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1.
Hepatol Res ; 54(3): 315-319, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37817425

RESUMO

A 72-year-old man with metastatic hepatocellular carcinoma previously received first-line systemic therapy with atezolizumab plus bevacizumab. His disease was judged to be progressing 5 months after treatment initiation. Comprehensive genomic profiling revealed cytoplasmic mesenchymal-epithelial transition factor amplification. On the basis of an expert panel's recommendation, he received cabozantinib as second-line therapy. The tumors shrank markedly and continued to shrink 6 months after treatment. Comprehensive genomic profiling could provide useful information for selecting effective second-line treatments for patients with hepatocellular carcinoma after first-line immunotherapy.

2.
Cancer Sci ; 114(3): 1015-1025, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36369895

RESUMO

Patients with advanced cancer undergo comprehensive genomic profiling in Japan only after treatment options have been exhausted. Patients with a very poor prognosis were not able to undergo profiling tests, resulting in a selection bias called length bias, which makes accurate survival analysis impossible. The actual impact of length bias on the overall survival of patients who have undergone profiling tests is unclear, yet appropriate methods for adjusting for length bias have not been developed. To assess the length bias in overall survival, we established a simulation-based model for length bias adjustment. This study utilized clinicogenomic data of 8813 patients with advanced cancer who underwent profiling tests at hospitals throughout Japan between June 2019 and April 2022. Length bias was estimated by the conditional Kendall τ statistics and was significantly positive for 13 of the 15 cancer subtypes, suggesting a worse prognosis for patients who underwent profiling tests in early timing. The median overall survival time in colorectal, breast, and pancreatic cancer from the initial survival-prolonging chemotherapy with adjustment for length bias was 937 (886-991), 1225 (1152-1368), and 585 (553-617) days, respectively (median; 95% credible interval). Adjusting for length bias made it possible to analyze the prognostic relevance of oncogenic mutations and treatments. In total, 12 tumor-specific oncogenic mutations correlating with poor survival were detected after adjustment. There was no difference in survival between FOLFIRINOX (leucovorin, fluorouracil, irinotecan, and oxaliplatin) or gemcitabine with nab-paclitaxel-treated groups as first-line chemotherapy for pancreatic cancer. Adjusting for length bias is an essential part of utilizing real-world clinicogenomic data.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica , Neoplasias Pancreáticas , Humanos , Viés de Seleção , Japão , Genômica , Neoplasias Pancreáticas
3.
Sensors (Basel) ; 23(13)2023 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-37447704

RESUMO

Microfluidic technology is a powerful tool to enable the rapid, accurate, and on-site analysis of forensically relevant evidence on a crime scene. This review paper provides a summary on the application of this technology in various forensic investigation fields spanning from forensic serology and human identification to discriminating and analyzing diverse classes of drugs and explosives. Each aspect is further explained by providing a short summary on general forensic workflow and investigations for body fluid identification as well as through the analysis of drugs and explosives. Microfluidic technology, including fabrication methodologies, materials, and working modules, are touched upon. Finally, the current shortcomings on the implementation of the microfluidic technology in the forensic field are discussed along with the future perspectives.


Assuntos
Ciências Forenses , Microfluídica , Humanos , Substâncias Explosivas/análise , Ciências Forenses/instrumentação , Ciências Forenses/métodos , Microfluídica/métodos , Microfluídica/tendências , Técnicas de Química Analítica , DNA/análise , Drogas Ilícitas/análise , Animais
4.
Ann Hematol ; 101(9): 1925-1929, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35779117

