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Association of HLA-DRB1 locus with treatment response to abatacept or TNF inhibitors in patients with seropositive rheumatoid arthritis. Sci Rep 2024; 14:6763. [PMID: 38514707 PMCID: PMC10957942 DOI: 10.1038/s41598-024-56987-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
The strongest genetic risk factor for rheumatoid arthritis (RA) has been known as HLA-DRB1 based on amino acid positions 11, 71, and 74. This study analyzed the association between specific HLA-DRB1 locus and treatment response to abatacept or TNF inhibitors (TNFi) in patients with seropositive RA. A total of 374 Korean RA patients were treated with abatacept (n = 110) or TNFi (n = 264). Associations between HLA-DRB1 and treatment response after 6 months were analyzed using multivariable logistic regression. Seropositive RA patients with HLA-DRB1 shared epitope (SE) had a favorable response to abatacept (OR = 3.67, P = 0.067) and an inversely associated response to TNFi (OR 0.57, P = 0.058) based on EULAR response criteria, but the difference was not statistically significant in comparison to those without SE. In analyses using amino acid positions of HLA-DRB1, a significant association was found between valine at amino acid position 11 of SE and good response to abatacept (OR = 6.46, P = 5.4 × 10-3). The VRA haplotype also showed a good response to abatacept (OR = 4.56, P = 0.013), but not to TNFi. Our results suggest that treatment response to abatacept or TNFi may differ depending on HLA-DRB1 locus in seropositive RA, providing valuable insights for selecting optimal therapy.
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Polygenic risk score-based phenome-wide association study of head and neck cancer across two large biobanks. BMC Med 2024; 22:120. [PMID: 38486201 PMCID: PMC10941505 DOI: 10.1186/s12916-024-03305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Numerous observational studies have highlighted associations of genetic predisposition of head and neck squamous cell carcinoma (HNSCC) with diverse risk factors, but these findings are constrained by design limitations of observational studies. In this study, we utilized a phenome-wide association study (PheWAS) approach, incorporating a polygenic risk score (PRS) derived from a wide array of genomic variants, to systematically investigate phenotypes associated with genetic predisposition to HNSCC. Furthermore, we validated our findings across heterogeneous cohorts, enhancing the robustness and generalizability of our results. METHODS We derived PRSs for HNSCC and its subgroups, oropharyngeal cancer and oral cancer, using large-scale genome-wide association study summary statistics from the Genetic Associations and Mechanisms in Oncology Network. We conducted a comprehensive investigation, leveraging genotyping data and electronic health records from 308,492 individuals in the UK Biobank and 38,401 individuals in the Penn Medicine Biobank (PMBB), and subsequently performed PheWAS to elucidate the associations between PRS and a wide spectrum of phenotypes. RESULTS We revealed the HNSCC PRS showed significant association with phenotypes related to tobacco use disorder (OR, 1.06; 95% CI, 1.05-1.08; P = 3.50 × 10-15), alcoholism (OR, 1.06; 95% CI, 1.04-1.09; P = 6.14 × 10-9), alcohol-related disorders (OR, 1.08; 95% CI, 1.05-1.11; P = 1.09 × 10-8), emphysema (OR, 1.11; 95% CI, 1.06-1.16; P = 5.48 × 10-6), chronic airway obstruction (OR, 1.05; 95% CI, 1.03-1.07; P = 2.64 × 10-5), and cancer of bronchus (OR, 1.08; 95% CI, 1.04-1.13; P = 4.68 × 10-5). These findings were replicated in the PMBB cohort, and sensitivity analyses, including the exclusion of HNSCC cases and the major histocompatibility complex locus, confirmed the robustness of these associations. Additionally, we identified significant associations between HNSCC PRS and lifestyle factors related to smoking and alcohol consumption. CONCLUSIONS The study demonstrated the potential of PRS-based PheWAS in revealing associations between genetic risk factors for HNSCC and various phenotypic traits. The findings emphasized the importance of considering genetic susceptibility in understanding HNSCC and highlighted shared genetic bases between HNSCC and other health conditions and lifestyles.
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Genome-wide association analyses using machine learning-based phenotyping reveal genetic architecture of occupational creativity and overlap with psychiatric disorders. Psychiatry Res 2024; 333:115753. [PMID: 38335777 DOI: 10.1016/j.psychres.2024.115753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
Creativity is known to be heritable and exhibits familial aggregation with psychiatric disorders; however, the complex nature of their relationship has not been well-established. In the present study, we demonstrate that using an expanded and validated machine learning (ML)-based phenotyping of occupational creativity (OC) can allow us to further understand the trait of creativity, which was previously difficult to define and study. We conducted the largest genome-wide association study (GWAS) on OC with 241,736 participants from the UK Biobank and identified 25 lead variants that have not yet been reported and three candidate causal genes that were previously associated with educational attainment and psychiatric disorders. We found extensive genetic overlap between OC and psychiatric disorders with mixed effect direction through various post-GWAS analyses, including the bivariate causal mixture model. In addition, we discovered a strongly genetic correlation between our original GWAS and the GWAS adjusted for education years (rg = 0.95). Our GWAS analysis via ML-based phenotyping contributes to the understanding of the genetic architecture of creativity, which may inform genetic discovery and genetic prediction in human cognition and psychiatric disorders.
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Machine learning model for circulating tumor DNA detection in chronic obstructive pulmonary disease patients with lung cancer. Transl Lung Cancer Res 2024; 13:112-125. [PMID: 38404987 PMCID: PMC10891398 DOI: 10.21037/tlcr-23-633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024]
Abstract
Background Patients with chronic obstructive pulmonary disease (COPD) have a high risk of developing lung cancer. Due to the high rates of complications from invasive diagnostic procedures in this population, detecting circulating tumor DNA (ctDNA) as a non-invasive method might be useful. However, clinical characteristics that are predictive of ctDNA mutation detection remain incompletely understood. This study aimed to investigate factors associated with ctDNA detection in COPD patients with lung cancer. Methods Herein, 177 patients with COPD and lung cancer were prospectively recruited. Plasma ctDNA was genotyped using targeted deep sequencing. Comprehensive clinical variables were collected, including the emphysema index (EI), using chest computed tomography. Machine learning models were constructed to predict ctDNA detection. Results At least one ctDNA mutation was detected in 54 (30.5%) patients. After adjustment for potential confounders, tumor stage, C-reactive protein (CRP) level, and milder emphysema were independently associated with ctDNA detection. An increase of 1% in the EI was associated with a 7% decrease in the odds of ctDNA detection (adjusted odds ratio =0.933; 95% confidence interval: 0.857-0.999; P=0.047). Machine learning models composed of multiple clinical factors predicted individuals with ctDNA mutations at high performance (AUC =0.774). Conclusions ctDNA mutations were likely to be observed in COPD patients with lung cancer who had an advanced clinical stage, high CRP level, or milder emphysema. This was validated in machine learning models with high accuracy. Further prospective studies are required to validate the clinical utility of our findings.
