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1.
Mol Cell ; 81(8): 1631-1639, 2021 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-33826920

RESUMEN

Spatial transcriptional profiling provides gene expression information within the important anatomical context of tissue architecture. This approach is well suited to characterizing solid tumors, which develop within a complex landscape of malignant cells, immune cells, and stroma. In a single assay, spatial transcriptional profiling can interrogate the role of spatial relationships among these cell populations as well as reveal spatial patterns of relevant oncogenic genetic events. The broad utility of this approach is reflected in the array of strategies that have been developed for its implementation as well as in the recent commercial development of several profiling platforms. The flexibility to apply these technologies to both hypothesis-driven and discovery-driven studies allows widespread applicability in research settings. This review discusses available technologies for spatial transcriptional profiling and several applications for their use in cancer research.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Neoplasias/genética , Transcripción Genética/genética , Animales , Expresión Génica/genética , Humanos
2.
Mol Psychiatry ; 27(9): 3842-3856, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35546635

RESUMEN

Bipolar disorder is an often-severe mental health condition characterized by alternation between extreme mood states of mania and depression. Despite strong heritability and the recent identification of 64 common variant risk loci of small effect, pathophysiological mechanisms remain unknown. Here, we analyzed genome sequences from 41 multiply-affected pedigrees and identified variants in 741 genes with nominally significant linkage or association with bipolar disorder. These 741 genes overlapped known risk genes for neurodevelopmental disorders and clustered within gene networks enriched for synaptic and nuclear functions. The top variant in this analysis - prioritized by statistical association, predicted deleteriousness, and network centrality - was a missense variant in the gene encoding D-amino acid oxidase (DAOG131V). Heterologous expression of DAOG131V in human cells resulted in decreased DAO protein abundance and enzymatic activity. In a knock-in mouse model of DAOG131, DaoG130V/+, we similarly found decreased DAO protein abundance in hindbrain regions, as well as enhanced stress susceptibility and blunted behavioral responses to pharmacological inhibition of N-methyl-D-aspartate receptors (NMDARs). RNA sequencing of cerebellar tissue revealed that DaoG130V resulted in decreased expression of two gene networks that are enriched for synaptic functions and for genes expressed, respectively, in Purkinje neurons or granule neurons. These gene networks were also down-regulated in the cerebellum of patients with bipolar disorder compared to healthy controls and were enriched for additional rare variants associated with bipolar disorder risk. These findings implicate dysregulation of NMDAR signaling and of gene expression in cerebellar neurons in bipolar disorder pathophysiology and provide insight into its genetic architecture.


Asunto(s)
Trastorno Bipolar , Receptores de N-Metil-D-Aspartato , Ratones , Animales , Humanos , Receptores de N-Metil-D-Aspartato/genética , Receptores de N-Metil-D-Aspartato/metabolismo , Trastorno Bipolar/genética , Trastorno Bipolar/metabolismo , D-Aminoácido Oxidasa/genética , D-Aminoácido Oxidasa/metabolismo , Redes Reguladoras de Genes/genética , Cerebelo/metabolismo
3.
Hum Mutat ; 43(11): 1590-1608, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-35510381

RESUMEN

While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.


Asunto(s)
Predisposición Genética a la Enfermedad , Variación Genética , Perfilación de la Expresión Génica , Pruebas Genéticas , Humanos , Intrones , ARN
4.
Nat Rev Genet ; 17(5): 257-71, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26996076

RESUMEN

With the emergence of RNA sequencing (RNA-seq) technologies, RNA-based biomolecules hold expanded promise for their diagnostic, prognostic and therapeutic applicability in various diseases, including cancers and infectious diseases. Detection of gene fusions and differential expression of known disease-causing transcripts by RNA-seq represent some of the most immediate opportunities. However, it is the diversity of RNA species detected through RNA-seq that holds new promise for the multi-faceted clinical applicability of RNA-based measures, including the potential of extracellular RNAs as non-invasive diagnostic indicators of disease. Ongoing efforts towards the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq.