RESUMO

The present study aims to evaluate the characteristics and treatment outcomes of adult Langerhans cell histiocytosis (LCH) patients with thyroid involvement. We retrospectively described the clinical, biological, and genomic characteristics of a series of 36 LCH patients with thyroid involvement in our center between January 2001 and December 2021. At the time of diagnosis, only one patient was classified as having single-system LCH, and 35 patients were classified as having multisystem (MS) LCH. Three patients had coexisting papillary thyroid carcinoma. Patients with thyroid gland involvement had higher frequencies of pituitary (88.6% vs. 53.4%, P < 0.001), liver (45.7% vs. 20.7%, P = 0.003), and lymph node (54.3% vs. 31.6%, P = 0.012) involvement and a lower frequency of bone (45.7% vs. 72.0%, P = 0.003) involvement than patients without thyroid gland involvement. Sixteen patients had abnormal thyroid function, including nine patients with primary hypothyroidism, one patient with central hypothyroidism, and six patients with subclinical hypothyroidism. BRAFV600E, BRAF N486_P490, and MAP2K1 mutations were detected in 14.3%, 57.1%, and 7.1% of patients, respectively. After a 43-month median follow-up, none of the patients died, and 15 patients experienced reactivation. The median event-free survival was 37.5 months. Two of 6 patients with subclinical hypothyroidism had normal thyroid function, and 12 patients still had hypothyroidism after treatment. As the largest adult LCH cohort with thyroid gland involvement to date, we found that patients with thyroid gland involvement had different clinical characteristics, genetic profiles, and outcomes than patients without thyroid gland involvement.


Assuntos
Histiocitose de Células de Langerhans , Hipotireoidismo , Adulto , Genômica , Histiocitose de Células de Langerhans/tratamento farmacológico , Histiocitose de Células de Langerhans/genética , Humanos , Proteínas Proto-Oncogênicas B-raf/genética , Estudos Retrospectivos
5.
Oncologist ; 26(3): e394-e402, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33219618

RESUMO

BACKGROUND: Carcinoma of unknown primary origin (CUP) accounts for 2%-5% of newly diagnosed advanced malignancies, with chemotherapy as the standard of care. CUPISCO (NCT03498521) is an ongoing randomized trial using comprehensive genomic profiling (CGP) to assign patients with CUP to targeted or immunotherapy treatment arms based on genomic profiling. We performed a retrospective analysis of CUP cases referred for CGP to determine how many were potentially eligible for enrollment into an experimental CUPISCO arm. MATERIALS AND METHODS: Centrally reviewed adenocarcinoma and undifferentiated CUP specimens in the FoundationCore database were analyzed using the hybrid capture-based FoundationOne CDx assay (mean coverage, >600×). Presence of genomic alterations, microsatellite instability (MSI), tumor mutational burden (TMB), genomic loss of heterozygosity (gLOH), and programmed death-ligand 1 (PD-L1) positivity were determined. RESULTS: A total of 96 of 303 patients (31.7%) could be matched to an experimental CUPISCO arm. Key genomic alterations included ERBB2 (7.3%), PIK3CA (6.3%), NF1 (5.6%), NF2 (4.6%), BRAF (4.3%), IDH1 (3.3%), PTEN, FGFR2, EGFR (3.6% each), MET (4.3%), CDK6 (3.0%), FBXW7, CDK4 (2.3% each), IDH2, RET, ROS1, NTRK (1.0% each), and ALK (0.7%). Median TMB was 3.75 mutations per megabase of DNA; 34 patients (11.6%) had a TMB ≥16 mutations per megabase. Three patients (1%) had high MSI, and 42 (14%) displayed high PD-L1 expression (tumor proportion score ≥50%). gLOH could be assessed in 199 of 303 specimens; 19.6% had a score of >16%. CONCLUSIONS: Thirty-two percent of patients would have been eligible for targeted therapy in CUPISCO. Future studies, including additional biomarkers such as PD-L1 positivity and gLOH, may identify a greater proportion potentially benefiting from CGP-informed treatment. Clinical trial identification number. NCT03498521 IMPLICATIONS FOR PRACTICE: The findings of this retrospective analysis of carcinoma of unknown primary origin (CUP) cases validate the experimental treatment arms being used in the CUPISCO study (NCT03498521), an ongoing randomized trial using comprehensive genomic profiling to assign patients with CUP to targeted or immunotherapy treatment arms based on the presence of pathogenic genomic alterations. The findings also suggest that future studies including additional biomarkers and treatment arms, such as programmed death-ligand 1 positivity and genomic loss of heterozygosity, may identify a greater proportion of patients with CUP potentially benefiting from comprehensive genomic profiling-informed treatment.