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An analysis of contributing factors of head and neck space infections of odontogenic origin: A long-term retrospective clinical study (including COVID-19 pandemic period). Med Oral Patol Oral Cir Bucal 2023; 28:e622-e629. [PMID: 37330958 PMCID: PMC10635621 DOI: 10.4317/medoral.26018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND The purpose of this study is to investigate predisposing factors for the head and neck infections (HNIs), regarding to the demographic data, anatomical spaces, microbiology and antibiotic sensitivity for affected patients. MATERIAL AND METHODS A 13-year of retrospective study evaluating 470 patients with HNIs, treated as inpatient management in the Department of Oral and Maxillofacial Surgery of KyungHee University school of Dentistry, Seoul, Korea, from January 2009 to February 2022. Statistical analysis of demographic, time-related, anatomic, microbiologic, and treatment variables were investigated for each patient. RESULTS The frequency of HNIs was significantly higher in 50's in males, followed by 70's in females. High Severity score (SS) were significantly associated with increased LOH (Length of hospital stay) and LOM (Length of medication), while LOH showed more intensive relationship compared with LOM. The most frequently involved space in abscess was submandibular space, though incidence and severity of HNIs shows declining tendency throughout 13-year research. Streptococcus viridans was the most predominant species isolated from pus culture growth, and a combination of ampicillin and sulbactam was the 1st choice of antibiotics intravenously. According to the comparison analysis between recommended antibiotics from resistance testing result and clinically administered antibiotics, final coincidence rate was estimated about 55%. CONCLUSIONS Due to HNIs being multifactorial, predicting progression and management of HNIs is still a challenge for oral and maxillofacial surgeons. The present study showed several predisposing factors of SHNIs and their correlations, which could contribute to earlier diagnosis and more effective treatment planning for clinicians, thereby leading to the improvement of prognosis for patients, ultimately.
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Leveraging genetic overlap between irritability and psychiatric disorders to identify genetic variants of major psychiatric disorders. Exp Mol Med 2023; 55:1193-1202. [PMID: 37258574 PMCID: PMC10317967 DOI: 10.1038/s12276-023-01005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/07/2023] [Accepted: 03/13/2023] [Indexed: 06/02/2023] Open
Abstract
Irritability is a heritable core mental trait associated with several psychiatric illnesses. However, the genomic basis of irritability is unclear. Therefore, this study aimed to 1) identify the genetic variants associated with irritability and investigate the associated biological pathways, genes, and tissues as well as single-nucleotide polymorphism (SNP)-based heritability; 2) explore the relationships between irritability and various traits, including psychiatric disorders; and 3) identify additional and shared genetic variants for irritability and psychiatric disorders. We conducted a genome-wide association study (GWAS) using 379,506 European samples (105,975 cases and 273,531 controls) from the UK Biobank. We utilized various post-GWAS analyses, including linkage disequilibrium score regression, the bivariate causal mixture model (MiXeR), and conditional and conjunctional false discovery rate approaches. This GWAS identified 15 independent loci associated with irritability; the total SNP heritability estimate was 4.19%. Genetic correlations with psychiatric disorders were most pronounced for major depressive disorder (MDD) and bipolar II disorder (BD II). MiXeR analysis revealed polygenic overlap with schizophrenia (SCZ), bipolar I disorder (BD I), and MDD. Conditional false discovery rate analyses identified additional loci associated with SCZ (number [n] of additional SNPs = 105), BD I (n = 54), MDD (n = 107), and irritability (n = 157). Conjunctional false discovery rate analyses identified 85, 41, and 198 shared loci between irritability and SCZ, BD I, and MDD, respectively. Multiple genetic loci were associated with irritability and three main psychiatric disorders. Given that irritability is a cross-disorder trait, these findings may help to elucidate the genomics of psychiatric disorders.
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First Direct Measurement Constraining the ^{34}Ar(α,p)^{37}K Reaction Cross Section for Mixed Hydrogen and Helium Burning in Accreting Neutron Stars. PHYSICAL REVIEW LETTERS 2023; 130:212701. [PMID: 37295108 DOI: 10.1103/physrevlett.130.212701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/19/2022] [Accepted: 05/02/2023] [Indexed: 06/12/2023]
Abstract
The rate of the final step in the astrophysical αp process, the ^{34}Ar(α,p)^{37}K reaction, suffers from large uncertainties due to a lack of experimental data, despite having a considerable impact on the observable light curves of x-ray bursts and the composition of the ashes of hydrogen and helium burning on accreting neutron stars. We present the first direct measurement constraining the ^{34}Ar(α,p)^{37}K reaction cross section, using the Jet Experiments in Nuclear Structure and Astrophysics gas jet target. The combined cross section for the ^{34}Ar,Cl(α,p)^{37}K,Ar reaction is found to agree well with Hauser-Feshbach predictions. The ^{34}Ar(α,2p)^{36}Ar cross section, which can be exclusively attributed to the ^{34}Ar beam component, also agrees to within the typical uncertainties quoted for statistical models. This indicates the applicability of the statistical model for predicting astrophysical (α,p) reaction rates in this part of the αp process, in contrast to earlier findings from indirect reaction studies indicating orders-of-magnitude discrepancies. This removes a significant uncertainty in models of hydrogen and helium burning on accreting neutron stars.
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P1.15-08 Phase 1: IMU-201 (PD1-Vaxx), a B-Cell Immunotherapy as Monotherapy or in Combination with Atezolizumab, in Adults with Non-Small Cell Lung Cancer. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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ADC Histogram Analysis of Pediatric Low-Grade Glioma Treated with Selumetinib: A Report from the Pediatric Brain Tumor Consortium. AJNR Am J Neuroradiol 2022; 43:455-461. [PMID: 35210278 PMCID: PMC8910799 DOI: 10.3174/ajnr.a7433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/01/2022] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND PURPOSE Selumetinib is a promising MAP (mitogen-activated protein) kinase (MEK) 1/2 inhibitor treatment for pediatric low-grade gliomas. We hypothesized that MR imaging-derived ADC histogram metrics would be associated with survival and response to treatment with selumetinib. MATERIALS AND METHODS Children with recurrent, refractory, or progressive pediatric low-grade gliomas who had World Health Organization grade I pilocytic astrocytoma with KIAA1549-BRAF fusion or the BRAF V600E mutation (stratum 1), neurofibromatosis type 1-associated pediatric low-grade gliomas (stratum 3), or sporadic non-neurofibromatosis type 1 optic pathway and hypothalamic glioma (OPHG) (stratum 4) were treated with selumetinib for up to 2 years. Quantitative ADC histogram metrics were analyzed for total and enhancing tumor volumes at baseline and during treatment. RESULTS Each stratum comprised 25 patients. Stratum 1 responders showed lower values of SD of baseline ADC_total as well as a larger decrease with time on treatment in ADC_total mean, mode, and median compared with nonresponders. Stratum 3 responders showed a greater longitudinal decrease in ADC_total. In stratum 4, higher baseline ADC_total skewness and kurtosis were associated with shorter progression-free survival. When all 3 strata were combined, responders showed a greater decrease with time in ADC_total mode and median. Compared with sporadic OPHG, neurofibromatosis type 1-associated OPHG had lower values of ADC_total mean, mode, and median as well as ADC_enhancement mean and median and higher values of ADC_total skewness and kurtosis at baseline. The longitudinal decrease in ADC_total median during treatment was significantly greater in sporadic OPHG compared with neurofibromatosis type 1-associated OPHG. CONCLUSIONS ADC histogram metrics are associated with progression-free survival and response to treatment with selumetinib in pediatric low-grade gliomas.