Asunto(s)
Pruebas Diagnósticas de Rutina/métodos , Enfermedad/genética , Perfilación de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , ARN/genética , Análisis de Secuencia de ARN/métodos , Biología Computacional/métodos , Humanos
5.
Breast Cancer Res Treat ; 186(2): 391-401, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33576900

RESUMEN

PURPOSE: Triple-negative breast cancer (TNBC) is an aggressive subtype most prevalent among women of Western Sub-Saharan African ancestry. It accounts for 15-25% of African American (AA) breast cancers (BC) and up to 80% of Ghanaian breast cancers, thus contributing to outcome disparities in BC for black women. The aggressive biology of TNBC has been shown to be regulated partially by breast cancer stem cells (BCSC) which mediate tumor recurrence and metastasis and are more abundant in African breast tumors. METHODS: We studied the biological differences between TNBC in women with African ancestry and those of Caucasian women by comparing the gene expression of the BCSC. From low-passage patient derived xenografts (PDX) from Ghanaian (GH), AA, and Caucasian American (CA) TNBCs, we sorted for and sequenced the stem cell populations and analyzed for differential gene enrichment. RESULTS: In our cohort of TNBC tumors, we observed that the ALDH expressing stem cells display distinct ethnic specific gene expression patterns, with the largest difference existing between the GH and AA ALDH+ cells. Furthermore, the tumors from the women of African ancestry [GH/AA] had ALDH stem cell (SC) enrichment for expression of immune related genes and processes. Among the significantly upregulated genes were CD274 (PD-L1), CXCR9, CXCR10 and IFI27, which could serve as potential drug targets. CONCLUSIONS: Further exploration of the role of immune regulated genes and biological processes in BCSC may offer insight into developing novel approaches to treating TNBC to help ameliorate survival disparities in women with African ancestry.


Asunto(s)
Neoplasias de la Mama Triple Negativas , Negro o Afroamericano/genética , Femenino , Ghana/epidemiología , Humanos , Recurrencia Local de Neoplasia , Neoplasias de la Mama Triple Negativas/genética , Población Blanca
6.
Br J Psychiatry ; 219(6): 659-669, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-35048876

RESUMEN

BACKGROUND: Studying phenotypic and genetic characteristics of age at onset (AAO) and polarity at onset (PAO) in bipolar disorder can provide new insights into disease pathology and facilitate the development of screening tools. AIMS: To examine the genetic architecture of AAO and PAO and their association with bipolar disorder disease characteristics. METHOD: Genome-wide association studies (GWASs) and polygenic score (PGS) analyses of AAO (n = 12 977) and PAO (n = 6773) were conducted in patients with bipolar disorder from 34 cohorts and a replication sample (n = 2237). The association of onset with disease characteristics was investigated in two of these cohorts. RESULTS: Earlier AAO was associated with a higher probability of psychotic symptoms, suicidality, lower educational attainment, not living together and fewer episodes. Depressive onset correlated with suicidality and manic onset correlated with delusions and manic episodes. Systematic differences in AAO between cohorts and continents of origin were observed. This was also reflected in single-nucleotide variant-based heritability estimates, with higher heritabilities for stricter onset definitions. Increased PGS for autism spectrum disorder (ß = -0.34 years, s.e. = 0.08), major depression (ß = -0.34 years, s.e. = 0.08), schizophrenia (ß = -0.39 years, s.e. = 0.08), and educational attainment (ß = -0.31 years, s.e. = 0.08) were associated with an earlier AAO. The AAO GWAS identified one significant locus, but this finding did not replicate. Neither GWAS nor PGS analyses yielded significant associations with PAO. CONCLUSIONS: AAO and PAO are associated with indicators of bipolar disorder severity. Individuals with an earlier onset show an increased polygenic liability for a broad spectrum of psychiatric traits. Systematic differences in AAO across cohorts, continents and phenotype definitions introduce significant heterogeneity, affecting analyses.


