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1.
Hereditas ; 159(1): 4, 2022 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-35042566

RESUMO

Maffucci syndrome (MS, OMIM 166000) is an extremely unusual, nonhereditary, multisystemic disorder that is characterized with multiple enchondromas and vascular lesions, most of which are spindle cell hemangiomas. Complications of MS, such as bone deformities and dysfunction caused by enchondromas, usually increase during childhood and adolescence. Malignant transformation of enchondromas and other malignancies are the most severe complications. MS is caused by somatic mosaic IDH1/2 mutations, 65% of which are the IDH1 p.Arg132Cys variant. Due to its rarity, there is no international consensus for the most appropriate treatment option of MS.Here, we report a case of a female patient presenting with multiple enchondromas and spindle cell hemangiomas (SCHs) on bilateral hand and feet diagnosed as MS. A detailed clinical, pathological and genetic diagnosis of MS was rendered. Integrative Genomics Viewer (IGV) visualization of next-generation sequencing (NGS) data revealed the consistent detection of the low-frequency somatic IDH1 p.Arg132Cys mutation between SCH tissue and cystic blood-derived cfDNA. This is the first successful molecular diagnosis of MS complicated with SCH utilizing minimally invasive cfDNA techniques. We suggest that cfDNA sequencing could potentially be used as an alternative, reliable and sensitive method to identify molecular information for genetic diagnosis and for future targeted therapies of MS.


Assuntos
Ácidos Nucleicos Livres , Encondromatose , Hemangioma , Encondromatose/genética , Feminino , Humanos , Isocitrato Desidrogenase/genética , Mutação
2.
Cancer Lett ; 524: 57-69, 2022 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-34656688

RESUMO

Growing bodies of evidence have demonstrated that the identification of prostate cancer (PCa) biomarkers in the patients' blood and urine may remarkably improve PCa diagnosis and progression monitoring. Among diverse cancer-derived circulating materials, extracellular RNA molecules (exRNAs) represent a compelling component to investigate cancer-related alterations. Once outside the intracellular environment, exRNAs circulate in biofluids either in association with protein complexes or encapsulated inside extracellular vesicles (EVs). Notably, EV-associated RNAs (EV-RNAs) were used for the development of several assays (such as the FDA-approved Progensa Prostate Cancer Antigen 3 (PCA3 test) aiming at improving early PCa detection. EV-RNAs encompass a mixture of species, including small non-coding RNAs (e.g. miRNA and circRNA), lncRNAs and mRNAs. Several methods have been proposed to isolate EVs and relevant RNAs, and to perform RNA-Seq studies to identify potential cancer biomarkers. However, EVs in the circulation of a cancer patient include a multitude of diverse populations that are released by both cancer and normal cells from different tissues, thereby leading to a heterogeneous EV-RNA-associated transcriptional signal. Decrypting the complexity of such a composite signal is nowadays the major challenge faced in the identification of specific tumor-associated RNAs. Multiple deconvolution algorithms have been proposed so far to infer the enrichment of cancer-specific signals from gene expression data. However, novel strategies for EVs sorting and sequencing of RNA associated to single EVs populations will remarkably facilitate the identification of cancer-related molecules. Altogether, the studies summarized here demonstrate the high potential of using EV-RNA biomarkers in PCa and highlight the urgent need of improving technologies and computational approaches to characterize specific EVs populations and their relevant RNA cargo.


Assuntos
Antígenos de Neoplasias/genética , Ácidos Nucleicos Livres/genética , MicroRNAs/genética , Neoplasias da Próstata/genética , Biomarcadores Tumorais/genética , Vesículas Extracelulares/genética , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Masculino , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/patologia , RNA-Seq
3.
Biochim Biophys Acta Mol Cell Res ; 1869(1): 119147, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34600918

RESUMO

Fragment size distribution, the important biological properties of cell-free DNA (cfDNA), provides useful information required for diagnostic assay development. However, besides methodological discrepancies, it varies due to the complicated origins and occurrences of in vivo cfDNA. In addition, limited data are available concerning the cfDNA associated with autophagy and distributional difference between cf-mitochondrial DNA (cf-mtDNA) and cf-nuclear DNA (cf-nDNA) fragments. Here we developed an in vitro model of mouse microglial cell (BV-2) with starvation-induced autophagy, in which cfDNA was isolated from the cell supernatant by ultrafiltration (UF) and column-based commercial kit (CC), respectively. Using Agilent 2100 Bioanalyzer, a DNA ladder pattern as the presence of peaks corresponding to mono-, di- and tri-nucleosomes was clearly visualized both in isolation products of UF and CC. However, we also detected shorter fragments than mono-nucleosome by UF. In comparing the UF and CC, we found that the former produced the higher recovery efficiency for spiked-in DNA of shorter fragments than mono-nucleosome in both water and medium, but the latter was superior for spiked-in DNA fragments which were longer than or equal to mono-nucleosome in medium. Combined with these two isolation methods, we have observed that autophagy-associated cf-mtDNA and cf-nDNA were both highly enriched in