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Genome-wide association study of occupational attainment as a proxy for cognitive reserve. Brain 2021; 145:1436-1448. [PMID: 34613391 DOI: 10.1093/brain/awab351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/22/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Occupational attainment, which represents middle-age cognitive activities, is a known proxy marker of cognitive reserve for Alzheimer's disease. Previous genome-wide association studies (GWAS) have identified numerous genetic variants and revealed the genetic architecture of educational attainment, another marker of cognitive reserve. However, the genetic architecture and heritability for occupational attainment remain elusive. We performed a large-scale GWAS of occupational attainment with 248,847 European individuals from the UK Biobank using the proportional odds logistic mixed model method. In this analysis, we defined occupational attainment using the classified job levels formulated in the UK Standard Occupational Classification system considering the individual professional skill and academic level. We identified 30 significant loci (P < 5 × 10-8); 12 were novel variants, unassociated with other traits. Among them, four lead variants were associated with genes expressed in brain tissues by expression quantitative trait loci mapping from 10 brain regions: rs13002946, rs3741368, rs11654986, and rs1627527. The single nucleotide polymorphism (SNP)-based heritability was estimated to be 8.5% (s.e. = 0.004) and partitioned heritability was enriched in the central nervous system and brain tissues. Genetic correlation analysis showed shared genetic backgrounds between occupational attainment and multiple traits, including education, intelligence, leisure activities, life satisfaction, and neuropsychiatric disorders. In two-sample Mendelian randomization (MR) analysis, we demonstrated that high occupation levels were associated with reduced risk for Alzheimer's disease (OR = 0.78, 95% CI = 0.65-0.92 in inverse variance weighted (IVW) method; OR = 0.73, 95% CI = 0.57-0.92 in the weighted median (WM) method). This causal relationship between occupational attainment and Alzheimer's disease was robust in additional sensitivity analysis that excluded potentially pleiotropic SNPs (OR = 0.72, 95% CI = 0.57-0.91 in the IVW method; OR = 0.72, 95% CI = 0.53-0.97 in the WM method). Multivariable MR confirmed that occupational attainment had an independent effect on the risk for Alzheimer's disease even after taking educational attainment into account (OR = 0.72, 95% CI = 0.54-0.95 in the IVW method; OR = 0.68, 95% CI = 0.48-0.97 in the WM method). Overall, our analyses provide insights into the genetic architecture of occupational attainment and demonstrate that occupational attainment is a potential causal protective factor for Alzheimer's disease as a proxy marker of cognitive reserve.
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Comprehensive characterization of distinct genetic alterations in metastatic breast cancer across various metastatic sites. NPJ Breast Cancer 2021; 7:93. [PMID: 34272397 PMCID: PMC8285498 DOI: 10.1038/s41523-021-00303-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 06/25/2021] [Indexed: 12/23/2022] Open
Abstract
Metastasis is the major cause of death in breast cancer patients. Although previous large-scale analyses have identified frequently altered genes specific to metastatic breast cancer (MBC) compared with those in primary breast cancer (PBC), metastatic site-specific altered genes in MBC remain largely uncharacterized. Moreover, large-scale analyses are required owing to the low expected frequency of such alterations, likely caused by tumor heterogeneity and late dissemination of breast cancer. To clarify MBC-specific genetic alterations, we integrated publicly available clinical and mutation data of 261 genes, including MBC drivers, from 4268 MBC and 5217 PBC patients from eight different cohorts. We performed meta-analyses and logistic regression analyses to identify MBC-enriched genetic alterations relative to those in PBC across 15 different metastatic site sets. We identified 11 genes that were more frequently altered in MBC samples from pan-metastatic sites, including four genes (SMARCA4, TSC2, ATRX, and AURKA) which were not identified previously. ARID2 mutations were enriched in treatment-naïve de novo and post-treatment MBC samples, compared with that in treatment-naïve PBC samples. In metastatic site-specific analyses, associations of ESR1 with liver metastasis and RICTOR with bone metastasis were significant, regardless of intrinsic subtypes. Among the 15 metastatic site sets, ESR1 mutations were enriched in the liver and depleted in the lymph nodes, whereas TP53 mutations showed an opposite trend. Seven potential MBC driver mutations showed similar preferential enrichment in specific metastatic sites. This large-scale study identified new MBC genetic alterations according to various metastatic sites and highlights their potential role in breast cancer organotropism.
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MRI Features May Predict Molecular Features of Glioblastoma in Isocitrate Dehydrogenase Wild-Type Lower-Grade Gliomas. AJNR Am J Neuroradiol 2021; 42:448-456. [PMID: 33509914 DOI: 10.3174/ajnr.a6983] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND PURPOSE Isocitrate dehydrogenase (IDH) wild-type lower-grade gliomas (histologic grades II and III) with epidermal growth factor receptor (EGFR) amplification or telomerase reverse transcriptase (TERT) promoter mutation are reported to behave similar to glioblastoma. We aimed to evaluate whether MR imaging features could identify a subset of IDH wild-type lower-grade gliomas that carry molecular features of glioblastoma. MATERIALS AND METHODS In this multi-institutional retrospective study, pathologically confirmed IDH wild-type lower-grade gliomas from 2 tertiary institutions and The Cancer Genome Atlas constituted the training set (institution 1 and The Cancer Genome Atlas, 64 patients) and the independent test set (institution 2, 57 patients). Preoperative MRIs were analyzed using the Visually AcceSAble Rembrandt Images and radiomics. The molecular glioblastoma status was determined on the basis of the presence of EGFR amplification and TERT promoter mutation. Molecular glioblastoma was present in 73.4% and 56.1% in the training and test sets, respectively. Models using clinical, Visually AcceSAble Rembrandt Images, and radiomic features were built to predict the molecular glioblastoma status in the training set; then they were validated in the test set. RESULTS In the test set, a model using both Visually AcceSAble Rembrandt Images and radiomic features showed superior predictive performance (area under the curve = 0.854) than that with only clinical features or Visually AcceSAble Rembrandt Images (areas under the curve = 0.514 and 0.648, respectively; P < . 001, both). When both Visually AcceSAble Rembrandt Images and radiomics were added to clinical features, the predictive performance significantly increased (areas under the curve = 0.514 versus 0.863, P < .001). CONCLUSIONS MR imaging features integrated with machine learning classifiers may predict a subset of IDH wild-type lower-grade gliomas that carry molecular features of glioblastoma.