Asunto(s)
Trastorno del Espectro Autista , Trastorno Bipolar , Trastorno Depresivo Mayor , Edad de Inicio , Trastorno Bipolar/diagnóstico , Trastorno Bipolar/epidemiología , Trastorno Bipolar/genética , Trastorno Depresivo Mayor/genética , Estudio de Asociación del Genoma Completo , Humanos , Herencia Multifactorial
7.
Hum Mutat ; 41(2): 412-419, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31660686

RESUMEN

We report a likely pathogenic splice-altering AP4S1 intronic variant in two sisters with progressive spastic paraplegia, global developmental delay, shy character, and foot deformities. Sequencing was completed on whole-blood messenger RNA (mRNA) and analyzed for gene expression outliers after exome sequencing analysis failed to identify a causative variant. AP4S1 was identified as an outlier and contained a rare homozygous variant located three bases upstream of exon 5 (NC_000014.8(NM_007077.4):c.295-3C>A). Confirmed by additional RNA-seq, reverse-transcription polymerase chain reaction, and Sanger sequencing, this variant corresponded with exon 5, including skipping, altered isoform usage, and loss of expression from the canonical isoform 2 (NM_001128126.3). Previously, loss-of-function variants within AP4S1 were associated with a quadriplegic cerebral palsy-6 phenotype, AP-4 Deficiency Syndrome. In this study, the inclusion of mRNA-seq allowed for the identification of a previously missed splice-altering variant, and thereby expands the mutational spectrum of AP-4 Deficiency Syndrome to include impacts to some tissue-dependent isoforms.


Asunto(s)
Complejo 4 de Proteína Adaptadora/genética , Empalme Alternativo , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Intrones , Hermanos , Paraplejía Espástica Hereditaria/diagnóstico , Paraplejía Espástica Hereditaria/genética , Alelos , Femenino , Estudios de Asociación Genética/métodos , Genotipo , Humanos , Linaje , Fenotipo
8.
Genome Res ; 27(4): 524-532, 2017 04.
Artículo en Inglés | MEDLINE | ID: mdl-28373299

RESUMEN

Genomic analyses of cutaneous melanoma (CM) have yielded biological and therapeutic insights, but understanding of non-ultraviolet (UV)-derived CMs remains limited. Deeper analysis of acral lentiginous melanoma (ALM), a rare sun-shielded melanoma subtype associated with worse survival than CM, is needed to delineate non-UV oncogenic mechanisms. We thus performed comprehensive genomic and transcriptomic analysis of 34 ALM patients. Unlike CM, somatic alterations were dominated by structural variation and absence of UV-derived mutation signatures. Only 38% of patients demonstrated driver BRAF/NRAS/NF1 mutations. In contrast with CM, we observed PAK1 copy gains in 15% of patients, and somatic TERT translocations, copy gains, and missense and promoter mutations, or germline events, in 41% of patients. We further show that in vitro TERT inhibition has cytotoxic effects on primary ALM cells. These findings provide insight into the role of TERT in ALM tumorigenesis and reveal preliminary evidence that TERT inhibition represents a potential therapeutic strategy in ALM.


Asunto(s)
Aberraciones Cromosómicas , Melanoma/genética , Mutación , Neoplasias Cutáneas/genética , Telomerasa/genética , Adulto , Anciano , Anciano de 80 o más Años , Células Cultivadas , Femenino , GTP Fosfohidrolasas/genética , Genes de Neurofibromatosis 1 , Humanos , Masculino , Melanoma/patología , Proteínas de la Membrana/genética , Persona de Mediana Edad , Proteínas Proto-Oncogénicas B-raf/genética , Neoplasias Cutáneas/patología , Telomerasa/metabolismo , Transcriptoma , Quinasas p21 Activadas/genética
9.
J Youth Adolesc ; 49(4): 849-868, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-31768740

RESUMEN

A detailed understanding of the factors associated with support among youth for reporting a knife or gun at school to an adult is essential to inform violence prevention initiatives. However, no studies have empirically assessed attitudes about support for reporting among secondary school students in Greater London nor perceived norms about such support among peers. Thus, this study explores whether students misperceive peer norms about support for telling adults about seeing weapons at school. Anonymous surveys were completed by 7401 youth (52% female; 43% White; mean age 11.8 years) in school years 4-11 in 45 school cohorts in a greater London borough between 2007 and 2012. Students reported both personal support about reporting weapons to several categories of adults and whether they perceived most other students at their school to support reporting weapons to adults in each category. Most students (64-78% on average) in most cohorts personally thought that students should report seeing a weapon at school to head teachers, police/security guard, teachers/counselors, and parent/other adult relatives. However, 34-44% of students erroneously thought that the majority of their peers did not support reporting to these adults. Perceived norms predicted personal support for reporting, adjusting for the prevalence of actual support at one's school and other factors. Pervasive norm misperceptions about reporting may contribute to a less safe environment.


