176,587 results match your criteria expression profiling


An enhancer-driven stem cell-like program mediated by SOX9 blocks intestinal differentiation in colorectal cancer.

Gastroenterology 2021 Sep 24. Epub 2021 Sep 24.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA;; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA; Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA;; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA;. Electronic address:

Background And Aims: Genomic alterations that encourage stem cell activity and hinder proper maturation are central to the development of colorectal cancer (CRC). Key molecular mediators that promote these malignant properties require further elucidation to galvanize translational advances. We therefore aimed to characterize a key factor that blocks intestinal differentiation, define its transcriptional and epigenetic program, and provide preclinical evidence for therapeutic targeting in CRC. Read More

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September 2021

Regulatory roles of three miRNAs on allergen mRNA expression in Tyrophagus putrescentiae.

Allergy 2021 Sep 27. Epub 2021 Sep 27.

Department of Clinical Laboratory, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, 214023, China.

Background: Tyrophagus putresecentiae is an important mite species in rural and urban environments, causing sensitization and allergic disease. While evidence suggests that microRNAs (miRNAs) may regulate the expression of allergen-encoding genes, no study has directly investigated this possibility. Here, this gap was addressed by profiling miRNAs and elucidating their target allergen messenger RNAs (mRNAs) in this mite species. Read More

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September 2021

Identification and validation of circulating miRNAs as potential new biomarkers for severe liver disease in patients with leptospirosis.

PLoS One 2021 27;16(9):e0257805. Epub 2021 Sep 27.

Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.

Background: Leptospirosis, a global zoonotic infectious disease, has various clinical manifestations ranging from mild self-limiting illness to life-threatening with multi-organ damage, including liver involvement. This study was aimed at identifying circulating microRNAs (miRNAs) as novel biomarkers for predicting severe liver involvement in patients with leptospirosis.

Methods: In a discovery set, 12 serum samples of patients with anicteric and icteric leptospirosis at initial clinical presentation were used for miRNA profiling by a NanoString nCounter miRNA assay. Read More

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September 2021

Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species.

PLoS Comput Biol 2021 Sep 27;17(9):e1009450. Epub 2021 Sep 27.

National Institutes of Health, National Cancer Institute, Center for Cancer Research, Comparative Oncology Program, Bethesda, Maryland, United States of America.

Understanding relationships between spontaneous cancer in companion (pet) canines and humans can facilitate biomarker and drug development in both species. Towards this end we developed an experimental-bioinformatic protocol that analyzes canine transcriptomics data in the context of existing human data to evaluate comparative relevance of canine to human cancer. We used this protocol to characterize five canine cancers: melanoma, osteosarcoma, pulmonary carcinoma, B- and T-cell lymphoma, in 60 dogs. Read More

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September 2021

RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.

PLoS Genet 2021 Sep 27;17(9):e1009821. Epub 2021 Sep 27.

Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.

RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3' ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. Read More

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September 2021

Intrahepatic cholangiocyte regeneration from an Fgf-dependent extrahepatic progenitor niche in a zebrafish model of Alagille Syndrome.

Hepatology 2021 Sep 27. Epub 2021 Sep 27.

Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, United States.

Alagille Syndrome (ALGS) is a congenital disorder caused by mutations in the Notch ligand gene, JAGGED1, leading to neonatal loss of intrahepatic duct (IHD) cells and cholestasis. Cholestasis can resolve in certain ALGS patients, suggesting regeneration of IHD cells. However, the mechanisms driving IHD cell regeneration following Jagged loss remains unclear. Read More

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September 2021

Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure.

Int J Cancer 2021 Sep 27. Epub 2021 Sep 27.

Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, WHO, Lyon, France.

Recurrent upper urinary tract carcinomas (UTUC) arise in the context of nephropathy linked to exposure to the herbal carcinogen aristolochic acid (AA). Here we delineated the molecular programs underlying UTUC tumorigenesis in patients from endemic aristolochic acid nephropathy (AAN) regions in Southern Europe. We applied an integrative multi-omics analysis of UTUCs, corresponding unaffected tissues and of patient urines. Read More

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September 2021

Integrating 31-Gene Expression Profiling With Clinicopathologic Features to Optimize Cutaneous Melanoma Sentinel Lymph Node Metastasis Prediction.

JCO Precis Oncol 2021 13;5. Epub 2021 Sep 13.

Oregon Health & Science University, Portland, OR.

National guidelines recommend sentinel lymph node biopsy (SLNB) be offered to patients with > 10% likelihood of sentinel lymph node (SLN) positivity. On the other hand, guidelines do not recommend SLNB for patients with T1a tumors without high-risk features who have < 5% likelihood of a positive SLN. However, the decision to perform SLNB is less certain for patients with higher-risk T1 melanomas in which a positive node is expected 5%-10% of the time. Read More

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September 2021

Comprehensive Analysis of mRNA Expression Profiling and Identification of Potential Diagnostic Biomarkers in Coronary Artery Disease.