Assuntos
Carcinoma , Neoplasias Pulmonares , Neoplasias Primárias Desconhecidas , Biomarcadores Tumorais/genética , Perfilação da Expressão Gênica , Genômica , Humanos , Mutação , Neoplasias Primárias Desconhecidas/genética , Proteínas Tirosina Quinases , Proteínas Proto-Oncogênicas , Estudos Retrospectivos
6.
Neuropathol Appl Neurobiol ; 47(5): 664-678, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-33393119

RESUMO

BACKGROUND: Autophagic vacuolar myopathies (AVMs) are an emerging group of heterogeneous myopathies sharing histopathological features on muscle pathology, in which autophagic vacuoles are the pathognomonic morphologic hallmarks. Glycogen storage disease type II (GSDII) caused by lysosomal acid α-glucosidase (GAA) deficiency is the best-characterised AVM. AIMS: This study aimed to investigate the mutational profiling of seven neuromuscular outpatients sharing clinical, myopathological and biochemical findings with AVMs. METHODS: We applied a diagnostic protocol, recently published by our research group for suspected late-onset GSDII (LO-GSDII), including counting PAS-positive lymphocytes on blood smears, dried blood spot (DBS)-GAA, muscle biopsy histological and immunofluorescence studies, GAA activity assay and expression studies on muscle homogenate, GAA sequencing, GAA multiplex ligation-dependent probe amplification (MLPA) and whole exome sequencing (WES). RESULTS: The patients had a limb girdle-like muscular pattern with persistent hyperCKaemia; vacuolated PAS-positive lymphocytes, glycogen accumulation and impaired autophagy at muscle biopsy. Decreased GAA activity was also measured. While GAA sequencing identified no pathogenic mutations, WES approach allowed us to identify for each patient an unexpected mutational pattern in genes cooperating in lysosomal-autophagic machinery, some of which have never been linked to human diseases. CONCLUSIONS: Our data suggest that reduced GAA activity may occur in any condition of impaired autophagy and that WES approach is advisable in all genetically undefined cases of autophagic myopathy. Therefore, deficiency of GAA activity and PAS-positive lymphocytes should be considered as AVM markers together with LC3/p62-positive autophagic vacuoles.


Assuntos
Autofagia/genética , Genótipo , Doenças por Armazenamento dos Lisossomos/patologia , Doenças Musculares/patologia , Fenótipo , Autofagia/fisiologia , Doença de Depósito de Glicogênio Tipo II/genética , Doença de Depósito de Glicogênio Tipo II/patologia , Humanos , Doenças por Armazenamento dos Lisossomos/genética , Lisossomos/metabolismo , Doenças Musculares/genética , Mutação/genética , Sequenciamento do Exoma/métodos , alfa-Glucosidases/genética , alfa-Glucosidases/metabolismo
7.
Future Oncol ; 17(16): 2057-2074, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33709779

RESUMO

Background: IDH1 mutations occur in approximately 13% of intrahepatic cholangiocarcinomas (IHCCs). The oral, targeted, mutant IDH1 (mIDH1) inhibitor ivosidenib (AG-120) suppresses production of the oncometabolite D-2-hydroxyglutarate, promoting disease stabilization and improved progression-free survival (PFS) in mIDH1 IHCC. Materials & methods: Harnessing matched baseline and on-treatment biopsies, we investigate the potential mechanisms underlying ivosidenib's efficacy. Results: mIDH1 inhibition leads to decreased cytoplasm and expression of hepatocyte lineage markers in patients with prolonged PFS. These findings are accompanied by downregulation of biliary fate, cell cycle progression and AKT pathway activity. Conclusion: Ivosidenib stimulates a hepatocyte differentiation program in mIDH1 IHCC, a phenotype associated with clinical benefit. mIDH1 inhibition could be a paradigm for differentiation-based therapy in solid tumors. Clinical trial registration: NCT02073994 (ClinicalTrials.gov).


Assuntos
Neoplasias dos Ductos Biliares/tratamento farmacológico , Colangiocarcinoma/tratamento farmacológico , Glicina/análogos & derivados , Isocitrato Desidrogenase/genética , Mutação , Piridinas/farmacologia , Antineoplásicos/administração & dosagem , Neoplasias dos Ductos Biliares/genética , Neoplasias dos Ductos Biliares/metabolismo , Neoplasias dos Ductos Biliares/patologia , Diferenciação Celular/efeitos dos fármacos , Colangiocarcinoma/genética , Colangiocarcinoma/metabolismo , Colangiocarcinoma/patologia , Ensaios Clínicos Fase I como Assunto , Glicina/farmacologia , Humanos , Isocitrato Desidrogenase/antagonistas & inibidores , Gradação de Tumores , Proteínas Proto-Oncogênicas c-akt/metabolismo , Taxa de Sobrevida , Resultado do Tratamento
8.
Phytochem Anal ; 32(2): 172-182, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32337813