Asunto(s)
Conducta del Adolescente/psicología , Revelación , Armas de Fuego , Conducta de Ayuda , Estudiantes/psicología , Violencia/prevención & control , Adolescente , Adulto , Femenino , Humanos , Londres , Masculino , Grupo Paritario , Percepción Social , Estudiantes/estadística & datos numéricos
10.
Hum Genet ; 138(11-12): 1409-1417, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31748968

RESUMEN

Pelizaeus-Merzbacher-like disease (PMLD) is an autosomal recessive hypomyelinating leukodystrophy, which is clinically and radiologically similar to X-linked Pelizaeus-Merzbacher disease (PMD). PMLD is characterized by early-onset nystagmus, delayed development (motor delay, speech delay and dysarthria), dystonia, hypotonia typically evolving into spasticity, ataxia, seizures, optic atrophy, and diffuse leukodystrophy on magnetic resonance imaging (MRI). We identified a 12-year-old Caucasian/Hispanic male with the classical clinical characteristics of PMLD with lack of myelination of the subcortical white matter, and absence of the splenium of corpus callosum. Exome sequencing in the trio revealed novel compound heterozygous pathogenic mutations in SNAP29 (p.Leu119AlafsX15, c.354DupG and p.0?, c.2T > C). Quantitative analysis of the patient's blood cells through RNA sequencing identified a significant decrease in SNAP29 mRNA expression, while western blot analysis on fibroblast cells revealed a lack of protein expression compared to parental and control cells. Mutations in SNAP29 have previously been associated with cerebral dysgenesis, neuropathy, ichthyosis, and keratoderma (CEDNIK) syndrome. Typical skin features described in CEDNIK syndrome, such as generalized ichthyosis and keratoderma, were absent in our patient. Moreover, the early onset nystagmus and leukodystrophy were consistent with a PMLD diagnosis. These findings suggest that loss of SNAP29 function, which was previously associated with CEDNIK syndrome, is also associated with PMLD. Overall, our study expands the genetic spectrum of PMLD.


Asunto(s)
Enfermedades Desmielinizantes del Sistema Nervioso Central Hereditarias/genética , Enfermedades Desmielinizantes del Sistema Nervioso Central Hereditarias/patología , Heterocigoto , Mutación , Proteínas Qb-SNARE/genética , Proteínas Qc-SNARE/genética , Niño , Humanos , Masculino , Pronóstico , Secuenciación del Exoma
11.
Invest New Drugs ; 37(4): 636-645, 2019 08.
Artículo en Inglés | MEDLINE | ID: mdl-30264293

RESUMEN

Malignant melanoma (MM) exhibits a high propensity for central nervous system dissemination with ~50% of metastatic MM patients developing brain metastases (BM). Targeted therapies and immune checkpoint inhibitors have improved overall survival for MM patients with BM. However, responses are usually of short duration and new agents that effectively penetrate the blood brain barrier (BBB) are needed. Here, we report a MM patient with BM who experienced an exceptional response to E6201, an ATP-competitive MEK1 inhibitor, on a Phase 1 study, with ongoing near-complete response and overall survival extending beyond 8 years. Whole exome and transcriptome sequencing revealed a high mutational burden tumor (22 mutations/Megabase) with homozygous BRAF V600E mutation. Correlative preclinical studies demonstrated broad activity for E6201 across BRAF V600E mutant melanoma cell lines and effective BBB penetration in vivo. Together, these results suggest that E6201 may represent a potential new treatment option for BRAF-mutant MM patients with BM.