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Involvement of the Olfactory Apparatus by Gliomas. AJNR Am J Neuroradiol 2020; 41:712-717. [PMID: 32165363 DOI: 10.3174/ajnr.a6471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/25/2020] [Indexed: 12/16/2022]
Abstract
The olfactory bulbs and tracts are central nervous system white matter tracts maintained by central neuroglia. Although rare, gliomas can originate from and progress to involve the olfactory apparatus. Through a Health Insurance Portability and Accountability Act-compliant retrospective review of the institutional teaching files and brain MR imaging reports spanning 10 years, we identified 12 cases of gliomas involving the olfactory bulbs and tracts, including 6 cases of glioblastoma, 2 cases of anaplastic oligodendroglioma, and 1 case each of pilocytic astrocytoma, diffuse (grade II) astrocytoma, anaplastic astrocytoma (grade III), and diffuse midline glioma. All except the pilocytic astrocytoma occurred in patients with known primary glial tumors elsewhere. Imaging findings of olfactory tumor involvement ranged from well-demarcated enhancing masses to ill-defined enhancing infiltrative lesions to nonenhancing masslike FLAIR signal abnormality within the olfactory tracts. Familiarity with the imaging findings of glioma involvement of the olfactory nerves is important for timely diagnosis and treatment of recurrent gliomas and to distinguish them from other disease processes.
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Diffusion Characteristics of Pediatric Diffuse Midline Gliomas with Histone H3-K27M Mutation Using Apparent Diffusion Coefficient Histogram Analysis. AJNR Am J Neuroradiol 2019; 40:1804-1810. [PMID: 31694820 DOI: 10.3174/ajnr.a6302] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 08/31/2019] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Diffuse midline gliomas with histone H3 K27M mutation are biologically aggressive tumors with poor prognosis defined as a new diagnostic entity in the 2016 World Health Organization Classification of Tumors of the Central Nervous System. There are no qualitative imaging differences (enhancement, border, or central necrosis) between histone H3 wildtype and H3 K27M-mutant diffuse midline gliomas. Herein, we evaluated the utility of diffusion-weighted imaging to distinguish H3 K27M-mutant from histone H3 wildtype diffuse midline gliomas. MATERIALS AND METHODS We identified 31 pediatric patients (younger than 21 years of age) with diffuse gliomas centered in midline structures that had undergone assessment for histone H3 K27M mutation. We measured ADC within these tumors using a voxel-based 3D whole-tumor measurement method. RESULTS Our cohort included 18 infratentorial and 13 supratentorial diffuse gliomas centered in midline structures. Twenty-three (74%) tumors carried H3-K27M mutations. There was no difference in ADC histogram parameters (mean, median, minimum, maximum, percentiles) between mutant and wild-type tumors. Subgroup analysis based on tumor location also did not identify a difference in histogram descriptive statistics. Patients who survived <1 year after diagnosis had lower median ADC (1.10 × 10-3mm2/s; 95% CI, 0.90-1.30) compared with patients who survived >1 year (1.46 × 10-3mm2/s; 95% CI, 1.19-1.67; P < .06). Average ADC values for diffuse midline gliomas were 1.28 × 10-3mm2/s (95% CI, 1.21-1.34) and 0.86 × 10-3mm2/s (95% CI, 0.69-1.01) for hemispheric glioblastomas with P < .05. CONCLUSIONS Although no statistically significant difference in diffusion characteristics was found between H3-K27M mutant and H3 wildtype diffuse midline gliomas, lower diffusivity corresponds to a lower survival rate at 1 year after diagnosis. These findings can have an impact on the anticipated clinical course for this patient population and offer providers and families guidance on clinical outcomes.
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A framework for automated conflict detection and resolution in medical guidelines. SCIENCE OF COMPUTER PROGRAMMING 2019; 182:42-63. [PMID: 32029957 PMCID: PMC6993806 DOI: 10.1016/j.scico.2019.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/09/2019] [Accepted: 07/01/2019] [Indexed: 05/30/2023]
Abstract
Common chronic conditions are routinely treated following standardised procedures known as clinical guidelines. For patients suffering from two or more chronic conditions, known as multimorbidity, several guidelines have to be applied simultaneously, which may lead to severe adverse effects when the combined recommendations and prescribed medications are inconsistent or incomplete. This paper presents an automated formal framework to detect, highlight and resolve conflicts in the treatments used for patients with multimorbidities focusing on medications. The presented extended framework has a front-end which takes guidelines captured in a standard modelling language and returns the visualisation of the detected conflicts as well as suggested alternative treatments. Internally, the guidelines are transformed into formal models capturing the possible unfoldings of the guidelines. The back-end takes the formal models associated with multiple guidelines and checks their correctness with a theorem prover, and inherent inconsistencies with a constraint solver. Key to our approach is the use of an optimising constraint solver which enables us to search for the best solution that resolves/minimises conflicts according to medication efficacy and the degree of severity in case of harmful combinations, also taking into account their temporal overlapping. The approach is illustrated throughout with a real medical example.
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Heritability estimates of individual psychological distress symptoms from genetic variation. J Affect Disord 2019; 252:413-420. [PMID: 31003110 DOI: 10.1016/j.jad.2019.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 02/16/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Psychological distress symptoms are associated with an increased risk of psychiatric disorders and medical illness. Although psychological distress is influenced by environmental factors, such as socioeconomic status, lifetime events, or interpersonal relationships, substantial interindividual variation also exists. However, heritability and genetic determinants of distress are poorly understood. METHODS In the Korean Genome and Epidemiology Study sample (n = 12,680), we estimated the heritability of individual psychological distress symptoms using the GCTA-REML method and carried out a genome-wide association study of individual psychological distress symptoms showing significant heritability. RESULTS We found three psychological distress items showing significant heritability: subjective well-being (9%), fatigue and appetite (11%), and enjoying daily life (8%). Additionally, we found genome-wide significant associations of rs6735649 located between STEAP3 and C1QL2 on chromosome 2 with subjective well-being (P = 1.32 × 10-8, odds ratio [OR] = 1.18, 95% confidence interval [CI]: 1.12-1.25) and rs35543418 located between SYT16 and KCNH5 on chromosome 14 with enjoying daily life (P = 1.33 × 10-8, OR = 1.59, 95% CI: 1.35-1.86). LIMITATIONS The lack of replication in independent cohorts and longitudinal assessment of distress may limit generalizability. CONCLUSIONS Our results indicate that distress symptoms are partly heritable. Further analysis in larger cohorts investigating gene-environment interactions is required to identify genetic variants that explain the proportion of variation in distress.