Assuntos
Autofagia , Ácidos Nucleicos Livres/química , Fragmentação do DNA , DNA Mitocondrial/química , Nucleossomos/química , Animais , Linhagem Celular , Ácidos Nucleicos Livres/genética , DNA Mitocondrial/genética , Camundongos , Microglia/metabolismo , Nucleossomos/genética , Inanição/metabolismo
4.
J Pharm Biomed Anal ; 208: 114441, 2022 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-34749106

RESUMO

Circulating cell free mitochondrial DNA (ccf-mtDNA) has emerged as a potential marker for diagnosis and prognosis of different chronic and age associated non-communicable diseases. Therefore, owing to its biomarker potential, we herein assessed a novel nano-photonic dual hybrid assay system for rapid and specific detection of ccf-mtDNA. The assay comprised of two systems, i.e. a capture and screen facet containing aminopyrene tethered carbon quantum dots for effective screening of circulating cell free nucleic acids (ccf-NAs) and a quantum dot conjugated probe for precise detection of ccf-mtDNA in the screened ccf-NAs. Our observations suggested that the developed dual-assay system possesses high feasibility and selectivity in screening of ccf-NAs and estimation of ccfmtDNA in a given sample. It also offers high versatility of measurement in different analytical platforms, indicating the translational potential of the method for possible disease risk assessment in control and field settings.


Assuntos
Ácidos Nucleicos Livres , Pontos Quânticos , Biomarcadores , DNA Mitocondrial/genética , Mitocôndrias
5.
Ann Lab Med ; 42(2): 141-149, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635607

RESUMO

Standardization of cell-free DNA (cfDNA) testing processes is necessary to obtain clinically reliable results. The pre-analytical phase of cfDNA testing greatly influences the results because of the low proportion and stability of circulating tumor DNA (ctDNA). In this review, we provide evidence-based clinical practice guidelines for pre-analytical phase procedures of plasma epidermal growth factor receptor gene (EGFR) variant testing. Specific recommendations for pre-analytical procedures were proposed based on evidence from the literature and our experimental data. Standardization of pre-analytical procedures can improve the analytical performance of cfDNA testing.


Assuntos
Ácidos Nucleicos Livres , DNA Tumoral Circulante , Receptores ErbB/genética , Humanos
6.
Curr Oncol ; 28(5): 3717-3728, 2021 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-34677235

RESUMO

Amplification (amp) of MET can be observed in cases of focal gene copy number gain, such as MET-driven amp, or with a gain of chromosome 7, such as aneuploidy. Several studies have shown that only high-level focal MET amp (MET/CEP7 ratio ≥5) is oncogenic, with such tumors responding to targeted therapy. However, there are few reports on how to distinguish between focal amplification and aneuploidy using next-generation sequencing (NGS). A total of 1025 patients with advanced solid tumors (typically pre-treated) were tested with a non-invasive comprehensive cfDNA NGS panel (Guardant360) from July 2014 to June 2019. Since bioinformatics upgrades of Guardant360 were undergoing in September 2018, focal MET amp was determined by our independent algorithm using the cohorts tested before September 2018 (291 patients), and validation was performed in the remaining cohort (734 patients). MET alterations (alts) associated with aberrant signaling were found in 110 patients (10.7%) among nine different cancer types, most commonly in non-small cell (12.2%, 62/510) and small cell (33.3%, 3/9) lung cancers, gastroesophageal cancer (19.4%, 7/36), and prostate adenocarcinoma (15.6%; 5/32). Among 291 patients tested before September 2018, 37 (12.7%) had MET alts. Among these, 24 (64.9%) had amps, 5 (13.5%) had exon 14 skipping, and 13 (35.1%) had single nucleotide variants (SNVs). Co-alterations, such as amp + SNVs, were found in four samples (10.8%). Among 24 MET amps, 29.2% (7/24) were focal according to our algorithm. MET copy number was significantly higher with focal amp compared to non-focal amp (mean copy number 3.26 vs. 2.44, respectively, p = 0.00304). In 734 patients tested after September 2018, our definition of focal MET amp was detected in 4.2% (31/734). Overall, focal amplification based on our algorithm was 3.7% (=38/1025). This study describes an approach to distinguish focal and non-focal MET amplification using comprehensive genomic profiling of cfDNA in advanced cancer patients. Focal MET amp accounted for ~30% of all MET amp, which was found in 3.7% of patients with diverse cancers and was associated with a higher plasma copy number. Clinical studies are warranted to assess the clinical utility of targeted therapies for tumors with focal MET amplification detected by NGS of cfDNA.