Asunto(s)
Antineoplásicos/uso terapéutico , Neoplasias Encefálicas/tratamiento farmacológico , Lactonas/uso terapéutico , Melanoma/tratamiento farmacológico , Inhibidores de Proteínas Quinasas/uso terapéutico , Proteínas Proto-Oncogénicas B-raf/genética , Neoplasias Cutáneas/tratamiento farmacológico , Anciano de 80 o más Años , Animales , Antineoplásicos/sangre , Antineoplásicos/farmacocinética , Encéfalo/metabolismo , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/metabolismo , Neoplasias Encefálicas/secundario , Línea Celular Tumoral , Femenino , Perfilación de la Expresión Génica , Humanos , Lactonas/sangre , Lactonas/farmacocinética , Masculino , Melanoma/genética , Melanoma/metabolismo , Melanoma/patología , Ratones Noqueados , Mutación , Inhibidores de Proteínas Quinasas/sangre , Inhibidores de Proteínas Quinasas/farmacocinética , Neoplasias Cutáneas/genética , Neoplasias Cutáneas/metabolismo , Neoplasias Cutáneas/patología , Resultado del Tratamiento , Secuenciación del Exoma
12.
Hum Mol Genet ; 25(15): 3383-3394, 2016 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-27329760

RESUMEN

Bipolar disorder (BD) is a genetically complex mental illness characterized by severe oscillations of mood and behaviour. Genome-wide association studies (GWAS) have identified several risk loci that together account for a small portion of the heritability. To identify additional risk loci, we performed a two-stage meta-analysis of >9 million genetic variants in 9,784 bipolar disorder patients and 30,471 controls, the largest GWAS of BD to date. In this study, to increase power we used ∼2,000 lithium-treated cases with a long-term diagnosis of BD from the Consortium on Lithium Genetics, excess controls, and analytic methods optimized for markers on the X-chromosome. In addition to four known loci, results revealed genome-wide significant associations at two novel loci: an intergenic region on 9p21.3 (rs12553324, P = 5.87 × 10 - 9; odds ratio (OR) = 1.12) and markers within ERBB2 (rs2517959, P = 4.53 × 10 - 9; OR = 1.13). No significant X-chromosome associations were detected and X-linked markers explained very little BD heritability. The results add to a growing list of common autosomal variants involved in BD and illustrate the power of comparing well-characterized cases to an excess of controls in GWAS.


Asunto(s)
Trastorno Bipolar/genética , Cromosomas Humanos X/genética , Estudio de Asociación del Genoma Completo , Receptor ErbB-2/genética , Femenino , Humanos , Masculino
13.
Am J Med Genet A ; 176(7): 1549-1558, 2018 07.
Artículo en Inglés | MEDLINE | ID: mdl-30160831

RESUMEN

Chromosome 1q41-q42 deletions have recently been associated with a recognizable neurodevelopmental syndrome of early childhood (OMIM 612530). Within this group, a predominant phenotype of developmental delay (DD), intellectual disability (ID), epilepsy, distinct dysmorphology, and brain anomalies on magnetic resonance imaging/computed tomography has emerged. Previous reports of patients with de novo deletions at 1q41-q42 have led to the identification of an evolving smallest region of overlap which has included several potentially causal genes including DISP1, TP53BP2, and FBXO28. In a recent report, a cohort of patients with de novo mutations in WDR26 was described that shared many of the clinical features originally described in the 1q41-q42 microdeletion syndrome (MDS). Here, we describe a novel germline FBXO28 frameshift mutation in a 3-year-old girl with intractable epilepsy, ID, DD, and other features which overlap those of the 1q41-q42 MDS. Through a familial whole-exome sequencing study, we identified a de novo FBXO28 c.972_973delACinsG (p.Arg325GlufsX3) frameshift mutation in the proband. The frameshift and resulting premature nonsense mutation have not been reported in any genomic database. This child does not have a large 1q41-q42 deletion, nor does she harbor a WDR26 mutation. Our case joins a previously reported patient also in whom FBXO28 was affected but WDR26 was not. These findings support the idea that FBXO28 is a monogenic disease gene and contributes to the complex neurodevelopmental phenotype of the 1q41-q42 gene deletion syndrome.