RESUMO

INTRODUCTION: Irises have been medicinally used in Ancient Egyptians, Anatolian, Chinese, British and Irish folk medicine. They are also well-known ornamental plants that have economic value in the perfume industry. The main obvious diagnostic difference between the different species is based on the morphology of the flowers. The flowering cycle is very short as well as the persistence of the fully opened flowers extends for a few days only. Moreover, the climatic conditions significantly causes fluctuation in their blooming time from year to year. This makes the morphological discrimination very difficult. The discrimination of different iris species is of a great importance, as each species is reported to possess different folk medicinal activities. OBJECTIVES: Finding genetic and metabolic markers for differentiation between Iris confusa Sealy (Subgen. Limniris Sect. Lophiris), I. pseudacorus L. (Subgen. Limniris Sect. Limniris) and I. germanica L. (Subgen. Iris Sect. Iris) on levels other than traditional taxonomic features. MATERIAL AND METHODS: Inter-simple sequence repeat (ISSR) and gas chromatography-mass spectrometry (GC-MS) analyses were performed. RESULTS: The highest similarity was found between I. pseudacorus L. and I. germanica L. and the least similarity was between I. confusa Sealy and I. pseudacorus L. The metabolic profiling of the leaves confirmed genetic profiling discriminating I. confusa from the other two species. The primary metabolites of the underground parts showed clear discrimination between the three species. CONCLUSIONS: This study represents the sole complete map for distinguishing the three Iris species on genetic and metabolic bases.


Assuntos
Gênero Iris , Egito , Flores/genética , Cromatografia Gasosa-Espectrometria de Massas , Gênero Iris/genética , Metabolômica
9.
Wien Med Wochenschr ; 171(11-12): 249-256, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33616797

RESUMO

Alzheimer's disease (AD) is the leading cause of neurodegeneration in the elderly and is clinically characterized by slowly progressing cognitive decline, which most commonly affects episodic memory function. This eventually leads to difficulties in activities of daily living. Biomarker studies show that the underlying pathology of AD begins 20 years before clinical symptoms. This results in the need to define specific targets and preclinical stages in order to address the problems of this disease at an earlier point in time. Genetic studies are indispensable for gaining insight into the etiology of neurodegenerative diseases and can play a major role in the early definition of the individual disease risk. This review provides an overview of the currently known genetic features of AD.


Assuntos
Doença de Alzheimer , Disfunção Cognitiva , Atividades Cotidianas , Idoso , Doença de Alzheimer/genética , Biomarcadores , Disfunção Cognitiva/genética , Progressão da Doença , Humanos
10.
Int J Mol Sci ; 21(23)2020 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-33260345

RESUMO

Liquid biopsy is a minimally-invasive diagnostic method that may improve access to molecular profiling for non-small cell lung cancer (NSCLC) patients. Although cell-free DNA (cf-DNA) isolation from plasma is the standard liquid biopsy method for detecting DNA mutations in cancer patients, the sensitivity can be highly variable. Vn96 is a peptide with an affinity for both extracellular vesicles (EVs) and circulating cf-DNA. In this study, we evaluated whether peptide-affinity (PA) precipitation of EVs and cf-DNA from NSCLC patient plasma improves the sensitivity of single nucleotide variants (SNVs) detection and compared observed SNVs with those reported in the matched tissue biopsy. NSCLC patient plasma was subjected to either PA precipitation or cell-free methods and total nucleic acid (TNA) was extracted; SNVs were then detected by next-generation sequencing (NGS). PA led to increased recovery of DNA as well as an improvement in NGS sequencing parameters when compared to cf-TNA. Reduced concordance with tissue was observed in PA-TNA (62%) compared to cf-TNA (81%), mainly due to identification of SNVs in PA-TNA that were not observed in tissue. EGFR mutations were detected in PA-TNA with 83% sensitivity and 100% specificity. In conclusion, PA-TNA may improve the detection limits of low-abundance alleles using NGS.


