49,847 results match your criteria Cancer Genomics & Proteomics[Journal]


A pan-cancer analysis of the oncogenic role of staphylococcal nuclease domain-containing protein 1 (SND1) in human tumors.

Genomics 2020 Jul 6. Epub 2020 Jul 6.

Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China. Electronic address:

Although emerging cell- or animal-based evidence supports the relationship between SND1 and cancers, no pan-cancer analysis is available. We thus first explored the potential oncogenic roles of SND1 across thirty-three tumors based on the datasets of TCGA (The cancer genome atlas) and GEO (Gene expression omnibus). SND1 is highly expressed in most cancers, and distinct associations exist between SND1 expression and prognosis of tumor patients. Read More

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http://dx.doi.org/10.1016/j.ygeno.2020.06.044DOI Listing

Analysis of relapse-associated alternative mRNA splicing and construction of a prognostic signature predicting relapse in I-III colon cancer.

Genomics 2020 Jul 6. Epub 2020 Jul 6.

Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China. Electronic address:

The literature comprehensively analyzed alternative splicing (AS) events in colon cancer is little and corresponding prognostic signature is still a lack. Based on data of TCGA, the relapse-associated ASs were comprehensively analyzed and a signature was further constructed to predict the relapse in I-III colon cancer. In total 1912 ASs of 1384 mRNA were identified as relapse-associated ASs, protein-protein interactions (PPI) and ASs-splicing factors (SF) interactions network were identified. Read More

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http://dx.doi.org/10.1016/j.ygeno.2020.07.002DOI Listing

Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices.

JCO Clin Cancer Inform 2020 Jul;4:602-613

Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC.

Purpose: The cancer research community is constantly evolving to better understand tumor biology, disease etiology, risk stratification, and pathways to novel treatments. Yet the clinical cancer genomics field has been hindered by redundant efforts to meaningfully collect and interpret disparate data types from multiple high-throughput modalities and integrate into clinical care processes. Bespoke data models, knowledgebases, and one-off customized resources for data analysis often lack adequate governance and quality control needed for these resources to be clinical grade. Read More

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http://dx.doi.org/10.1200/CCI.19.00169DOI Listing

Sugar-sweetened beverage consumption and risk of hyperuricemia: a longitudinal analysis of the Health Workers Cohort Study participants in Mexico.

Am J Clin Nutr 2020 Jul 9. Epub 2020 Jul 9.

Research Center in Policy, Population, and Health, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico.

Background: The elevated consumption of sugar-sweetened beverages (SSBs) in Mexico is an important public health concern. However, the association between SSB consumption and hyperuricemia has been scarcely studied and not well documented.

Objectives: To prospectively evaluate the association between SSB consumption and risk of hyperuricemia in Mexican adults. Read More

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http://dx.doi.org/10.1093/ajcn/nqaa160DOI Listing

Rewired signaling network in T cells expressing the chimeric antigen receptor (CAR).

EMBO J 2020 Jul 9:e104730. Epub 2020 Jul 9.

Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.

The chimeric antigen receptor (CAR) directs T cells to target and kill specific cancer cells. Despite the success of CAR T therapy in clinics, the intracellular signaling pathways that lead to CAR T cell activation remain unclear. Using CD19 CAR as a model, we report that, similar to the endogenous T cell receptor (TCR), antigen engagement triggers the formation of CAR microclusters that transduce downstream signaling. Read More

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http://dx.doi.org/10.15252/embj.2020104730DOI Listing

Corrigendum to: Gene expression profiling of cells of origin of squamous cell carcinomas in head-and-neck, esophagus, and lung.

Acta Biochim Biophys Sin (Shanghai) 2020 Jul 9. Epub 2020 Jul 9.

Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.

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http://dx.doi.org/10.1093/abbs/gmaa079DOI Listing

Medulloblastoma: an Old Diagnosis with New Promises.

Curr Oncol Rep 2020 Jul 9;22(9):90. Epub 2020 Jul 9.

Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA.

Purpose Of Review: Molecular subtyping in medulloblastoma (MB) has diagnostic and prognostic values which impact therapy. This paper provides guidance for the clinician caring for pediatric and adult patients with medulloblastoma in the modern era.

Recent Findings: Medulloblastoma comprises four molecularly distinct subgroups: wingless activated (WNT), sonic hedgehog activated (SHH), group 3, and group 4. Read More

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http://dx.doi.org/10.1007/s11912-020-00953-4DOI Listing

Whole exome sequencing reveals the maintained polyclonal nature from primary to metastatic malignant peripheral nerve sheath tumor in two patients with NF1.