Asunto(s)
Trastorno Dismórfico Corporal/genética , Deleción Cromosómica , Cromosomas Humanos Par 1/genética , Discapacidades del Desarrollo/genética , Epilepsia Refractaria/genética , Mutación del Sistema de Lectura , Proteínas Ligasas SKP Cullina F-box/genética , Trastorno Dismórfico Corporal/patología , Preescolar , Discapacidades del Desarrollo/patología , Epilepsia Refractaria/patología , Exoma , Femenino , Humanos , Fenotipo , Pronóstico , Secuenciación del Exoma
14.
Appetite ; 129: 82-93, 2018 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-29890185

RESUMEN

Perceptions of peer food and beverage consumption norms may predict personal consumption. Yet actual peer norms may be misperceived. Data were collected from adolescents in grades 6-12 (n = 5841) in 13 schools across six regionally diverse states via an anonymous online survey. The male and female averages for the number of sugar-sweetened beverages (SSBs) personally consumed per day were significantly lower than average perceptions of the typical number of SSBs consumed by peers. Inversely, the male and female averages for the number of fruit and vegetable (FV) servings personally consumed per day were significantly higher than average perceptions of typical FVs consumed by peers. Among the majority of male and female grade cohorts, the median SSB consumption was 1 drink per day and the median FV intake was 3 servings per day. Regression analyses found a strong relationship between personal consumption and perceived peer norms about male and female consumption (ß â€¯= 0.56, p < .001 for perceived male norm among male students and ß â€¯= 0.52, p < .001 for perceived female norm among female students about SSB consumption, for example), adjusting for sociodemographic characteristics and actual consumption norms. Overall, 65% and 67% of students overestimated average SSB consumption among males and females in their grade cohort, respectively, while less than 5% underestimated these norms. In addition, 49% and 52% of students underestimated average FV intake among males and females in their grade cohort, respectively, while only about 25-30% overestimated the norm. There was little difference in male and female students' estimations of peer norms. Unhealthy misperceptions of SSB norms and FV norms existed across all student categories and grade cohorts, which may contribute to unhealthy personal dietary patterns.


Asunto(s)
Bebidas , Dieta , Frutas , Normas Sociales , Edulcorantes , Verduras , Adolescente , Niño , Sacarosa en la Dieta , Femenino , Humanos , Masculino , Grupo Paritario , Estudiantes , Encuestas y Cuestionarios , Estados Unidos , Adulto Joven
15.
Nat Rev Genet ; 12(10): 730-6, 2011 09 16.
Artículo en Inglés | MEDLINE | ID: mdl-21921928

RESUMEN

Access to genetic data across studies is an important aspect of identifying new genetic associations through genome-wide association studies (GWASs). Meta-analysis across multiple GWASs with combined cohort sizes of tens of thousands of individuals often uncovers many more genome-wide associated loci than the original individual studies; this emphasizes the importance of tools and mechanisms for data sharing. However, even sharing summary-level data, such as allele frequencies, inherently carries some degree of privacy risk to study participants. Here we discuss mechanisms and resources for sharing data from GWASs, particularly focusing on approaches for assessing and quantifying the privacy risks to participants that result from the sharing of summary-level data.


Asunto(s)
Recolección de Datos , Variación Genética , Estudio de Asociación del Genoma Completo , Difusión de la Información/métodos , Estudios de Cohortes , Confidencialidad , Recolección de Datos/legislación & jurisprudencia , Bases de Datos Genéticas , Variación Genética/fisiología , Estudio de Asociación del Genoma Completo/métodos , Estudio de Asociación del Genoma Completo/estadística & datos numéricos , Humanos , Difusión de la Información/legislación & jurisprudencia , Metaanálisis como Asunto , Polimorfismo de Nucleótido Simple , Medición de Riesgo
16.
PLoS Genet ; 10(2): e1004135, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24550739