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Point-of-Care Local Failure and Overall Survival Prediction Models for Meningioma. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas. AJNR Am J Neuroradiol 2018; 39:1201-1207. [PMID: 29748206 DOI: 10.3174/ajnr.a5667] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/20/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND PURPOSE The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation. MATERIALS AND METHODS MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify isocitrate dehydrogenase 1 (IDH1) mutation status, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase (MGMT) promotor methylation status. Principal component analysis of the final convolutional neural network layer was used to extract the key imaging features critical for successful classification. RESULTS Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. Each genetic category was also associated with distinctive imaging features such as definition of tumor margins, T1 and FLAIR suppression, extent of edema, extent of necrosis, and textural features. CONCLUSIONS Our results indicate that for The Cancer Imaging Archives dataset, machine-learning approaches allow classification of individual genetic mutations of both low- and high-grade gliomas. We show that relevant MR imaging features acquired from an added dimensionality-reduction technique demonstrate that neural networks are capable of learning key imaging components without prior feature selection or human-directed training.
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Sex-related demographic and symptomatologic characteristics of patients with fibromyalgia. Ann Phys Rehabil Med 2018. [DOI: 10.1016/j.rehab.2018.05.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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338 Necrobiosis lipoidica comorbidities and complications. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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1036 Necrobiosis lipoidica histopathology & inflammatory composition. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.1048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Differentiation of brain tumor-related edema based on 3D T1rho imaging. Eur J Radiol 2017; 91:88-92. [PMID: 28629576 PMCID: PMC5563444 DOI: 10.1016/j.ejrad.2017.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/22/2017] [Accepted: 03/28/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND AND PURPOSE Cerebral edema associated with brain tumors is an important source of morbidity. Its type depends largely on the capillary ultra-structures of the histopathologic subtype of underlying brain tumor. The purpose of our study was to differentiate vasogenic edema associated with brain metastases and infiltrative edema related to diffuse gliomas using quantitative 3D T1 rho (T1ρ) imaging. MATERIALS AND METHODS Preoperative MR examination including whole brain 3D T1ρ imaging was performed in 23 patients with newly diagnosed brain tumors (9 with metastasis, 8 with lower grade glioma, LGG, 6 with glioblastoma, GBM). Mean T1ρ values were measured in regions of peritumoral non-enhancing T2 signal hyperintensity, excluding both enhancing and necrotic or cystic component, and normal-appearing white matter. RESULTS Mean T1ρ values were significantly elevated in the vasogenic edema surrounding intracranial metastases when compared to the infiltrative edema associated with either LGG or GBM (p=0.02 and <0.01, respectively). No significant difference was noted between T1ρ values of infiltrative edema between LGG and GBM (p=0.84 and 0.96, respectively). CONCLUSION Our study demonstrates the feasibility and potential diagnostic role of T1ρ in the quantitative differentiation between edema related to intracranial metastases and gliomas and as a potentially complementary tool to standard MR techniques in further characterizing pathophysiology of vasogenic and infiltrative edema.
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Angiogenic effects of 3 dimensional cell culture system. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Cellular aging and senescence characteristics of mesenchymal stem cells. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Application of hydrogel scaffolds on 3d culture of adipose tissue-derived mesenchymal stem cells. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Proliferating effects of soy peptide on mesenchymal stem cells. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Effects of long-term cryopreservation in stem cell stability. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cell protectant of clinical grade for cell delivery without cryopreservation. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Imaging Characteristics of Pediatric Diffuse Midline Gliomas with Histone H3 K27M Mutation. AJNR Am J Neuroradiol 2017; 38:795-800. [PMID: 28183840 DOI: 10.3174/ajnr.a5076] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/06/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND PURPOSE The 2016 World Health Organization Classification of Tumors of the Central Nervous System includes "diffuse midline glioma with histone H3 K27M mutation" as a new diagnostic entity. We describe the MR imaging characteristics of this new tumor entity in pediatric patients. MATERIALS AND METHODS We retrospectively reviewed imaging features of pediatric patients with midline gliomas with or without the histone H3 K27 mutation. We evaluated the imaging features of these tumors on the basis of location, enhancement pattern, and necrosis. RESULTS Among 33 patients with diffuse midline gliomas, histone H3 K27M mutation was present in 24 patients (72.7%) and absent in 9 (27.3%). Of the tumors, 27.3% (n = 9) were located in the thalamus; 42.4% (n = 14), in the pons; 15% (n = 5), within the vermis/fourth ventricle; and 6% (n = 2), in the spinal cord. The radiographic features of diffuse midline gliomas with histone H3 K27M mutation were highly variable, ranging from expansile masses without enhancement or necrosis with large areas of surrounding infiltrative growth to peripherally enhancing masses with central necrosis with significant mass effect but little surrounding T2/FLAIR hyperintensity. When we compared diffuse midline gliomas on the basis of the presence or absence of histone H3 K27M mutation, there was no significant correlation between enhancement or border characteristics, infiltrative appearance, or presence of edema. CONCLUSIONS We describe, for the first time, the MR imaging features of pediatric diffuse midline gliomas with histone H3 K27M mutation. Similar to the heterogeneous histologic features among these tumors, they also have a diverse imaging appearance without distinguishing features from histone H3 wildtype diffuse gliomas.