Assuntos
Ácidos Nucleicos Livres , DNA Tumoral Circulante , Aneuploidia , Ácidos Nucleicos Livres/genética , DNA Tumoral Circulante/genética , Genômica , Humanos , Neoplasias/diagnóstico , Neoplasias/genética
7.
In Vivo ; 35(6): 3449-3457, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34697181

RESUMO

BACKGROUND/AIM: Preimplantation genetic testing (PGT) for chromosomal screening, based on embryo biopsy, has significant limitations. Cell-free DNA (cf-DNA) has been detected in spent culture medium (SCM), opening new horizons for the development of non-invasive PGT (ni-PGT). In this study, we evaluated the diagnostic performance of ni-PGT for aneuploidy (niPGT-A), comparing the results of trophectoderm biopsies (TE) and respective SCM from individually cultured embryos via Next Generation Sequencing (NGS). MATERIALS AND METHODS: Forty fresh embryos were analyzed. TE and SCM from blastocysts were collected and analyzed. RESULTS: We detected cfDNA in 100% of samples tested. The overall concordance rate between the ni-PGT-A and PGT-A was 27/33 (81.8%). The full concordance rate was 21/33 (63.6%). The aneuploidy agreement was 91.66%, and the euploidy agreement was 76.19%. CONCLUSION: We found a good accordance between TE and SCM analysis, suggesting that niPGT-A could be a reliable alternative for chromosomal abnormalities assessment of in vitro cultured embryos.


Assuntos
Ácidos Nucleicos Livres , Diagnóstico Pré-Implantação , Aneuploidia , Blastocisto , Ácidos Nucleicos Livres/genética , Feminino , Testes Genéticos , Humanos , Gravidez
8.
Pediatrics ; 148(5)2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34716219

RESUMO

Lymphomatous involvement of the larynx is a rare entity. We present a case of atypical laryngotracheitis as the initial manifestation of non-Hodgkin's lymphoma in a pediatric patient. The diagnosis was aided through the use of microbial cell-free DNA (mcfDNA) testing, which detected the presence of Epstein-Barr virus in the patient's plasma. This enabled the consideration of an Epstein-Barr virus-related lymphoproliferative process, leading to additional workup and the final diagnosis of lymphoma. To our knowledge, this is the first case of mcfDNA testing leading not simply to an infectious organism, but further to a new oncologic diagnosis. Plasma mcfDNA testing has the potential to inform clinical practice beyond classic infectious disease manifestations. In this article, we review both the possible future applications and the areas of further investigation that remain.


Assuntos
Infecções por Vírus Epstein-Barr/diagnóstico , Herpesvirus Humano 4/genética , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias Laríngeas/diagnóstico , Linfoma não Hodgkin/diagnóstico , Ácidos Nucleicos Livres/sangue , Criança , Citomegalovirus/genética , Herpesvirus Humano 4/isolamento & purificação , Humanos , Neoplasias Infratentoriais/terapia , Neoplasias Laríngeas/complicações , Neoplasias Laríngeas/virologia , Laringite/diagnóstico , Laringite/etiologia , Linfoma não Hodgkin/complicações , Linfoma não Hodgkin/virologia , Masculino , Meduloblastoma/terapia , Neoplasias da Coluna Vertebral/terapia , Tomografia Computadorizada por Raios X , Traqueíte/diagnóstico , Traqueíte/etiologia
9.
Can J Vet Res ; 85(4): 271-278, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34602731