Assuntos
Ácidos Nucleicos Livres/genética , Vesículas Extracelulares/química , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias Pulmonares/sangue , Neoplasias Pulmonares/genética , Mutação/genética , Peptídeos/química , Adulto , Idoso , Idoso de 80 Anos ou mais , Alelos , Biomarcadores Tumorais/sangue , Biomarcadores Tumorais/genética , Carcinoma Pulmonar de Células não Pequenas/sangue , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Receptores ErbB/genética , Feminino , Humanos , Biópsia Líquida , Neoplasias Pulmonares/patologia , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética
11.
Mol Cell Neurosci ; 88: 300-307, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29505902

RESUMO

Considerable evidence suggests that autism spectrum disorders (ASD), schizophrenia (SCZ), bipolar disorder (BD) and obsessive-compulsive disorder (OCD) share a common molecular aetiology, despite their unique clinical diagnostic criteria. The aim of this study was therefore to determine and characterise the common and unique molecular architecture of ASD, SCZ, BD and OCD. Gene lists were obtained from previously published studies for ASD, BD, SCZ and for OCD. Genes identified to be common to all disorders, or unique to one specific disorder, were included for enrichment analyses using the web-server tool Enrichr. Ten genes were identified to be commonly associated with the aetiology of ASD, SCZ, BD and OCD. Enrichment analyses determined that these genes are predominantly involved in the dopaminergic and serotonergic pathways, the voltage-gated calcium ion channel gene network, folate metabolism, regulation of the hippo signaling pathway, and the regulation of gene silencing and expression. In addition to well-characterised and previously described pathways, regulation of the hippo signaling pathway was commonly associated with ASD, SCZ, BD and OCD, implicating neural development and neuronal maintenance as key in neuropsychiatric disorders. In contrast, a large number of previously associated genes were shown to be disorder-specific. And unique disorder-specific pathways and biological processes were presented for ASD, BD, SCZ and OCD aetiology. Considering the current global incidence and prevalence rates of mental health disorders, focus should be placed on cross-disorder commonalities in order to realise actionable and translatable results to combat mental health disorders.


Assuntos
Transtorno do Espectro Autista/genética , Transtorno Bipolar/genética , Predisposição Genética para Doença , Transtorno Obsessivo-Compulsivo/genética , Esquizofrenia/genética , Expressão Gênica/genética , Humanos
12.
Annu Rev Nutr ; 37: 395-422, 2017 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-28715990

RESUMO

There is a great deal of interest in personalized, individualized, or precision interventions for disease and health-risk mitigation. This is as true of nutrition-based intervention and prevention strategies as it is for pharmacotherapies and pharmaceutical-oriented prevention strategies. Essentially, technological breakthroughs have enabled researchers to probe an individual's unique genetic, biochemical, physiological, behavioral, and exposure profile, allowing them to identify very specific and often nuanced factors that an individual might possess, which may make it more or less likely that he or she responds favorably to a particular intervention (e.g., nutrient supplementation) or disease prevention strategy (e.g., specific diet). However, as compelling and intuitive as personalized nutrition might be in the current era in which data-intensive biomedical characterization of individuals is possible, appropriately and objectively vetting personalized nutrition strategies is not trivial and requires novel study designs and data analytical methods. These designs and methods must consider a very integrated use of the multiple contemporary biomedical assays and technologies that motivate them, which adds to their complexity. Single-subject or N-of-1 trials can be used to assess the utility of personalized interventions and, in addition, can be crafted in such a way as to accommodate the necessarily integrated use of many emerging biomedical technologies and assays. In this review, we consider the motivation, design, and implementation of N-of-1 trials in translational nutrition research that are meant to assess the utility of personalized nutritional strategies. We provide a number of example studies, discuss appropriate analytical methods given the complex data they generate and require, and consider how such studies could leverage integration of various biomarker assays and clinical end points. Importantly, we also consider the development of strategies and algorithms for matching nutritional needs to individual biomedical profiles and the issues surrounding them. Finally, we discuss the limitations of personalized nutrition studies, possible extensions of N-of-1 nutritional intervention studies, and areas of future research.