ACS Omega 2021 Sep 6;6(37):24016-24026. Epub 2021 Sep 6.

Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, China.

The aim of this study is to investigate mRNA expression profiling by RNA sequencing (RNA-seq) in patients with coronary artery disease (CAD) and validate differentially expressed genes (DEGs) as novel biomarkers for CAD. Transcriptome-wide mRNA expression analysis of peripheral blood mononuclear cells was performed in five CAD patients and five controls. Functional enrichment analyses, protein-protein interaction network construction, and hub gene selection were further conducted. Read More

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September 2021

MCL-1 Inhibition Overcomes Anti-apoptotic Adaptation to Targeted Therapies in B-Cell Precursor Acute Lymphoblastic Leukemia.

Front Cell Dev Biol 2021 9;9:695225. Epub 2021 Sep 9.

Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.

Multiple targeted therapies are currently explored for pediatric and young adult B-cell precursor acute lymphoblastic leukemia (BCP-ALL) treatment. However, this new armamentarium of therapies faces an old problem: choosing the right treatment for each patient. The lack of predictive biomarkers is particularly worrying for pediatric patients since it impairs the implementation of new treatments in the clinic. Read More

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September 2021

ASF1B Promotes Oncogenesis in Lung Adenocarcinoma and Other Cancer Types.

Front Oncol 2021 9;11:731547. Epub 2021 Sep 9.

Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, China.

Anti-silencing function 1B histone chaperone (ASF1B) is known to be an important modulator of oncogenic processes, yet its role in lung adenocarcinoma (LUAD) remains to be defined. In this study, an integrated assessment of The Cancer Genome Atlas (TCGA) and genotype-tissue expression (GTEx) datasets revealed the overexpression of ASF1B in all analyzed cancer types other than LAML. Genetic, epigenetic, microsatellite instability (MSI), and tumor mutational burden (TMB) analysis showed that ASF1B was regulated by single or multiple factors. Read More

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September 2021

Comprehensive Genomic Landscape in Chinese Clear Cell Renal Cell Carcinoma Patients.

Front Oncol 2021 9;11:697219. Epub 2021 Sep 9.

Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma (RCC). The genomic landscape in Chinese ccRCC needs to be elucidated. Herein, we investigated the molecular features of Chinese ccRCC patients. Read More

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September 2021

Identification and Evaluation of Autoantibody to a Novel Tumor-Associated Antigen GNA11 as a Biomarker in Esophageal Squamous Cell Carcinoma.

Front Oncol 2021 10;11:661043. Epub 2021 Sep 10.

Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.

The study aims to explore the diagnostic value of anti-GNA11 autoantibody in esophageal squamous cell carcinoma (ESCC) from multiple levels. Autoantibody against GNA11 with the highest diagnostic performance was screened out from the customized protein microarray. A total of 486 subjects including ESCC patients and matched normal controls were recruited in the verification and validation phases by using enzyme-linked immunosorbent assay (ELISA). Read More

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September 2021

Comprehensive analysis of abnormal expression, prognostic value and oncogenic role of the hub gene FN1 in pancreatic ductal adenocarcinoma bioinformatic analysis and experiments.

PeerJ 2021 6;9:e12141. Epub 2021 Sep 6.

Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.

Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most commonly diagnosed cancers with a poor prognosis worldwide. Although the treatment of PDAC has made great progress in recent years, the therapeutic effects are still unsatisfactory. Methods. Read More

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September 2021

Untargeted Metabolomic Profiling of Cuprizone-Induced Demyelination in Mouse Corpus Callosum by UPLC-Orbitrap/MS Reveals Potential Metabolic Biomarkers of CNS Demyelination Disorders.

Oxid Med Cell Longev 2021 14;2021:7093844. Epub 2021 Sep 14.

Department of Neurosurgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China.

Multiple sclerosis (MS) is a neurodegenerative disorder characterized by periodic neuronal demyelination, which leads to a range of symptoms and eventually to disability. The goal of this research was to use UPLC-Orbitrap/MS to identify validated biomarkers and explore the metabolic mechanisms of MS in mice. Thirty-two C57BL/6 male mice were randomized into two groups that were fed either normal food or 0. Read More

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September 2021

Expression Pattern of Genes in Condyloma Acuminata Treated with Lindau Cream versus Podophyllin.

Evid Based Complement Alternat Med 2021 17;2021:5579520. Epub 2021 Sep 17.

Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.

Lindua (), a strong antiviral traditional medicine, can be used to treat condyloma acuminata (CA) caused by the human papillomavirus (HPV). However, its molecular mechanism for CA elimination is unknown. Herein, we conducted a randomized clinical trial to evaluate the effectiveness of and its molecular mechanism compared with podophyllin, the gold standard treatment. Read More

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September 2021

Profiling of MicroRNAs in Midguts of Provides Novel Insights Into the Resistance.