RESUMO

This study aimed to identify potential biomarkers of canine pyometra and their correlations with clinical parameters. First, 90 dogs with pyometra and 26 healthy female dogs were compared. Then, paired samples (before and after ovariohysterectomy) from 22 dogs with pyometra and 9 healthy controls from the initial cohort were compared. Concentrations of acute inflammatory proteins, C-reactive protein (CRP) and serum amyloid A (SAA), and cell-free DNA (cfDNA), were significantly higher in dogs with pyometra than in clinically healthy dogs. Cell-free DNA was the most sensitive biomarker for systemic inflammation, based on the receiver operating characteristic curve analysis (area under the curve = 0.959). In addition, cfDNA and CRP were significantly associated with inflammation and organ injury-related clinical parameters. Following the surgical removal of the inflamed uterus, interleukin-6 (IL-6), high-mobility group box 1 (HMGB1), and procalcitonin (PCT) significantly decreased, whereas changes in CRP, SAA, and cfDNA were not significant. These findings indicate that cfDNA, CRP, and SAA are potential clinical biomarkers of systemic inflammation in dogs with pyometra and PCT, IL-6, and HMGB1 are potential biomarkers of clinical recovery.


Assuntos
Doenças do Cão/patologia , Histerectomia/veterinária , Inflamação/sangue , Ovariectomia/veterinária , Piometra/veterinária , Animais , Biomarcadores/sangue , Proteína C-Reativa/análise , Estudos de Casos e Controles , Ácidos Nucleicos Livres/sangue , Estudos de Coortes , Doenças do Cão/terapia , Cães , Feminino , Inflamação/metabolismo , Piometra/patologia , Piometra/terapia , Curva ROC , Proteína Amiloide A Sérica/análise
10.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(10): 1025-1029, 2021 Oct 10.
Artigo em Chinês | MEDLINE | ID: mdl-34625947

RESUMO

Fetal cell free DNA (cfDNA) in maternal blood circulation mainly originates from placental trophoblasts which have dual characteristics of apoptotic cells and the embryo, and can be affected by maternal factors. Pregnancy-related diseases including preeclampsia, gestational diabetes mellitus, preeclampsia, macrosomia and fetal growth restriction can seriously affect maternal health and pregnancy outcome. Early prediction and timely intervention are important means to reduce the risk. Fetal cfDNA and prediction of pregnancy-related diseases have become a hot topicfor current research. This paper reviews the latest progress made in the field.


Assuntos
Ácidos Nucleicos Livres , Complicações na Gravidez , Ácidos Nucleicos Livres/genética , Feminino , Feto , Humanos , Placenta , Gravidez , Resultado da Gravidez
11.
Nat Commun ; 12(1): 5955, 2021 10 12.
Artigo em Inglês | MEDLINE | ID: mdl-34642316

RESUMO

Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials. Here, we investigate the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We recover immune and malignant cell types in the CSF, characterize cell behavior changes following ICI, and identify genomic features associated with relevant clinical phenomena. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and demonstrates clinical utility of cell-free and single-cell genomic measurements for LMD research.


Assuntos
Neoplasias Encefálicas/tratamento farmacológico , Antígeno CTLA-4/imunologia , Inibidores de Checkpoint Imunológico/uso terapêutico , Carcinomatose Meníngea/tratamento farmacológico , Neoplasias Meníngeas/tratamento farmacológico , Receptor de Morte Celular Programada 1/imunologia , Microambiente Tumoral/efeitos dos fármacos , Adulto , Idoso , Anticorpos Monoclonais Humanizados/uso terapêutico , Neoplasias Encefálicas/imunologia , Neoplasias Encefálicas/mortalidade , Neoplasias Encefálicas/secundário , Linfócitos T CD8-Positivos/efeitos dos fármacos , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/patologia , Antígeno CTLA-4/antagonistas & inibidores , Antígeno CTLA-4/genética , Ácidos Nucleicos Livres/genética , Ácidos Nucleicos Livres/imunologia , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Imunoterapia , Interferon gama/genética , Interferon gama/imunologia , Ipilimumab/uso terapêutico , Masculino , Carcinomatose Meníngea/imunologia , Carcinomatose Meníngea/mortalidade , Carcinomatose Meníngea/patologia , Neoplasias Meníngeas/imunologia , Neoplasias Meníngeas/mortalidade , Neoplasias Meníngeas/patologia , Pessoa de Meia-Idade , Nivolumabe/uso terapêutico , Receptor de Morte Celular Programada 1/antagonistas & inibidores , Receptor de Morte Celular Programada 1/genética , Análise de Célula Única , Análise de Sobrevida , Microambiente Tumoral/genética , Microambiente Tumoral/imunologia
13.
BMC Cancer ; 21(1): 1075, 2021 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-34600526