Assuntos
Dieta , Nutrigenômica , Medicina de Precisão , Pesquisa Translacional Biomédica , Humanos , Modelos Biológicos
14.
Rinsho Ketsueki ; 59(10): 2127-2135, 2018.
Artigo em Japonês | MEDLINE | ID: mdl-30305518

RESUMO

Adult T-cell leukemia/lymphoma (ATL) is a peripheral T-cell neoplasm with a dismal prognosis. This disease is caused by human T-cell leukemia virus type-1 (HTLV-1) retrovirus. Not only viral proteins, such as Tax and HBZ, but also additional genetic and epigenetic aberrations, including gain-of-function alterations in the components of T-cell receptor/NF-κB pathway or deteriorating alterations responsible for immune surveillance, are essential for ATL development and progression. Furthermore, recent investigation has demonstrated the effects of genetic and epigenetic alterations prevalently identified in ATL on the disease phenotype and its clinical outcomes. Aggressive ATL is associated with an increased burden of genetic and epigenetic abnormalities. Higher frequencies of TP53 and IRF4 mutations and several copy number alterations, including PD-L1 amplifications and CDKN2A deletions, are more predominant in aggressive than indolent diseases. In contrast, STAT3 mutations are more frequent in indolent ATL. Several genetic alterations, such as PD-L1 amplification, can predict the clinical outcomes independent of established clinical factors. Therefore, ATL subtypes can further be subdivided into genetically distinct subgroups with different prognoses. The genetic profiling of ATL cases has revealed its molecular pathology and should contribute to improved prognostication and management of patients with ATL.


Assuntos
Vírus Linfotrópico T Tipo 1 Humano , Leucemia-Linfoma de Células T do Adulto/genética , Antígeno B7-H1/genética , Fatores de Transcrição de Zíper de Leucina Básica , Inibidor p16 de Quinase Dependente de Ciclina/genética , Produtos do Gene tax , Testes Genéticos , Humanos , Fatores Reguladores de Interferon/genética , Leucemia-Linfoma de Células T do Adulto/virologia , NF-kappa B/genética , Prognóstico , Proteínas dos Retroviridae , Fator de Transcrição STAT3/genética , Proteína Supressora de Tumor p53/genética
15.
J Infect Dis ; 216(6): 703-712, 2017 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-28934431

RESUMO

Background: The difficulty in distinguishing infection by Zika virus (ZIKV) from other flaviviruses is a global health concern, particularly given the high risk of neurologic complications (including Guillain-Barré syndrome [GBS]) with ZIKV infection. Methods: We developed quantitative frameworks to compare and explore infectome, diseasome, and comorbidity of ZIKV infections. We analyzed gene expression microarray and RNA-Seq data from ZIKV, West Nile fever (WNF), chikungunya, dengue, yellow fever, Japanese encephalitis virus, GBS, and control datasets. Using neighborhood-based benchmarking and multilayer network topology, we constructed relationship networks based on the Online Mendelian Inheritance in Man database and our identified significant genes. Results: ZIKV infections showed dysregulation in expression of 929 genes. Forty-seven genes were highly expressed in both ZIKV and dengue infections. However, ZIKV shared <15 significant transcripts with other flavivirus infections. Notably, dysregulation of MAFB and SELENBP1 was common to ZIKV, dengue, and GBS infection; ATF5, TNFAIP3, and BAMB1 were common to ZIKV, dengue, and WNF; and NAMPT and PMAlP1 were common to ZIKV, GBS, and WNF. Phylogenetic, ontologic, and pathway analyses showed that ZIKV infection most resembles dengue fever. Conclusions: We have developed methodologies to investigate disease mechanisms and predictions for infectome, diseasome, and comorbidities quantitatively, and identified particular similarities between ZIKV and dengue infections.