Front Genet 2021 8;12:739849. Epub 2021 Sep 8.

State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.

The diamondback moth (DBM), , one of the most destructive lepidopteran pests worldwide, has developed field resistance to (Bt) Cry toxins. Although miRNAs have been reported to be involved in insect resistance to multiple insecticides, our understanding of their roles in mediating Bt resistance is limited. In this study, we constructed small RNA libraries from midguts of the Cry1Ac-resistant (Cry1S1000) strain and the Cry1Ac-susceptible strain (G88) using a high-throughput sequencing analysis. Read More

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September 2021

MicroRNA Profiling During Mulberry ( Roxb) Fruit Development and Regulatory Pathway of miR477 for Anthocyanin Accumulation.

Front Plant Sci 2021 8;12:687364. Epub 2021 Sep 8.

College of Forestry, Shandong Agricultural University, Tai'an, China.

To understand the mechanism of small non-coding RNAs (miRNA)-mediated development and ripening of mulberry fruits, three small RNA libraries from mulberry fruits at different development stages were constructed, and 159 conserved miRNAs as well as 86 novel miRNAs were successfully identified. Among the miRNAs identified, there were 90 miRNAs which showed differential expression patterns at different stages of fruit development and ripening. The target genes of these differential expressed (DE) miRNAs were involved in growth and development, transcription and regulation of transcription, metabolic processes, and etc. Read More

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September 2021

Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Supportive Anti-Inflammatory Cytokines.

Front Immunol 2021 9;12:646043. Epub 2021 Sep 9.

Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States.

Background: Microglia safeguard the CNS against injuries and pathogens, and in the presence of certain harmful stimuli are capable of inducing a disease-dependent inflammatory response. When exposed to anti-inflammatory cytokines, however, these cells possess the ability to switch from an inflammatory to an immunosuppressive phenotype. Cancer cells exploit this property to evade the immune system, and elicit an anti-inflammatory microenvironment that facilitates tumor attachment and growth. Read More

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September 2021

Accelerated Barrier Repair in Human Skin Explants Induced with a Plant-Derived PPAR-α Activating Complex via Cooperative Interactions.

Clin Cosmet Investig Dermatol 2021 18;14:1271-1293. Epub 2021 Sep 18.

Rodan & Fields, San Francisco, CA, 94105, USA.

Background: Peroxisome proliferator-activated receptors (PPARs) govern epidermal lipid synthesis and metabolism. In skin, PPAR activation has been shown to regulate genes responsible for permeability barrier homeostasis, epidermal differentiation, lipid biosynthesis, and inflammation.

Objective: Given the known dermatologic benefits of PPARs, we set out to discover a naturally derived, multi-molecule complex that would be superior to the more commonly formulated conjugated linoleic acids (CLAs). Read More

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September 2021

PD-L1 Expression and Comprehensive Molecular Profiling Predict Survival in Nonsmall Cell Lung Cancer: A Real-World Study of a Large Chinese Cohort.

Clin Lung Cancer 2021 Aug 28. Epub 2021 Aug 28.

Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. Electronic address:

Background: Programmed death ligand 1 (PD-L1) expression is the current standard biomarker used to predict non-smallcell lung cancer (NSCLC) response to immunotherapy. Gene expression signatures also seem to be related to the response to immunotherapy. Understanding the clinical and prognostic impact of molecular phenotype and tumor features on PD-L1 expression in NSCLC patients may improve the prediction of immunotherapy response. Read More

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Modifications of Ribosome Profiling that Provide New Data on the Translation Regulation.

Biochemistry (Mosc) 2021 Sep;86(9):1095-1106

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.

Ribosome profiling (riboseq) has opened the possibilities for the genome-wide studies of translation in all living organisms. This method is based on deep sequencing of mRNA fragments protected by the ribosomes from hydrolysis by ribonucleases, the so-called ribosomal footprints (RFPs). Ribosomal profiling together with RNA sequencing allows not only to identify with a reasonable accuracy translated reading frames in the transcriptome, but also to track changes in gene expression in response to various stimuli. Read More

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September 2021

Silencing aurora-kinase-A (AURKA) reinforced the sensitivity of diffuse large B-cell lymphoma cells to cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) via suppressing β-Catenin and RAS-extracellular signal-regulated protein kinase (ERK1/2) pathway.

Bioengineered 2021 Sep 26. Epub 2021 Sep 26.

Department of Hematology, Quanzhou First Hospital.