RESUMO

BACKGROUND: Monitoring circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs), known as liquid biopsies, continue to be developed as diagnostic and prognostic markers for a wide variety of cancer indications, mainly due to their minimally invasive nature and ability to offer a wide range of phenotypic and genetic information. While liquid biopsies maintain significant promising benefits, there is still limited information regarding the kinetics of ctDNA and CTCs following radiation therapy which remains a vital treatment modality in head and neck cancers. This study aims to describe the kinetics of ctDNA and CTCs following radiation exposure in a preclinical rabbit model with VX2 induced buccal carcinoma. METHODS: Seven rabbits were inoculated with VX2 cells in the buccal mucosa and subjected to radiation. At selected time points, blood sampling was performed to monitor differing levels of ctDNA and CTC. Plasma ctDNA was measured with quantitative PCR for papillomavirus E6 while CTCs were quantified using an immunomagnetic nanoparticles within a microfluidic device. Comparisons of CTC detection with EpCAM compared to multiple surface markers (EGFR, HER2 and PSMA) was evaluated and correlated with the tumor size. RESULTS: Plasma ctDNA reflects the overall tumor burden within the animal model. Analysis of correlations between ctDNA with tumor and lymph node volumes showed a positive correlation (R = 0.452 and R = 0.433 [p < 0.05]), respectively. Over the course of treatment, ctDNA levels declined and quickly becomes undetectable following tumor eradication. While during the course of treatment, ctDNA levels were noted to rise particularly upon initiation of radiation following scheduled treatment breaks. Levels of CTCs were observed to increase 1 week following inoculation of tumor to the primary site. For CTC detection, the use of multiple surface markers showed a greater sensitivity when compared to detection using only EpCAM. Plasma CTC levels remained elevated following radiation therapy which may account for an increased shedding of CTCs following radiation. CONCLUSION: This study demonstrates the utility of ctDNA and CTCs detection in response to radiation treatment in a preclinical head and neck model, allowing for better understanding of liquid biopsy applications in both clinical practice and research development.


Assuntos
Carcinoma de Células Escamosas/sangue , Carcinoma de Células Escamosas/radioterapia , Ácidos Nucleicos Livres/sangue , Neoplasias Bucais/sangue , Neoplasias Bucais/radioterapia , Animais , Biomarcadores Tumorais/sangue , Carcinoma de Células Escamosas/induzido quimicamente , DNA Tumoral Circulante/sangue , Papillomavirus de Coelho Cottontail , Molécula de Adesão da Célula Epitelial/sangue , Neoplasias de Cabeça e Pescoço/sangue , Neoplasias de Cabeça e Pescoço/induzido quimicamente , Neoplasias de Cabeça e Pescoço/radioterapia , Separação Imunomagnética/métodos , Biópsia Líquida/métodos , Masculino , Neoplasias Bucais/induzido quimicamente , Neoplasias Bucais/virologia , Nanopartículas , Transplante de Neoplasias , Fases de Leitura Aberta , Coelhos , Dosagem Radioterapêutica , Carga Tumoral
14.
PLoS One ; 16(10): e0244332, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34610014

RESUMO

BACKGROUND: Colorectal cancer (CRC) is one of the leading causes of cancer-related death. Early detection is critical to reduce CRC morbidity and mortality. In order to meet this need, we developed a molecular clamping assay called the ColoScape TM assay for early colorectal cancer diagnostics. METHODS: Nineteen mutations in four genes (APC, KRAS, BRAF and CTNNB1) associated with early events in CRC pathogenesis are targeted in the ColoScapeTM assay. Xenonucleic Acid (XNA)-mediated qPCR clamping technology was applied to minimize the wild-type background amplification in order to improve assay sensitivity of CRC mutation detection. The assay analytical performance was verified and validated, cfDNA and FFPE CRC patient samples were evaluated, and an ROC curve was applied to evaluate its performance. RESULTS: The data showed that the assay analytical sensitivity was 0.5% Variant Allele Frequency, corresponding to ~7-8 copies of mutant DNA with 5 ng total DNA input per test. This assay is highly reproducible with intra-assay CV of <3% and inter-assay CV of <5%. We have investigated 380 clinical samples including plasma cfDNA and FFPE samples from patients with precancerous and different stages of CRC. The preliminary assay clinical specificity and sensitivity for CRC cfDNA were: 100% (95% CI, 80.3-97.5%) and 92.2% (95% CI, 94.7-100%), respectively, with AUC of 0.96; 96% specificity (95% CI, 77.6-99.7%) and 92% sensitivity (95% CI, 86.1-95.6%) with AUC of 0.94 for CRC FFPE; 95% specificity (95% CI, 82.5%-99.1%) and 62.5% sensitivity (95% CI, 35.8%-83.7%) with AUC of 0.79 for precancerous lesions cfDNA. CONCLUSIONS: The XNA-mediated molecular clamping assay is a rapid, precise, and sensitive assay for the detection of precancerous lesions cfDNA and CRC cfDNA or FFPE samples.