Assuntos
Comorbidade , Perfilação da Expressão Gênica , Interações Hospedeiro-Patógeno/genética , Infecções por Vírus de RNA/diagnóstico , Infecção por Zika virus/diagnóstico , Zika virus/isolamento & purificação , Regulação da Expressão Gênica , Ontologia Genética , Humanos , Filogenia , Infecções por Vírus de RNA/classificação , Vírus de RNA/classificação , Vírus de RNA/genética , Vírus de RNA/isolamento & purificação , Análise de Sequência de RNA , Zika virus/genética
16.
Pathobiology ; 84(6): 306-322, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28178700

RESUMO

Massive parallel sequencing technologies (next-generation sequencing) have enabled us to draw a comprehensive landscape of the genomic aberrations underlying common cancers of the digestive system, and they have thus revolutionized our understanding of the genomic makeup and biology of these tumors. Apart from the commonly mutated founder genes, e.g., KRAS and TP53, we now have detailed information on additional and less frequent genomic events for every major digestive system cancer. However, many challenging issues remain when it comes to translating these findings into clinical applications. Recent examples are the precise definition of the role of genomic heterogeneity and tumor evolution in metastatic spread and their impact on oncologic therapy. Other unresolved issues include the usefulness of identified drivers as novel drug targets and predictive biomarkers, as well as the development of strategies to implement broad genomic testing in individualized patient care. This review aims to dissect and discuss these topics for selected major cancers.


Assuntos
Sistema Digestório/patologia , Neoplasias Gastrointestinais/genética , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Biomarcadores Tumorais/genética , Anormalidades do Sistema Digestório/diagnóstico , Sistemas de Liberação de Medicamentos , Humanos , Mutação , Sequenciamento Completo do Genoma
17.
J Clin Densitom ; 20(3): 353-359, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28729043

RESUMO

Over the past decade, several genetic variants or genes for osteoporosis have been identified through genome-wide association studies and candidate gene association studies. These genetic variants are common in the general population but have modest effect sizes, with odds ratio ranging from 1.1 to 1.5. Thus, the utility of any single variant is limited. However, theoretical and empirical studies have suggested that a profiling of multiple variants that are associated with bone phenotypes (i.e., "osteogenomic profile") can improve the accuracy of fracture prediction and classification beyond that obtained by conventional clinical risk factors. These results support the view that an osteogenomic profile, when integrated into existing models, can help clinicians and patients alike to better assess the risk fracture for an individual, and raise the possibility of personalized osteoporosis care.


Assuntos
Variação Genética , Osteoporose/genética , Fraturas por Osteoporose/genética , Densidade Óssea/genética , Estudo de Associação Genômica Ampla , Genômica , Humanos , Medicina de Precisão , Medição de Risco/métodos
18.
Adv Exp Med Biol ; 994: 143-167, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28560673

RESUMO

Cancer kills by metastasizing beyond the primary site. Early detection, surgical intervention and other treatments have improved the survival rates of patients with cancer, however, once metastasis occurs, responses to conventional therapies become significantly less effective, and this remains the leading cause of death. Circulating tumor cells (CTCs) are tumor cells that have preferentially disseminated from the primary tumor mass into the hematological system, and are en route to favorable distant sites where if they survive, can develop into metastases. They may be the earliest detectable cells with metastatic ability, and are gaining increasing attention because of their prognostic value in many types of cancers including breast, prostate, colon and lung. Recent technological advances have removed barriers that previously hindered the detection and isolation of these rare cells from blood, and have exponentially improved the genetic resolution at which we can characterize signatures that define CTCs. Some of the most significant observations from such examinations are described here. Firstly, aberrations that were thought to be unique to CTCs are detected at subclonal frequencies within primary tumors with measurable heterogeneity, indicating pre-existing genetic signatures for metastasis. Secondly, these subclonal events are enriched in CTCs and metastases, pointing towards the selection of a more 'fit' component of tumor cells with survival advantages. Lastly, this component of cancer cells may also be the chemoresistant portion that escapes systemic treatment, or acquires resistance during progression of the disease. The future of cancer management may include a standardized method of measuring intratumor heterogeneity of the primary as well as matched CTCs. This will help identify and target rare aberrations within primary tumors that make them more adept to disseminate, and also to monitor the development of treatment resistant subclones as cancer progresses.