Neurooncol Adv 2020 Jul 10;2(Suppl 1):i75-i84. Epub 2019 Sep 10.

Division of Medical Oncology, Department of Medicine Washington University School of Medicine, St. Louis, Missouri.

Background: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas with high metastatic rates and poor overall patient survival. There are currently no effective therapies, underscoring the pressing need to define the molecular etiologies that underlie MPNST progression. The aim of this study was to examine clonal progression and identify the molecular events critical for MPNST spread. Read More

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http://dx.doi.org/10.1093/noajnl/vdz026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317063PMC

KIF11 and KIF15 mitotic kinesins are potential therapeutic vulnerabilities for malignant peripheral nerve sheath tumors.

Neurooncol Adv 2020 Jul 4;2(Suppl 1):i62-i74. Epub 2020 Jan 4.

Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias & Pujol Research Institute (IGTP), Badalona, Barcelona, Spain.

Background: Malignant peripheral nerve sheath tumor (MPNST) constitutes the leading cause of neurofibromatosis type 1-related mortality. MPNSTs contain highly rearranged hyperploid genomes and exhibit a high division rate and aggressiveness. We have studied in vitro whether the mitotic kinesins KIF11, KIF15, and KIF23 have a functional role in maintaining MPNST cell survival and can represent potential therapeutic vulnerabilities. Read More

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http://dx.doi.org/10.1093/noajnl/vdz061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317059PMC

Genetics of human malignant peripheral nerve sheath tumors.

Neurooncol Adv 2020 Jul 28;2(Suppl 1):i50-i61. Epub 2019 Nov 28.

Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.

Malignant peripheral nerve sheath tumors (MPNSTs) are heterogeneous, highly aggressive tumors with no widely effective treatment other than surgery. Genomic architecture of MPNST is similar to other soft tissue sarcomas, with a relatively modest burden of single nucleotide variants and an elevated frequency of copy-number alterations. Recent advances in genomic studies identified previously unrecognized critical involvement of polycomb repressor complex 2 (PRC2) core components and in transition to malignancy. Read More

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http://dx.doi.org/10.1093/noajnl/vdz049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317054PMC

Proteins inform survival-based differences in patients with glioblastoma.

Neurooncol Adv 2020 Jan-Dec;2(1):vdaa039. Epub 2020 Mar 17.

Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.

Background: Improving the care of patients with glioblastoma (GB) requires accurate and reliable predictors of patient prognosis. Unfortunately, while protein markers are an effective readout of cellular function, proteomics has been underutilized in GB prognostic marker discovery.

Methods: For this study, GB patients were prospectively recruited and proteomics discovery using liquid chromatography-mass spectrometry analysis (LC-MS/MS) was performed for 27 patients including 13 short-term survivors (STS) (≤10 months) and 14 long-term survivors (LTS) (≥18 months). Read More

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http://dx.doi.org/10.1093/noajnl/vdaa039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212893PMC

Gliomas display distinct sex-based differential methylation patterns based on molecular subtype.

Neurooncol Adv 2020 Jan-Dec;2(1):vdaa002. Epub 2020 Jan 8.

Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.

Background: Gliomas are the most common type of primary brain tumor and one of many cancers where males are diagnosed with greater frequency than females. However, little is known about the sex-based molecular differences in glioblastomas (GBMs) or lower grade glioma (non-GBM) subtypes. DNA methylation is an epigenetic mechanism involved in regulating gene transcription. Read More

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http://dx.doi.org/10.1093/noajnl/vdaa002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212920PMC
January 2020

Sexually dimorphic impact of the iron-regulating gene, , on survival in glioblastoma.

Neurooncol Adv 2020 Jan-Dec;2(1):vdaa001. Epub 2020 Feb 17.

Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.

Background: The median survival for patients with glioblastoma (GBM), the most common primary malignant brain tumor in adults, has remained approximately 1 year for more than 2 decades. Recent advances in the field have identified GBM as a sexually dimorphic disease. It is less prevalent in females and they have better survival compared to males. Read More

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http://dx.doi.org/10.1093/noajnl/vdaa001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212901PMC
February 2020

Involvement of hepatic lipid droplets and their associated proteins in the detoxification of aflatoxin B in aflatoxin-resistance BALB/C mouse.

Toxicol Rep 2020 22;7:795-804. Epub 2020 Jun 22.

Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria.