Assuntos
Neoplasias Colorretais/diagnóstico , Detecção Precoce de Câncer/métodos , Sequência de Bases , Linhagem Celular Tumoral , Ácidos Nucleicos Livres/genética , DNA Tumoral Circulante/genética , Neoplasias Colorretais/genética , DNA de Neoplasias/genética , Células HCT116 , Humanos , Mutação/genética , Reação em Cadeia da Polimerase em Tempo Real
15.
J Hematol Oncol ; 14(1): 175, 2021 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-34702327

RESUMO

Previous studies on liquid biopsy-based early detection of advanced colorectal adenoma (advCRA) or adenocarcinoma (CRC) were limited by low sensitivity. We performed a prospective study to establish an integrated model using fragmentomic profiles of plasma cell-free DNA (cfDNA) for accurately and cost-effectively detecting early-stage CRC and advCRA. The training cohort enrolled 310 participants, including 149 early-stage CRC patients, 46 advCRA patients and 115 healthy controls. Plasma cfDNA samples were prepared for whole-genome sequencing. An ensemble stacked model differentiating healthy controls from advCRA/early-stage CRC patients was trained using five machine learning models and five cfDNA fragmentomic features based on the training cohort. The model was subsequently validated using an independent test cohort (N = 311; including 149 early-stage CRC, 46 advCRA and 116 healthy controls). Our model showed an area under the curve (AUC) of 0.988 for differentiating advCRA/early-stage CRC patients from healthy individuals in an independent test cohort. The model performed even better for identifying early-stage CRC (AUC 0.990) compared to advCRA (AUC 0.982). At 94.8% specificity, the sensitivities for detecting advCRA and early-stage CRC reached 95.7% and 98.0% (0: 94.1%; I: 98.5%), respectively. Promisingly, the detection sensitivity has reached 100% and 97.6% in early-stage CRC patients with negative fecal occult or CEA blood test results, respectively. Finally, our model maintained promising performances (AUC: 0.982, 94.4% sensitivity at 94.8% specificity) even when sequencing depth was down-sampled to 1X. Our integrated predictive model demonstrated an unprecedented detection sensitivity for advCRA and early-stage CRC, shedding light on more accurate noninvasive CRC screening in clinical practice.


Assuntos
Adenocarcinoma/diagnóstico , Adenoma/diagnóstico , Ácidos Nucleicos Livres/genética , Neoplasias Colorretais/diagnóstico , Adenocarcinoma/sangue , Adenocarcinoma/genética , Adenoma/sangue , Adenoma/genética , Biomarcadores Tumorais/sangue , Biomarcadores Tumorais/genética , Ácidos Nucleicos Livres/sangue , Neoplasias Colorretais/sangue , Neoplasias Colorretais/genética , Detecção Precoce de Câncer , Humanos , Estudos Prospectivos
16.
BMC Med ; 19(1): 243, 2021 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-34641873