Assuntos
Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica , Neoplasias/sangue , Células Neoplásicas Circulantes/metabolismo , Humanos , Neoplasias/patologia , Neoplasias/terapia , Células Neoplásicas Circulantes/patologia , Especificidade de Órgãos
19.
Int J Mol Sci ; 18(3)2017 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-28264500

RESUMO

Bipolar disorder (BPD) and schizophrenia (SCH) show similar neuropsychiatric behavioral disturbances, including impaired social interaction and communication, seen in autism spectrum disorder (ASD) with multiple overlapping genetic and environmental influences implicated in risk and course of illness. GeneAnalytics software was used for pathway analysis and genetic profiling to characterize common susceptibility genes obtained from published lists for ASD (792 genes), BPD (290 genes) and SCH (560 genes). Rank scores were derived from the number and nature of overlapping genes, gene-disease association, tissue specificity and gene functions subdivided into categories (e.g., diseases, tissues or functional pathways). Twenty-three genes were common to all three disorders and mapped to nine biological Superpathways including Circadian entrainment (10 genes, score = 37.0), Amphetamine addiction (five genes, score = 24.2), and Sudden infant death syndrome (six genes, score = 24.1). Brain tissues included the medulla oblongata (11 genes, score = 2.1), thalamus (10 genes, score = 2.0) and hypothalamus (nine genes, score = 2.0) with six common genes (BDNF, DRD2, CHRNA7, HTR2A, SLC6A3, and TPH2). Overlapping genes impacted dopamine and serotonin homeostasis and signal transduction pathways, impacting mood, behavior and physical activity level. Converging effects on pathways governing circadian rhythms support a core etiological relationship between neuropsychiatric illnesses and sleep disruption with hypoxia and central brain stem dysfunction.


Assuntos
Transtorno do Espectro Autista/genética , Transtorno Bipolar/genética , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Estudos de Associação Genética , Predisposição Genética para Doença , Esquizofrenia/genética , Transtorno do Espectro Autista/diagnóstico , Transtorno Bipolar/diagnóstico , Relógios Circadianos/genética , Biologia Computacional/métodos , Bases de Dados Genéticas , Perfilação da Expressão Gênica , Humanos , Especificidade de Órgãos/genética , Fenótipo , Esquizofrenia/diagnóstico
20.
Adv Exp Med Biol ; 890: 149-74, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26703804

RESUMO

Small cell lung cancer (SCLC) is an aggressive, poorly differentiated neuroendocrine carcinoma with distinct clinical, pathological and molecular characteristics. Despite robust responses to initial chemotherapy and radiation, the prognosis of patients with SCLC remains poor with an overall 5-year survival rate of less than 10 %. Despite the fact that numerous molecularly targeted approaches have thus far failed to demonstrate clinical utility in SCLC, further advances will rely on better definition of the biological pathways that drive survival, proliferation and metastasis. Recent next-generation, molecular profiling studies have identified many new therapeutic targets in SCLC, as well as extreme genomic instability which explains the high degree of resistance. A wide variety of anti-angiogenic agents, growth factor inhibitors, pro-apoptotic agents, and epigenetic modulators have been evaluated in SCLC and many studies of these strategies are on-going. Perhaps the most promising approaches involve agents targeting cancer stem cell pathways and immunomodulatory drugs that interfere with the PD1 and CTLA-4 pathways. SCLC offers many barriers to the development of successful therapy, including limited tumor samples, inadequate preclinical models, high mutational burden, and aggressive tumor growth which impairs functional status and hampers enrollment on clinical trials.


Assuntos
Antineoplásicos/uso terapêutico , Regulação Neoplásica da Expressão Gênica , Fatores Imunológicos/uso terapêutico , Neoplasias Pulmonares/tratamento farmacológico , Proteínas de Neoplasias/genética , Carcinoma de Pequenas Células do Pulmão/tratamento farmacológico , Antígeno CTLA-4/antagonistas & inibidores , Antígeno CTLA-4/genética , Antígeno CTLA-4/imunologia , Proliferação de Células/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/genética , Instabilidade Genômica , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/mortalidade , Neoplasias Pulmonares/patologia , Proteínas de Neoplasias/antagonistas & inibidores , Proteínas de Neoplasias/imunologia , Células-Tronco Neoplásicas/efeitos dos fármacos , Células-Tronco Neoplásicas/metabolismo , Células-Tronco Neoplásicas/patologia , Medicina de Precisão , Receptor de Morte Celular Programada 1/antagonistas & inibidores , Receptor de Morte Celular Programada 1/genética , Receptor de Morte Celular Programada 1/imunologia , Carcinoma de Pequenas Células do Pulmão/genética , Carcinoma de Pequenas Células do Pulmão/mortalidade , Carcinoma de Pequenas Células do Pulmão/patologia , Análise de Sobrevida
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