,Radiosurgery ,030218 nuclear medicine & medical imaging ,Target dose ,03 medical and health sciences ,0302 clinical medicine ,Medicine ,Radiology ,business ,Radiation treatment planning ,030217 neurology & neurosurgery - Abstract
Objective: The present proof-of-principle study investigated radiobiological effects of redistributing central target dose hot spots across different treatment fractions during hypofractionated stereotactic radiosurgery (HSRS) of large intracranial tumors.
- Published
- 2021
50. Irradiation of Nf1 mutant mouse models of spinal plexiform neurofibromas drives pathologic progression and decreases survival
- Author
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Jean L. Nakamura, Marc S. Mendonca, D. Wade Clapp, Waylan K. Bessler, Martina Descovich, Andrew E. Horvai, Danny Laurent, Abbi Smith, and Helen Chin-Sinex
- Subjects
0301 basic medicine ,Pathology ,medicine.medical_specialty ,business.industry ,medicine.medical_treatment ,Cancer ,Context (language use) ,medicine.disease ,Malignant transformation ,Radiation therapy ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Peripheral nervous system ,Conditional gene knockout ,medicine ,Neoplastic transformation ,Neurofibromatosis ,business - Abstract
Background Genetically susceptible individuals can develop malignancies after irradiation of normal tissues. In the context of therapeutic irradiation, it is not known whether irradiating benign neoplasms in susceptible individuals promotes neoplastic transformation and worse clinical outcomes. Individuals with Neurofibromatosis 1 (NF1) are susceptible to both radiation-induced second malignancies and spontaneous progression of plexiform neurofibromas (PNs) to malignant peripheral nerve sheath tumors (MPNSTs). The role of radiotherapy in the treatment of benign neoplasms such as PNs is unclear. Methods To test whether radiotherapy promotes neoplastic progression of PNs and reduces overall survival, we administered spinal irradiation (SI) to conditional knockout mouse models of NF1-associated PNs in 2 germline contexts: Nf1fllfl; PostnCre+ and Nf1fl/-; PostnCre+. Both genotypes develop extensive Nf1 null spinal PNs, modeling PNs in NF1 patients. A total of 101 mice were randomized to 0 Gy, 15 Gy (3 Gy × 5), or 30 Gy (3 Gy × 10) of spine-focused, fractionated SI and aged until signs of illness. Results SI decreased survival in both Nf1fllfl mice and Nf1fl/- mice, with the worst overall survival occurring in Nf1fl/- mice receiving 30 Gy. SI was also associated with increasing worrisome histologic features along the PN-MPNST continuum in PNs irradiated to higher radiation doses. Conclusions This preclinical study provides experimental evidence that irradiation of pre-existing PNs reduces survival and may shift PNs to higher grade neoplasms.
- Published
- 2021
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