The therapeutic effects of standard cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) therapy for prevalent lymphoma diffuse large B-cell lymphoma (DLBC, DLBCL) still require improvement. Cancer related aurora-kinase-A (AURKA) may work as a target for DLBCL treatment and its effect on CHOP therapy was investigated in present study. The Gene Expression Profiling Interactive Analysis 2 was applied to analyze AURKA expression in DLBC tumor tissues and normal lymphoid tissues. Read More

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September 2021

Mucosal melanomas of different anatomic sites share a common global DNA methylation profile with cutaneous melanoma but show location-dependent patterns of genetic and epigenetic alterations.

J Pathol 2021 Sep 26. Epub 2021 Sep 26.

German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.

Cutaneous, ocular, and mucosal melanomas are histologically indistinguishable tumors that are driven by a different spectrum of genetic alterations. With current methods, identification of the site of origin of a melanoma metastasis is challenging. DNA methylation profiling has shown promise for the identification of the site of tumor origin in various settings. Read More

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September 2021

Chronic Ethanol Exposure Induces Deleterious Changes in Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells.

Stem Cell Rev Rep 2021 Sep 25. Epub 2021 Sep 25.

Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, GA, 30322, USA.

Chronic alcohol consumption in adults can induce cardiomyopathy, arrhythmias, and heart failure. In newborns, prenatal alcohol exposure can increase the risk of congenital heart diseases. Understanding biological mechanisms involved in the long-term alcohol exposure-induced cardiotoxicity is pivotal to the discovery of therapeutic strategies. Read More

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September 2021

Evaluation of Signaling Pathways Profiling in Human Dermal Endothelial Cells Treated by Snake Venom Cysteine-Rich Secretory Proteins (svCRiSPs) from North American Snakes Using Reverse Phase Protein Array (RPPA).

Toxins (Basel) 2021 Aug 31;13(9). Epub 2021 Aug 31.

National Natural Toxins Research Center (NNTRC), Texas A&M University-Kingsville, MSC 224, 975 West Avenue B, Kingsville, TX 78363, USA.

Cysteine-Rich Secretory Proteins (CRiSPs) are typically found in many snake venoms; however, the role that these toxins play in the pathophysiology of snakebites is still unclear. Herein, we compared the effects of snake venom CRiSPs (svCRiSPs) from the most medically important species of North American snakes on endothelial cell permeability and vascular permeability. We used reverse phase protein array (RPPA) to identify key signaling molecules on human dermal lymphatic (HDLECs) and blood (HDBECs) endothelial cells treated with svCRiSPs. Read More

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Metabolic Profiling during Acute Myeloid Leukemia Progression Using Paired Clinical Bone Marrow Serum Samples.

Metabolites 2021 Aug 31;11(9). Epub 2021 Aug 31.

Soonchunhyang Institute of Medi-Bio Science (SIMS), Soon Chun Hyang University, Cheonan 31151, Korea.

Cellular metabolic changes reflect the characteristics of patients with acute myeloid leukemia (AML) caused by genetic variations, which are important in establishing AML treatment. However, little is known about the metabolic profile of patients with genetic variation-induced AML. Furthermore, the metabolites differ with disease progression. Read More

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Quantitative proteome analysis reveals changes of membrane transport proteins in Sedum plumbizincicola under cadmium stress.

Chemosphere 2021 Sep 18;287(Pt 3):132302. Epub 2021 Sep 18.

State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, PR China; Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, 311400, PR China. Electronic address:

Sedum plumbizincicola is an herbaceous species tolerant of excessive cadmium accumulation in above-ground tissues. The implications of membrane proteins, especially integrative membrane proteins, in Cd detoxification of plants have received attention in recent years, but a comprehensive profiling of Cd-responsive membrane proteins from Cd hyperaccumulator plants is lacking. In this study, the membrane proteins of root, stem, and leaf tissues of S. Read More

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September 2021

Assessment of immune biomarkers and establishing a triple negative phenotype in gynecologic cancers.

Gynecol Oncol 2021 Sep 22. Epub 2021 Sep 22.

Wayne State University and Karmanos Cancer Institute, 4100 John R. St., Detroit, MI 48201, United States of America.

Objective: Immuno-oncology (IO) has rapidly evolved, with many IO therapies either approved or under investigation for multiple malignancies. Biomarkers exist that can predict response to IO therapies including PD-L1 expression, microsatellite instability (MSI), and total mutation burden (TMB). This paper serves to analyze the presence of these biomarkers across gynecologic cancers. Read More

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September 2021

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica PO1f for production of erythritol from glycerol.

Biotechnol Biofuels 2021 Sep 25;14(1):188. Epub 2021 Sep 25.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Background: Sugar alcohols are widely used as low-calorie sweeteners in the food and pharmaceutical industries. They can also be transformed into platform chemicals. Yarrowia lipolytica, an oleaginous yeast, is a promising host for producing many sugar alcohols. Read More

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September 2021