More than 25% of patients with AML carry no mutations in genes known to be associated with leukemia. Analyses of genomes, transcriptomes, and methylomes of AML samples implicate mutations in ...cytogenetically normal AML and provide insight into the relationships among causative genes.
The molecular pathogenesis of acute myeloid leukemia (AML) has been studied with the use of cytogenetic analysis for more than three decades. Recurrent chromosomal structural variations are well established as diagnostic and prognostic markers, suggesting that acquired genetic abnormalities (i.e., somatic mutations) have an essential role in pathogenesis.
1
,
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However, nearly 50% of AML samples have a normal karyotype, and many of these genomes lack structural abnormalities, even when assessed with high-density comparative genomic hybridization or single-nucleotide polymorphism (SNP) arrays
3
–
5
(see Glossary). Targeted sequencing has identified recurrent mutations in
FLT3, NPM1, KIT, CEBPA,
and
TET2
.
6
–
8
Massively parallel . . .
Abstract
A major hurdle for targeted cancer therapies is the development of resistance, with many agents showing promising initial results but not providing significant overall survival benefits. To ...address resistance we need to know the genetic and epigenetic alterations that drive resistance. This knowledge will contribute to modified treatment protocols, new targets, and predictive biomarkers. We are working on a system to model evolution of tumor resistance in a the patient-derived xenograft (PDX) mouse system. Compared to xenografts, PDXs are closer to the tumor biology of the patient, having a higher degree of molecular subtypes and intratumor heterogeneity, and a mixture of human and mouse stroma. In this study, we implanted 1-3mm chunks from a primary colorectal cancer tumor carrying the BRAF V600>E mutation into immunosuppressed NOD/SCID CB.17 mice. Once the tumors were established (100-150mmˆ3 tumor burden), the mice were stratified into two groups, control and fed chow containing the BRAF inhibitor PLX4720, 417 mg/kg (Scientific Diets). The tumors in most of the PDXs in the group fed PLX4720 chow regressed and became very small by day 77. In several cases PDXs that were allowed to develop beyond day 77 became resistant to PLX4720 treatment.
To identify mechanisms of PLX4720 resistance we sequenced DNA and RNA from two resistant PDXs, one untreated control PDX, and a sample of the original patient tumor. We used the Ion AmpliSeq Comprehensive Cancer Panel from Life Technologies to sequence exons from 409 cancer related genes on the Ion Torrent PGM. Additionally, we performed SOLiD 5500 paired-end (50x25 nt) next generation sequencing (NGS) of the whole transcriptome of these samples. Since the stromal component of the PDXs is a mixture of cells of human and mouse origin, and sequence reads of mouse origin could contribute to false positive mutation calls or skew expression analysis of the resistant data, we needed to develop a method for filtering mouse reads out of our sequencing data. To this end, we have developed and applied a read filtering protocol that sorts reads that align to the human genome into three groups, better in human, better in mouse, or ambiguous. 97.7% of the reads from human tissue were defined as better in human with the remaining 2.3% being ambiguous, or better in mouse. PDX derived reads had between 8% and 13% of reads being better in mouse. Only reads defined as better in human were used for expression analysis and SNP calling in this work. In one of the two resistant tumors analyzed this method has identified a candidate resistance mutation, NRAS G13>D. The NRAS mutation is seen in both the RNA-seq and DNA-seq data, and is not seen in the original patient tumor, the control untreated PDX, or in the second resistant tumor. Based on these findings, we feel that PDX provide a powerful model system for examining the evolution of resistance to targeted agents.
Citation Format: Brian P. James, Robert J. Lemos, Feng Tian, Thomas C. Motter, Amin Momin, Nastaran D. Neishaboori, Galina M. Kiriakova, Scott Kopetz, Garth Powis. Modeling evolution of resistance in patient-derived xenografts: resistance to the BRAF inhibitor PLX4720. abstract. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3233. doi:10.1158/1538-7445.AM2013-3233
Previous studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers display distinct biological and ...clinical features. HPV is known to drive cancer by the actions of the E6 and E7 oncoproteins, but the molecular architecture of HPV infection and its interaction with the host genome in head and neck cancers have not been comprehensively described. We profiled a cohort of 279 head and neck cancers with next generation RNA and DNA sequencing and show that 35 (12.5%) tumors displayed evidence of high-risk HPV types 16, 33, or 35. Twenty-five cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and both inter- and intrachromosomal rearrangements. Many of these events involved genes with documented roles in cancer. Cancers with integrated vs. nonintegrated HPV displayed different patterns of DNA methylation and both human and viral gene expressions. Together, these data provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viral oncogenesis.