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P569Diastolic dyssynchrony is associated with exercise intolerance in hypertensive patients with left ventricular hypertrophyP570Echocardiographic pattern of acute pulmonary embolism, analysis of consecutive 511 patientsP571Clinical significance of ventricular interdependence and left ventricular function in patients with pulmonary hypertension receiving specific vasodilator therapyP572Haemodynamic characteristics and ventricular mechanics in post-capillary and combined pre- and post-capillary pulmonary hypertensionP573Relationship between hematological response and echocardiographic features in patients with light chains systemic amyloidosisP574Myocardial changes in patients with anorexia nervosaP575Giant cell arteritis presenting as fever of unknown origin: role of clinical history, early positron emission tomography and ultrasound screeningP576Subclinical systolic dysfunction in systemic sclerosis is not influenced by standard rheumatologic therapy - a 4D echocardiographic studyP577Cardiac index correlates with the degree of hepatic steathosis in obese patients with obstructive sleep apneaP578Myocardial mechanics in top-level endurance athletes: a three-dimensional speckle tracking studyP579The athlete heart: what happens to myocardial deformation in physiological adaptation to sportsP580Association between left ventricle intrinsic function and urine protein-creatinine ratio in preeclampsia before and after deliveryP581Dilatation of the aorta in children with bicuspid aortic valveP582Cardiovascular functional abnormalities in patients with osteogenesis imperfectaP583Dobutamine stress test fast protocol: diagnostic accuracy and securityP584Prognostic value of non-positive exercise echocardiography in the patients submitted to percutaneous coronary interventionP585The use of myocardial strain imaging in the detection of coronary artery disease during stress echocardiographyP586Preserved O2 extraction exercise response in heart failure patients with chronotropic insufficiency: evidence for a central cardiac rather than peripheral oxygen uptake limitationP587Major determinant of O2 artero-venous difference at peak exercise in heart failure and healthy subjectsP588Stress echocardiography with contrast perfusion analysis for a more sensitive test for ischemic heart diseaseP589Assessment of mitral annular physiology in myxomatous mitral disease with 3D transesophageal echocardiography: comparison between early severe mitral regurgitation and decompensated groupP590Three-dimensional transesophageal echocardiographic assessment of the mitral valve geometry in patients with mild, moderate and severe chronic ischemic mitral regurgitationP591Left atrial appendage closure. Multimodality imaging in device size selectionP592Contributions of three-dimensional transesophageal echocardiography in the evaluation of aortic atherosclerotic plaquesP593Agitated blood-saline is superior to agitated air-saline for echocardiographic shunt studies. Eur Heart J Cardiovasc Imaging 2016; 17:ii102-ii109. [DOI: 10.1093/ehjci/jew248.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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52 Physician-level Differences in Emergency Department Length of Stay. Ann Emerg Med 2016. [DOI: 10.1016/j.annemergmed.2016.08.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Clinical application of genomic profiling to find druggable targets for adolescent and young adult (AYA) cancer patients with metastasis. BMC Cancer 2016; 16:170. [PMID: 26925973 PMCID: PMC4772349 DOI: 10.1186/s12885-016-2209-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 02/20/2016] [Indexed: 11/26/2022] Open
Abstract
Background Although adolescent and young adult (AYA) cancers are characterized by biological features and clinical outcomes distinct from those of other age groups, the molecular profile of AYA cancers has not been well defined. In this study, we analyzed cancer genomes from rare types of metastatic AYA cancers to identify driving and/or druggable genetic alterations. Methods Prospectively collected AYA tumor samples from seven different patients were analyzed using three different genomics platforms (whole-exome sequencing, whole-transcriptome sequencing or OncoScan™). Using well-known bioinformatics tools (bwa, Picard, GATK, MuTect, and Somatic Indel Detector) and our annotation approach with open access databases (DAVID and DGIdb), we processed sequencing data and identified driving genetic alterations and their druggability. Results The mutation frequencies of AYA cancers were lower than those of other adult cancers (median = 0.56), except for a germ cell tumor with hypermutation. We identified patient-specific genetic alterations in candidate driving genes: RASA2 and NF1 (prostate cancer), TP53 and CDKN2C (olfactory neuroblastoma), FAT1, NOTCH1, and SMAD4 (head and neck cancer), KRAS (urachal carcinoma), EML4-ALK (lung cancer), and MDM2 and PTEN (liposarcoma). We then suggested potential drugs for each patient according to his or her altered genes and related pathways. By comparing candidate driving genes between AYA cancers and those from all age groups for the same type of cancer, we identified different driving genes in prostate cancer and a germ cell tumor in AYAs compared with all age groups, whereas three common alterations (TP53, FAT1, and NOTCH1) in head and neck cancer were identified in both groups. Conclusion We identified the patient-specific genetic alterations and druggability of seven rare types of AYA cancers using three genomics platforms. Additionally, genetic alterations in cancers from AYA and those from all age groups varied by cancer type. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2209-1) contains supplementary material, which is available to authorized users.
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The Combined Performance of ADC, CSF CXC Chemokine Ligand 13, and CSF Interleukin 10 in the Diagnosis of Central Nervous System Lymphoma. AJNR Am J Neuroradiol 2016; 37:74-9. [PMID: 26381553 DOI: 10.3174/ajnr.a4450] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/12/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE CXC chemokine ligand 13 and interleukin 10 have emerged as CSF biomarkers for the diagnosis of CNS lymphoma. Our hypothesis is that the combined use of ADC, CXC chemokine ligand 13, and interleukin 10 will result in increased diagnostic performance compared with the use of ADC values alone. MATERIALS AND METHODS Eighty-seven patients were included in this study, including 43 with CNS lymphoma and 44 without CNS lymphoma (21 metastases, 14 high-grade gliomas, 9 tumefactive demyelinating lesions) who had undergone CSF proteomic analysis and had a new enhancing mass on brain MR imaging. Average ADC was derived by contouring the contrast-enhancing tumor volume. Group means were compared via t tests for average ADC, CXC chemokine ligand 13, and interleukin 10. Receiver operating characteristic analysis was performed for each individual variable. Multiple-variable logistic regression with receiver operating characteristic analysis was performed, and the multiple-variable receiver operating characteristic was compared with single-variable receiver operating characteristics. RESULTS The average ADC was lower and CSF CXC chemokine ligand 13 and interleukin 10 values were higher in CNS lymphoma (P < .001). Areas under the curve ranged from 0.739 to 0.832 for single-variable ROC. Multiple-variable logistic regression yielded statistically significant individual effects for all 3 variables in a combined model. Multiple-variable receiver operating characteristics (area under the curve, 0.928) demonstrated statistically significantly superior diagnostic performance compared with the use of single variables alone. CONCLUSIONS The combined use of ADC, CSF CXC chemokine ligand 13, and interleukin 10 results in increased diagnostic performance for the diagnosis of CNS lymphoma. This finding highlights the importance of CSF analysis when the diagnosis of CNS lymphoma is considered on the basis of MR imaging.
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Pro-angiogenic cellular and genomic expression patterns within glioblastoma influences dynamic susceptibility weighted perfusion MRI. Clin Radiol 2015; 70:1087-95. [DOI: 10.1016/j.crad.2015.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 11/19/2014] [Accepted: 03/19/2015] [Indexed: 12/15/2022]
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Abstract 75: Patient-specific genomic profiling for advanced cancers in young adults. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: Large-scale cancer genome analyses have uncovered the genetic landscape of common cancers. However, rate tumor types in adolescent, young adult (AYA) have not been well-characterized genetically. We performed a pilot study of patient-specific cancer genome analysis to know whether we can analyze individual cancer genome without the existing large-scale genomics data of same tumor types in advanced and rare AYA tumors.