RESUMEN

Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited. During the course of a clinical trial of whole genomic sequencing seeking druggable targets, we examined six patients with advanced cholangiocarcinoma. Integrated genome-wide and whole transcriptome sequence analyses were performed on tumors from six patients with advanced, sporadic intrahepatic cholangiocarcinoma (SIC) to identify potential therapeutically actionable events. Among the somatic events captured in our analysis, we uncovered two novel therapeutically relevant genomic contexts that when acted upon, resulted in preliminary evidence of anti-tumor activity. Genome-wide structural analysis of sequence data revealed recurrent translocation events involving the FGFR2 locus in three of six assessed patients. These observations and supporting evidence triggered the use of FGFR inhibitors in these patients. In one example, preliminary anti-tumor activity of pazopanib (in vitro FGFR2 IC50≈350 nM) was noted in a patient with an FGFR2-TACC3 fusion. After progression on pazopanib, the same patient also had stable disease on ponatinib, a pan-FGFR inhibitor (in vitro, FGFR2 IC50≈8 nM). In an independent non-FGFR2 translocation patient, exome and transcriptome analysis revealed an allele specific somatic nonsense mutation (E384X) in ERRFI1, a direct negative regulator of EGFR activation. Rapid and robust disease regression was noted in this ERRFI1 inactivated tumor when treated with erlotinib, an EGFR kinase inhibitor. FGFR2 fusions and ERRFI mutations may represent novel targets in sporadic intrahepatic cholangiocarcinoma and trials should be characterized in larger cohorts of patients with these aberrations.


Asunto(s)
Neoplasias de los Conductos Biliares/tratamiento farmacológico , Colangiocarcinoma/tratamiento farmacológico , Receptores ErbB/metabolismo , Receptor Tipo 2 de Factor de Crecimiento de Fibroblastos/genética , Transducción de Señal/genética , Neoplasias de los Conductos Biliares/genética , Neoplasias de los Conductos Biliares/patología , Conductos Biliares Intrahepáticos/patología , Línea Celular Tumoral , Colangiocarcinoma/genética , Colangiocarcinoma/patología , Receptores ErbB/antagonistas & inhibidores , Receptores ErbB/genética , Clorhidrato de Erlotinib , Genoma Humano , Humanos , Imidazoles/administración & dosificación , Indazoles , Terapia Molecular Dirigida , Mutación , Pronóstico , Inhibidores de Proteínas Quinasas , Piridazinas/administración & dosificación , Pirimidinas/administración & dosificación , Quinazolinas/administración & dosificación , Receptor Tipo 2 de Factor de Crecimiento de Fibroblastos/antagonistas & inhibidores , Receptor Tipo 2 de Factor de Crecimiento de Fibroblastos/metabolismo , Sulfonamidas/administración & dosificación , Transcriptoma
17.
Nucleic Acids Res ; 42(2): e8, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24071583

RESUMEN

As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900-1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300-400-bp inserts. A priori analyses show that LI-WGS requires less sequencing compared with short insert WGS to achieve a target physical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a power of 0.99. We thus developed an LI-WGS library preparation protocol based off of Illumina's WGS library preparation protocol and illustrate the feasibility of performing LI-WGS. We additionally applied LI-WGS to three separate tumor/normal DNA pairs collected from patients diagnosed with different cancers to demonstrate our application of LI-WGS on actual patient samples for identification of somatic copy number alterations and translocations. With the evolution of sequencing technologies and bioinformatics analyses, we show that modifications to current approaches may improve our ability to interrogate cancer genomes.


Asunto(s)
Variaciones en el Número de Copia de ADN , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Neoplasias/genética , Análisis de Secuencia de ADN/métodos , Translocación Genética , Biblioteca de Genes , Genoma Humano , Genómica/métodos , Humanos
18.
Hum Mol Genet ; 22(17): 3534-46, 2013 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-23666530

RESUMEN

Multiple research groups have observed neuropathological phenotypes and molecular symptoms in vitro using induced pluripotent stem cell (iPSC)-derived neural cell cultures (i.e. patient-specific neurons and glia). However, the global differences/similarities that may exist between in vitro neural cells and their tissue-derived counterparts remain largely unknown. In this study, we compared temporal series of iPSC-derived in vitro neural cell cultures to endogenous brain tissue from the same autopsy donor. Specifically, we utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, and the following three results support this conclusion: (i) there was a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain; (ii) there was an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue; and (iii) there was a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. Taken together, these results are consistent with in vitro neural development and physiological progression occurring predominantly by transcriptional activation of downregulated genes rather than deactivation of upregulated genes.