Significance A significant proportion of head and neck cancer is driven by human papillomavirus (HPV) infection, and the expression of viral oncogenes is involved in the development of these tumors. However, the role of HPV integration in primary tumors beyond increasing the expression of viral oncoproteins is not understood. Here, we describe how HPV integration impacts the host genome by amplification of oncogenes and disruption of tumor suppressors as well as driving inter- and intrachromosomal rearrangements. Tumors that do and do not have HPV integrants display distinct gene expression profiles and DNA methylation patterns, which further support the view that the mechanisms by which tumors with integrated and nonintegrated HPV arise are distinct.
The first sustained increase in live kidney donation in the United States in 15 years was observed from 2017 to 2019. To help sustain this surge, we studied 35 900 donors (70.3% white, 14.5% ...Hispanic, 9.3% black, 4.4% Asian) to understand the increase in 2017‐2019 vs 2014‐2016 using Poisson regression. Among biologically related donors aged <35, 35‐49, and ≥50 years, the number of donors did not change across race/ethnicity but increased by 38% and 29% for Hispanic and black ≥50. Among unrelated donors <35, 35‐49, and ≥50, white donors increased by 18%, 14%, and 27%; Hispanic donors <35 did not change but increased by 22% and 35% for 35‐49 and ≥50; black donors <35 declined by 23% and did not change for 35‐49 and ≥50; Asian donors did not change. Among kidney paired donors <35, 35‐49, and ≥50, white donors increased by 42%, 50%, and 68%; Hispanic donors <35 and 35‐49 increased by 36% and 55% and did not change for ≥50; black donors did not change; Asian donors <35 did not change but increased by 107% and 82% for 35‐49 and ≥50. The increase in donation was driven predominantly by unrelated and paired white donors. Donation among unrelated black individuals should be promoted.
Unrelated and paired white donors are the principal drivers of the recent surge in live kidney donation in the US, with no substantive increase among unrelated and paired Black donors.
OBJECTIVE: To evaluate cerebrospinal fluid (CSF) levels of amyloid beta protein ending at amino acid 42 (Abeta42) and tau as markers for Alzheimer disease (AD) and to determine whether clinical ...variables influence these levels. DESIGN: Cohort study. SETTING: Six academic research centers with expertise in dementia. SUBJECTS: Eighty-two patients with probable AD, including 24 with very mild dementia (Mini-Mental State Examination score >23/30) (AD group); 60 cognitively normal elderly control subjects (NC group); and 74 subjects with neurological disorders, including dementia (ND group). MAIN OUTCOME MEASURES: Levels of Abeta42 and tau were compared among AD, NC, and ND groups. Relationships of age, sex, Mini-Mental State Examination score, and apolipoprotein E (Apo E) genotype with these levels were examined using multiple linear regression. Classification tree models were developed to optimize distinguishing AD from NC groups. RESULTS: Levels of Abeta42 were significantly lower, and levels of tau were significantly higher, in the AD group than in the NC or ND group. In the AD group, Abeta42 level was inversely associated with Apo E epsilon4 allele dose and weakly related to Mini-Mental State Examination score; tau level was associated with male sex and 1 Apo E epsilon4 allele. Classification tree analysis, comparing the AD and NC subjects, was 90% sensitive and 80% specific. With specificity set at greater than 90%, the tree was 77% sensitive for AD. This tree classified 26 of 74 members of the ND group as having AD. They had diagnoses difficult to distinguish from AD clinically and a high Apo E epsilon4 allele frequency. Markers in CSF were used to correctly classify 12 of 13 patients who later underwent autopsy, including 1 with AD not diagnosed clinically. CONCLUSIONS: Levels of CSF Abeta42 decrease and levels of CSF tau increase in AD. Apolipoprotein E epsilon4 had a dose-dependent relationship with CSF levels of Abeta42, but not tau. Other covariates influenced CSF markers minimally. Combined analysis of CSF Abeta42 and tau levels discriminated patients with AD, including patients with mild dementia, from the NC group, supporting use of these proteins to identify AD and to distinguish early AD from aging. In subjects in the ND group with an AD CSF profile, autopsy follow-up will be required to decide whether CSF results are false positive, or whether AD is a primary or concomitant cause of dementia.