Methods: The patients were prospectively enrolled from a medical oncology clinic in a university hospital. Tissue samples of the study patients were acquired from the fresh tissue, formalin-fixed paraffin-embedded (FFPE) tissue and cancer cells from pleural effusion as well. Cancer genome data was acquired using massive parallel sequencing technique from seven AYA patients with advanced solid tumors. WES and WTS data were generated from 6 tumors with matched normal and 4 tumors, respectively. Somatic alterations of cancer genome were classified with 2 distinct categories with heuristic ways and level 1 to 3 depends on differences of genetic alterations based on clinical and biological relevance, and mutation context.
Results: Each different tumor types of 7 study patients were as follows; atypical prostate cancer (AYA01, 30 years old), olfactory neuroblastoma (AYA02, 30 years old), tongue cancer (AYA04, 33 years old), urachal carcinoma (AYA06, 32 years old), germ cell tumor (AYA07, 21 years old), lung cancer (AYA09, 34 years old) and liposarcoma (AYA10, 33 years old). Patients with GCT and tongue cancer had higher mutation rate based on WES data; 476 and 97 non-synonymous somatic nucleotide variations respectively. However, there were only 13∼16 non-synonymous somatic nucleotide variations and 7∼18 indel somatic variations in patients with other four cancers. We identified one level-1 (strong) oncogenic alterations and eight level-1 tumor suppressor alterations as well as 19 level-2 (moderate) and level-3 (modest) alterations were found from 5 WES data (we excluded 1 hypermutated germ cell tumor sample). Some level-1/2 alterations were considered as targetable by developed or developing drugs. Each tumor was characterized by tumor-unique manner. AYA01 was characterized with concurrent tumor suppressor alterations of RasGAP family genes (NF1 and RASA2), AYA02 with chromosome-level copy number alteration and CDKN2C stopgain mutation, AYA04 with concurrent oncogenic (AMER3) and tumor suppressor (FAT1, LGR6, MSX1) alterations of Wnt signaling, AYA06 with KRAS mutation and AYA09 with a fusion of EML4-ALK.
Conclusion: Our study showed that we can characterize rare AYA tumors with WES or WTS data without pre-existing large-scale genomics data of same tumor types, although there are much hurdles in identifying major driver and/or druggable genetic alterations.
Citation Format: Soojin Cha, Jeongeun Lee, Jong-Yeon Shin, Ji-Yeon Kim, Jong-Il Kim, Se-Hoon Lee. Patient-specific genomic profiling for advanced cancers in young adults. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 75. doi:10.1158/1538-7445.AM2015-75
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Abstract 2994: Clinical applications of comprehensive genome analysis of papillary renal cell carcinoma, type II. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose
Papillary renal cell carcinoma (PRCC) is the most common type of non-clear cell renal cell carcinoma (NCCRCC). Of PRCC, PRCC,type2(PRCC2) is known to have highly aggressiveness and relative drug resistance. In contrast of clear cell renal cell carcinoma (CCRCC), we poorly understand genetic alterations to drive PRCC2. Moreover, though many tyrosine kinase inhibitors (TKIs) are now available to treat PRCC, the predictive marker of TKIs is not in existence. Therefore, we aimed to analyze genetic alteration of PRCC2.
Patients and Methods
We performed whole-exome sequencing (WES) of DNA from 9 PRCC2 samples and matched normal tissue. In addition, whole-transcriptome sequencing (WTS) was conducted for 7 of these samples. We analyzed somatic mutations, copy number alterations, germ line mutations using WES data, pathway alterations and gene fusions through RNA expression data. We investigated the relationship between clinical prognosis and genetic alterations.
Results
Of nine samples, average non-silent mutation rate is 1.13 mutations per Mb (range, 0.49 to 2.14 mutations per Mbs). Forty-seven somatic mutations including SRRD(four), PKD1L2(three) and MX1(three) are discovered in more than 2 specimens. The genes associated to histone modification and ubiqutination are frequently altered. We found FH somatic mutation, a potent target of VEGFR TKI, in young female PRCC2 patient. Her tumor is extremely shrunk after 6cycles treatment and after that she received pazopanib for 52weeks maintaining effective response.
Conclusion
We suggest the possibility of translational research from sequencing data to real medical treatment of PRCC2. This pivotal study demonstrates that novel somatic FH mutation is the therapeutic target of VEGFR TKI. Therefore, further large scaled comprehensive genetic analysis of PRCC2 is required to propose personalized medicine for conquering papillary renal cell carcinoma, type 2.
Note: This abstract was not presented at the meeting.
Citation Format: Ji-Yeon Kim, Se-Hoon Lee, Soojin Cha, Kyung Chul Moon, Jong-Il Kim, Dae Seog Heo. Clinical applications of comprehensive genome analysis of papillary renal cell carcinoma, type II. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2994. doi:10.1158/1538-7445.AM2015-2994
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Direct Cranial Nerve Involvement by Gliomas: Case Series and Review of the Literature. AJNR Am J Neuroradiol 2015; 36:1349-54. [PMID: 25857757 DOI: 10.3174/ajnr.a4287] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/17/2014] [Indexed: 11/07/2022]
Abstract
Malignant gliomas are characterized by infiltrative growth of tumor cells, including along white matter tracts. This may result in clinical cranial neuropathy due to direct involvement of a cranial nerve rather than by leptomeningeal spread along cranial nerves. Gliomas directly involving cranial nerves III-XII are rare, with only 11 cases reported in the literature before 2014, including 8 with imaging. We present 8 additional cases demonstrating direct infiltration of a cranial nerve by a glioma. Asymmetric cisternal nerve expansion compared with the contralateral nerve was noted with a mean length of involvement of 9.4 mm. Based on our case series, the key imaging feature for recognizing direct cranial nerve involvement by a glioma is the detection of an intra-axial mass in the pons or midbrain that is directly associated with expansion, signal abnormality, and/or enhancement of the adjacent cranial nerves.