RESUMO

BACKGROUND: Plasma cell-free DNA (cfDNA) methylation has shown promising results in the early detection of multiple cancers recently. Here, we conducted a study to investigate the performance of cfDNA methylation in the early detection of esophageal cancer (ESCA). METHODS: Specific methylation markers for ESCA were identified and optimized based on esophageal tumor and paired adjacent tissues (n = 24). Age-matched participants with ESCA (n = 85), benign esophageal diseases (n = 10), and healthy controls (n = 125) were randomized into the training and test sets to develop a classifier to differentiate ESCA from healthy controls and benign esophageal disease. The classifier was further validated in an independent plasma cohort of ESCA patients (n = 83) and healthy controls (n = 98). RESULTS: In total, 921 differentially methylated regions (DMRs) between tumor and adjacent tissues were identified. The early detection classifier based on those DMRs was first developed and tested in plasma samples, discriminating ESCA patients from benign and healthy controls with a sensitivity of 76.2% (60.5-87.9%) and a specificity of 94.1% (85.7-98.4%) in the test set. The performance of the classifier was consistent irrespective of sex, age, and pathological diagnosis (P > 0.05). In the independent plasma validation cohort, similar performance was observed with a sensitivity of 74.7% (64.0-83.6%) and a specificity of 95.9% (89.9-98.9%). Sensitivity for stage 0-II was 58.8% (44.2-72.4%). CONCLUSION: We demonstrated that the cfDNA methylation patterns could distinguish ESCAs from healthy individuals and benign esophageal diseases with promising sensitivity and specificity. Further prospective evaluation of the classifier in the early detection of ESCAs in high-risk individuals is warranted.


Assuntos
Ácidos Nucleicos Livres , Neoplasias Esofágicas , Biomarcadores Tumorais/genética , Estudos de Casos e Controles , Metilação de DNA , Detecção Precoce de Câncer , Neoplasias Esofágicas/diagnóstico , Neoplasias Esofágicas/genética , Humanos
17.
World J Gastroenterol ; 27(34): 5666-5681, 2021 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-34629793

RESUMO

Gastrointestinal (GI) cancers are among the most common cancer types and leading causes of cancer-related deaths worldwide. There is a tremendous clinical need for effective early diagnosis for better healthcare of GI cancer patients. In this article, we provide a short overview of the recent advances in GI cancer diagnosis. In the first part, we discuss the applications of blood-based biomarkers, such as plasma circulating cell-free DNA, circulating tumor cells, extracellular vesicles, and circulating cell-free RNA, for cancer liquid biopsies. In the second part, we review the current trends of artificial intelligence (AI) for pathology image and tissue biopsy analysis for GI cancer, as well as deep learning-based approaches for purity assessment of tissue biopsies. We further provide our opinions on the future directions in blood-based and AI-enhanced approaches for GI cancer diagnosis, and we think that these fields will have more intensive integrations with clinical needs in the near future.


Assuntos
Ácidos Nucleicos Livres , Neoplasias Gastrointestinais , Inteligência Artificial , Detecção Precoce de Câncer , Neoplasias Gastrointestinais/diagnóstico , Humanos , Biópsia Líquida
18.
Prog Orthod ; 22(1): 33, 2021 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-34657984

RESUMO

OBJECTIVES: Literature shows that the expression of various biomarkers in peri-miniscrew crevicular fluid (PMICF) is related to the stability of miniscrew implants (MSIs). The present study investigated the role and alterations in levels of circulating cell-free nucleic acids (cfNAs) in PMICF before and after orthodontic loading. MATERIAL AND METHODS: This prospective study consisted of forty-six MSIs placed between the second premolar and first molar in the maxillary and mandibular arches. Direct loading was done after 3 weeks of MSI insertion with nickel-titanium closed coil spring exerting a force of 200 g. The PMICF sample was collected at various time intervals, and the level of cfNA was determined. Clinical parameters, including implant mobility and gingival health, were also assessed. Pre-loading and post-loading parameters were assessed using Wilcoxon's rank-sum test. RESULTS: Among 46 MSIs, 36 were stable during the study and 10 MSIs showed peri-implant inflammation and increased mobility. There was a significant rise in the cfNA concentration 24 h after implant insertion (0.4 ± 0.86 ng/µl). The level of cfNAs significantly decreased over 3 weeks and reached the baseline level (0.2 ± 0.31 ng/µl). There was also a significant rise in the levels of cfNA (0.8 ± 0.70 ng/µl) at 24 h after loading MSIs, which gradually decreased to 0.2 ± 0.24 ng/µl after 63 days. The expression of cfNAs was on the average 0.32 units more in the cases with failed implants (P = 0.05). CONCLUSIONS: cfNA levels in PMICF showed an upward trend 24 h after MSI insertion and 24 h after orthodontic loading. The expression of cfNA was more in cases with failed MSIs. Hence, the cfNAs can be considered as a prognostic biomarker of MSI stability.