Asunto(s)
Encéfalo/citología , Encéfalo/metabolismo , Células Madre Pluripotentes Inducidas/fisiología , Células-Madre Neurales/fisiología , Neurogénesis , Neuronas/fisiología , Anciano , Células Cultivadas , Islas de CpG , Metilación de ADN , Humanos , Células Madre Pluripotentes Inducidas/citología , Masculino , Células-Madre Neurales/citología , Neurogénesis/genética , Neuronas/citología , Neuronas/metabolismo , Especificidad de Órganos/genética , ARN Largo no Codificante/genética , Activación Transcripcional
19.
N Engl J Med ; 366(2): 141-9, 2012 Jan 12.
Artículo en Inglés | MEDLINE | ID: mdl-22236224

RESUMEN

BACKGROUND: Family history is a significant risk factor for prostate cancer, although the molecular basis for this association is poorly understood. Linkage studies have implicated chromosome 17q21-22 as a possible location of a prostate-cancer susceptibility gene. METHODS: We screened more than 200 genes in the 17q21-22 region by sequencing germline DNA from 94 unrelated patients with prostate cancer from families selected for linkage to the candidate region. We tested family members, additional case subjects, and control subjects to characterize the frequency of the identified mutations. RESULTS: Probands from four families were discovered to have a rare but recurrent mutation (G84E) in HOXB13 (rs138213197), a homeobox transcription factor gene that is important in prostate development. All 18 men with prostate cancer and available DNA in these four families carried the mutation. The carrier rate of the G84E mutation was increased by a factor of approximately 20 in 5083 unrelated subjects of European descent who had prostate cancer, with the mutation found in 72 subjects (1.4%), as compared with 1 in 1401 control subjects (0.1%) (P=8.5x10(-7)). The mutation was significantly more common in men with early-onset, familial prostate cancer (3.1%) than in those with late-onset, nonfamilial prostate cancer (0.6%) (P=2.0x10(-6)). CONCLUSIONS: The novel HOXB13 G84E variant is associated with a significantly increased risk of hereditary prostate cancer. Although the variant accounts for a small fraction of all prostate cancers, this finding has implications for prostate-cancer risk assessment and may provide new mechanistic insights into this common cancer. (Funded by the National Institutes of Health and others.).


Asunto(s)
Mutación de Línea Germinal , Proteínas de Homeodominio/genética , Neoplasias de la Próstata/genética , Cromosomas Humanos Par 17 , Ligamiento Genético , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Persona de Mediana Edad , Linaje , Próstata/patología , Neoplasias de la Próstata/patología , Análisis de Secuencia de ADN
20.
Prev Sci ; 16(1): 70-9, 2015 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24488532

RESUMEN

Previous research has revealed pervasive misperceptions of peer norms for a variety of behaviors among adolescents such as alcohol use, smoking, and bullying and that these misperceptions are predictors of personal behavior. Similarly, misperception of peer weight norms may be a pervasive and important risk factor for adolescent weight status. Thus, the comparative association of actual and perceived peer weight norms is examined in relation to personal weight status. Secondary school students in 40 middle and high schools (n = 40,328) were surveyed about their perceptions of the peer weight norm for same gender and grade within their school. Perceived norms were compared to aggregate self-reports of weight for these same groups. Overestimation of peer weight norms by more than 5 % occurred among 26 % of males and 20 % of females (by 22 and 16 lb on average, respectively). Underestimation occurred among 38 % of males as well as females (by 16 and 13 lb on average, respectively). Personal overweight status based on body mass index (BMI) was much more prevalent among respondents who overestimated peer weight norms as was personal underweight status among respondents who underestimated norms. Perception of the peer norm was the strongest predictor of personal BMI among all personal and school variables examined for both male and female students. Thus, reducing misperceived weight norms should be given more attention as a potential avenue for preventing obesity and eating disorders.


Asunto(s)
Sobrepeso/psicología , Grupo Paritario , Normas Sociales , Delgadez/psicología , Adolescente , Imagen Corporal , Femenino , Humanos , Masculino , Estados Unidos
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