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GE-42 * INTEGRATED RADIOGRAPHIC AND PHYLOGENETIC CASE STUDY OF A PRIMARY AND CONTRALATERAL RECURRENT GLIOMA. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou256.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Acetylation changes at lysine 5 of histone H4 associated with lytic gene promoters during reactivation of Kaposi's sarcoma-associated herpesvirus. Acta Virol 2014; 58:282-6. [PMID: 25283865 DOI: 10.4149/av_2014_03_282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a pathogenic agent of Kaposi's sarcoma, primary effusion lymphoma and multicentric Castleman's disease in humans. Similarly to other gammaherpesviruses such as Epstein-Barr virus (EBV) and herpesvirus saimiri (HVS), KSHV displays two alternative life cycles, latent and lytic one. The transactivation from latency to the lytic phase is the result of transcriptional changes in the KSHV genome caused by the replication and transcriptional activator (RTA). During KSHV reactivation, epigenetic modifications of histone protein on the viral genome occur, which regulate the transcriptional activation of a number of lytic genes. The reactivation of EBV from latency to lytic cycle, induced by an immediate-early Zta protein, was shown to be accompanied by acetylation of specific lysines in histone H4. Accordingly, we hypothesized that the RTA-induced transactivation of KSHV could also be accompanied by histone acetylation. To validate this hypothesis, we assayed alterations of acetyl-histone H4-lysine 5 (acH4K5) during the RTA-mediated KSHV reactivation. While the modified histone protein in a total cell lysate was not distinguished between control and RTA-expressed cells, upregulated acH4K5 was detected on several lytic gene promoter regions during KSHV reactivation. Our results clearly indicate that this epigenetic change is related to transcription of genes expressed in the lytic cycle of KSHV.
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IMAGING BIOMARKERS OF MALIGNANT PROGRESSION OF DIFFUSE LOW-GRADE GLOMA (LGG). Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou206.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Application of cancer genomics to solve unmet clinical needs. Genomics Inform 2013; 11:174-9. [PMID: 24465227 PMCID: PMC3897843 DOI: 10.5808/gi.2013.11.4.174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 12/12/2022] Open
Abstract
The large amount of data on cancer genome research has contributed to our understanding of cancer biology. Indeed, the genomics approach has a strong advantage for analyzing multi-factorial and complicated problems, such as cancer. It is time to think about the actual usage of cancer genomics in the clinical field. The clinical cancer field has lots of unmet needs in the management of cancer patients, which has been defined in the pre-genomic era. Unmet clinical needs are not well known to bioinformaticians and even non-clinician cancer scientists. A personalized approach in the clinical field will bring potential additional challenges to cancer genomics, because most data to now have been population-based rather than individual-based. We can maximize the use of cancer genomics in the clinical field if cancer scientists, bioinformaticians, and clinicians think and work together in solving unmet clinical needs. In this review, we present one imaginary case of a cancer patient, with which we can think about unmet clinical needs to solve with cancer genomics in the diagnosis, prediction of prognosis, monitoring the status of cancer, and personalized treatment decision.
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RADIOBIOLOGY. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Primary care hospitalization risk score is associated with coronary revascularization in older adults. Eur Geriatr Med 2013. [DOI: 10.1016/j.eurger.2013.07.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Geriatric syndromes as predictors of one-year mortality in an outpatient practice. Eur Geriatr Med 2013. [DOI: 10.1016/j.eurger.2013.07.634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Can longitudinal strain by 2 dimensional speckle tracking echocardiography provide diagnostic and prognostic value in immunoglobulin light chain and hereditary transthyretin cardiac amyloidosis? Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht308.p1192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
We report a very rare case of isolated multiple pulmonary arterial calcification with severe bilateral peripheral pulmonary arterial stenosis diagnosed in utero. Despite treatment with bisphosphonate for 6 months, systolic right ventricular pressure increased persistently and surpassed left ventricular pressure. After successful bilateral pulmonary arterioplasty at 13 months of age, the patient showed decreased systolic right ventricular pressure with normal interventricular septal configuration. This is the first case report for an isolated pulmonary artery calcification without other arterial calcification proven by non-contrast computed tomography of a living patient.
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Super-resolution track density imaging of glioblastoma: histopathologic correlation. AJNR Am J Neuroradiol 2013; 34:1319-25. [PMID: 23413250 DOI: 10.3174/ajnr.a3400] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND PURPOSE Super-resolution track density imaging generates anatomic images with submillimeter voxel resolution by using high-angular-resolution diffusion imaging and fiber-tractography. TDI within the diseased human brain has not been previously described. The purpose of this study was to correlate TDI with histopathologic features of GBM. MATERIALS AND METHODS A total of 43 tumor specimens (24 contrast-enhancing, 12 NE, and 7 centrally necrotic regions) were collected from 18 patients with treatment-naïve GBM by use of MR imaging-guided neurosurgical techniques. Immunohistochemical stains were used to evaluate the following histopathologic features: hypoxia, architectural disruption, microvascular hyperplasia, and cellular proliferation. We reconstructed track density maps at a 0.25-mm isotropic spatial resolution by using probabilistic streamline tractography combined with constrained spheric deconvolution (model order, 8; 0.1-mm step size; 1 million seed points). Track density values were obtained from each tissue site. A P value of .05 was considered significant and was adjusted for multiple comparisons by use of the false discovery rate method. RESULTS Track density was not significantly different between contrast-enhancing and NE regions but was more likely to be elevated within regions demonstrating aggressive histopathologic features (P < .05). Significant correlation between relative track density and hypoxia (odds ratio, 3.52; P = .01), architectural disruption (odds ratio, 3.49; P = .03), and cellular proliferation (odds ratio, 1.70; P = .05) was observed irrespective of the presence or absence of contrast enhancement. CONCLUSIONS Numeric values of track density correlate with GBM biologic features and may be clinically useful for identification of regions of tumor infiltration within both enhancing and NE components of GBM.
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Combined diffusion and perfusion MR imaging as biomarkers of prognosis in immunocompetent patients with primary central nervous system lymphoma. AJNR Am J Neuroradiol 2013; 34:35-40. [PMID: 22936096 DOI: 10.3174/ajnr.a3165] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND AND PURPOSE ADC derived from DWI has been shown to correlate with PFS and OS in immunocompetent patients with PCNSL. The purpose of our study was to confirm the validity of ADC measurements as a prognostic biomarker and to determine whether rCBV measurements derived from DSC perfusion MR imaging provide prognostic information. MATERIALS AND METHODS Pretherapy baseline DWI and DSC perfusion MR imaging in 25 patients with PCNSL was analyzed before methotrexate-based induction chemotherapy. Contrast-enhancing tumor was segmented and coregistered with ADC and rCBV maps, and mean and minimum values were measured. Patients were separated into high or low ADC groups on the basis of previously published threshold values of ADC(min) < 384 × 10(-6) mm(2)/s. High and low rCBV groups were defined on the basis of receiver operating curve analysis. High and low ADC and rCBV groups were analyzed independently and in combination. Multivariate Cox survival analysis was performed. RESULTS Patients with ADC(min) values < 384 × 10(-6) mm(2)/s or rCBV(mean) values < 1.43 had worse PFS and OS. The patient cohort with combined low ADC(min)-low rCBV(mean) had the worst prognosis. No other variables besides ADC and rCBV significantly affected survival. CONCLUSIONS Our study reinforces the validity of ADC values as a prognostic biomarker and provides the first evidence of low tumor rCBV as a novel risk factor for adverse prognosis in immunocompetent patients with PCNSL.
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