OBJECTIVE To evaluate cerebrospinal fluid (CSF) levels of amyloid β protein ending at amino acid 42 (Aβ42) and tau as markers for Alzheimer disease (AD) and to determine whether clinical variables ...influence these levels. DESIGN Cohort study. SETTING Six academic research centers with expertise in dementia. SUBJECTS Eighty-two patients with probable AD, including 24 with very mild dementia (Mini-Mental State Examination score >23/30) (AD group); 60 cognitively normal elderly control subjects (NC group); and 74 subjects with neurological disorders, including dementia (ND group). MAIN OUTCOME MEASURES Levels of Aβ42 and tau were compared among AD, NC, and ND groups. Relationships of age, sex, Mini-Mental State Examination score, and apolipoprotein E (Apo E) genotype with these levels were examined using multiple linear regression. Classification tree models were developed to optimize distinguishing AD from NC groups. RESULTS Levels of Αβ42 were significantly lower, and levels of tau were significantly higher, in the AD group than in the NC or ND group. In the AD group, Αβ42 level was inversely associated with Apo E ϵ4 allele dose and weakly related to Mini-Mental State Examination score; tau level was associated with male sex and 1 Apo E ϵ4 allele. Classification tree analysis, comparing the AD and NC subjects, was 90% sensitive and 80% specific. With specificity set at greater than 90%, the tree was 77% sensitive for AD. This tree classified 26 of 74 members of the ND group as having AD. They had diagnoses difficult to distinguish from AD clinically and a high Apo E ϵ4 allele frequency. Markers in CSF were used to correctly classify 12 of 13 patients who later underwent autopsy, including 1 with AD not diagnosed clinically. CONCLUSIONS Levels of CSF Αβ42 decrease and levels of CSF tau increase in AD. Apolipoprotein E ϵ4 had a dose-dependent relationship with CSF levels of Αβ42, but not tau. Other covariates influenced CSF markers minimally. Combined analysis of CSF Αβ42 and tau levels discriminated patients with AD, including patients with mild dementia, from the NC group, supporting use of these proteins to identify AD and to distinguish early AD from aging. In subjects in the ND group with an AD CSF profile, autopsy follow-up will be required to decide whether CSF results are false positive, or whether AD is a primary or concomitant cause of dementia.Arch Neurol. 1998;55:937-945-->
To evaluate cerebrospinal fluid (CSF) levels of amyloid beta protein ending at amino acid 42 (Abeta42) and tau as markers for Alzheimer disease (AD) and to determine whether clinical variables ...influence these levels.
Cohort study.
Six academic research centers with expertise in dementia.
Eighty-two patients with probable AD, including 24 with very mild dementia (Mini-Mental State Examination score >23/30) (AD group); 60 cognitively normal elderly control subjects (NC group); and 74 subjects with neurological disorders, including dementia (ND group).
Levels of Abeta42 and tau were compared among AD, NC, and ND groups. Relationships of age, sex, Mini-Mental State Examination score, and apolipoprotein E (Apo E) genotype with these levels were examined using multiple linear regression. Classification tree models were developed to optimize distinguishing AD from NC groups.
Levels of Abeta42 were significantly lower, and levels of tau were significantly higher, in the AD group than in the NC or ND group. In the AD group, Abeta42 level was inversely associated with Apo E epsilon4 allele dose and weakly related to Mini-Mental State Examination score; tau level was associated with male sex and 1 Apo E epsilon4 allele. Classification tree analysis, comparing the AD and NC subjects, was 90% sensitive and 80% specific. With specificity set at greater than 90%, the tree was 77% sensitive for AD. This tree classified 26 of 74 members of the ND group as having AD. They had diagnoses difficult to distinguish from AD clinically and a high Apo E epsilon4 allele frequency. Markers in CSF were used to correctly classify 12 of 13 patients who later underwent autopsy, including 1 with AD not diagnosed clinically.
Levels of CSF Abeta42 decrease and levels of CSF tau increase in AD. Apolipoprotein E epsilon4 had a dose-dependent relationship with CSF levels of Abeta42, but not tau. Other covariates influenced CSF markers minimally. Combined analysis of CSF Abeta42 and tau levels discriminated patients with AD, including patients with mild dementia, from the NC group, supporting use of these proteins to identify AD and to distinguish early AD from aging. In subjects in the ND group with an AD CSF profile, autopsy follow-up will be required to decide whether CSF results are false positive, or whether AD is a primary or concomitant cause of dementia.
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