Assuntos
Ácidos Nucleicos Livres , Procedimentos de Ancoragem Ortodôntica , Parafusos Ósseos , Humanos , Estudos Prospectivos , Técnicas de Movimentação Dentária
19.
J Immunol ; 207(10): 2433-2444, 2021 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-34663619

RESUMO

Throughout gestation, the maternal immune system is tightly modulated to allow growth of a semiallogeneic fetus. During the third trimester, the maternal immune system shifts to a proinflammatory phenotype in preparation for labor. What induces this shift remains unclear. Cell-free fetal DNA (cffDNA) is shed by the placenta and enters maternal circulation throughout pregnancy. Levels of cffDNA are increased as gestation progresses and peak before labor, coinciding with a shift to proinflammatory maternal immunity. Furthermore, cffDNA is abnormally elevated in plasma from women with complications of pregnancy, including preterm labor. Given the changes in maternal immunity at the end of pregnancy and the role of sterile inflammation in the pathophysiology of spontaneous preterm birth, we hypothesized that cffDNA can act as a damage-associated molecular pattern inducing an inflammatory cytokine response that promotes hallmarks of parturition. To test this hypothesis, we stimulated human maternal leukocytes with cffDNA from primary term cytotrophoblasts or maternal plasma and observed significant IL-1ß and CXCL10 secretion, which coincides with phosphorylation of IFN regulatory factor 3 and caspase-1 cleavage. We then show that human maternal monocytes are crucial for the immune response to cffDNA and can activate bystander T cells to secrete proinflammatory IFN-γ and granzyme B. Lastly, we find that the monocyte response to cffDNA leads to vascular endothelium activation, induction of myometrial contractility, and PGE2 release in vitro. Our results suggest that the immune response to cffDNA can promote key features of the parturition cascade, which has physiologic consequences relevant to the timing of labor.


Assuntos
Ácidos Nucleicos Livres/imunologia , Feto/imunologia , Monócitos/imunologia , Parto/imunologia , Trofoblastos/imunologia , Feminino , Humanos , Gravidez
20.
Biomed Res Int ; 2021: 5517786, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34513991

RESUMO

Objective: Increasing evidence emphasizes the implications of dysregulated apoptosis and autophagy cellular processes in coronary artery disease (CAD). Herein, we aimed to explore apoptosis- and autophagy-related long noncoding RNAs (lncRNAs) in peripheral blood of CAD patients. Methods: The mRNA and lncRNA expression profiles were retrieved from the Gene Expression Omnibus (GEO) database. With ∣fold change | >1.5 and adjusted p value < 0.05, differentially expressed apoptosis- and autophagy-related mRNAs were screened between CAD and healthy blood samples. Also, differentially expressed lncRNAs were identified for CAD. Using the psych package, apoptosis- and autophagy-related lncRNAs were defined with Spearson's correlation analysis. Receiver operating characteristic (ROC) curves were conducted for the assessment of the diagnosed efficacy of these apoptosis- and autophagy-related lncRNAs. Results: Our results showed that 24 apoptosis- and autophagy-related mRNAs were abnormally expressed in CAD than normal controls. 12 circulating upregulated and 1 downregulated apoptosis- and autophagy-related lncRNAs were identified for CAD. The ROCs confirmed that AC004485.3 (AUC = 0.899), AC004920.3 (AUC = 0.93), AJ006998.2 (AUC = 0.776), H19 (AUC = 0.943), RP5-902P8.10 (AUC = 0.956), RP5-1114G22.2 (AUC = 0.883), RP11-247A12.1 (AUC = 0.885), RP11-288L9.4 (AUC = 0.928), RP11-344B5.2 (AUC = 0.858), RP11-452C8.1 (AUC = 0.929), RP11-565A3.1 (AUC = 0.893), and XXbac-B33L19.4 (AUC = 0.932) exhibited good performance in differentiating CAD from healthy controls. Conclusion: Collectively, our findings proposed that circulating apoptosis- and autophagy-related lncRNAs could become underlying diagnostic markers for CAD in clinical practice.


Assuntos
Ácidos Nucleicos Livres/genética , Doença da Artéria Coronariana/genética , RNA Longo não Codificante/genética , Apoptose/genética , Autofagia/genética , Biomarcadores/sangue , Ácidos Nucleicos Livres/análise , Ácidos Nucleicos Livres/sangue , China , Doença da Artéria Coronariana/diagnóstico , Doença da Artéria Coronariana/fisiopatologia , Bases de Dados Genéticas , Feminino , Expressão Gênica/genética , Perfilação da Expressão Gênica/métodos , Humanos , Masculino , RNA Longo não Codificante/análise , RNA Mensageiro/genética , Curva ROC , Transcriptoma/genética
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