The highly potent carcinogen, Aflatoxin B, induces liver cancer in many animals including humans but some mice strains are highly resistant. This murine resistance is due to a rapid detoxification of AFB. Hepatic lipid droplets (LDs) ultimately impact the liver functions but their potential role in AFB detoxification has not been addressed. Read More

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http://dx.doi.org/10.1016/j.toxrep.2020.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334552PMC

Pharmacophore-based virtual screening for the identification of the novel Src inhibitor SJG-136 against lung cancer cell growth and motility.

Am J Cancer Res 2020 1;10(6):1668-1690. Epub 2020 Jun 1.

Institute of Biomedical Sciences, National Chung Hsing University Taichung, Taiwan.

Aberrant elevated Src activity is related to lung cancer growth and metastasis. Therefore, the development of potent small molecule inhibitors to target Src kinase is a potential therapeutic strategy for lung cancer. This study aimed to develop a computational model for the in silico screening of Src inhibitors and then assess the suppressive effect of candidate compounds on cellular functions. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7339285PMC

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy.

Nat Commun 2020 Jul 8;11(1):3406. Epub 2020 Jul 8.

Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada.

Cancer stem cells are critical for cancer initiation, development, and treatment resistance. Our understanding of these processes, and how they relate to glioblastoma heterogeneity, is limited. To overcome these limitations, we performed single-cell RNA sequencing on 53586 adult glioblastoma cells and 22637 normal human fetal brain cells, and compared the lineage hierarchy of the developing human brain to the transcriptome of cancer cells. Read More

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http://dx.doi.org/10.1038/s41467-020-17186-5DOI Listing

Genetic characteristics of gastric-type mucinous carcinoma of the uterine cervix.

Mod Pathol 2020 Jul 8. Epub 2020 Jul 8.

Department of Pathology, Yonsei University College of Medicine, Seoul, Korea.

Gastric-type mucinous carcinoma (GAS) is a recently established variant of endocervical mucinous adenocarcinoma that is characterized as being unrelated to HPV and having aggressive behavior and chemoresistance. GAS has a distinct morphology resembling nonneoplastic gastric glands or pancreaticobiliary adenocarcinoma, and their possible genetic similarity has been posed. In this study, next-generation sequencing was performed in 21 GAS cases using a customized panel including 94 cancer-associated genes. Read More

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http://dx.doi.org/10.1038/s41379-020-0614-0DOI Listing

Accumulation of molecular aberrations distinctive to hepatocellular carcinoma progression.

Cancer Res 2020 Jul 8. Epub 2020 Jul 8.

Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo.

Cancer develops through the accumulation of genetic and epigenetic aberrations. To identify sequential molecular alterations that occur during the development of hepatocellular carcinoma (HCC), we compared 52 early and 108 overt HCC samples by genome sequencing. Gene mutations in the p53/RB1 pathway, WNT pathway, MLL protein family, SWI/SNF complexes, and AKT/PI3K pathway were common in HCC. Read More

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http://dx.doi.org/10.1158/0008-5472.CAN-20-0225DOI Listing

Genome-wide association study data reveal genetic susceptibility to chronic inflammatory intestinal diseases and pancreatic ductal adenocarcinoma risk.

Cancer Res 2020 Jul 8. Epub 2020 Jul 8.

Division of Cancer Epidemiology and Genetics, National Cancer Institute

Registry-based epidemiologic studies suggest associations between chronic inflammatory intestinal diseases and pancreatic ductal adenocarcinoma (PDAC). As genetic susceptibility contributes to a large proportion of chronic inflammatory intestinal diseases, we hypothesize that the genomic regions surrounding established genome-wide associated variants for these chronic inflammatory diseases are associated with PDAC. We examined the association between PDAC and genomic regions (+/- 500 kb) surrounding established common susceptibility variants for ulcerative colitis, Crohn's disease, inflammatory bowel disease, celiac disease, chronic pancreatitis, and primary sclerosing cholangitis. Read More

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http://dx.doi.org/10.1158/0008-5472.CAN-20-0447DOI Listing

Calibration of pathogenicity due to variant-induced leaky splicing defects by using BRCA2 exon 3 as a model system.

Cancer Res 2020 Jul 8. Epub 2020 Jul 8.

Inserm U1245, Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine

BRCA2 is a clinically actionable gene implicated in breast and ovarian cancer predisposition that has become a high priority target for improving the classification of variants of unknown significance (VUS). Amongst all BRCA2 VUS, those causing partial/leaky splicing defects are the most challenging to classify because the minimal level of full-length transcripts (FL) required for normal function remains to be established. Here, we explored BRCA2 exon 3 (BRCA2e3) as a model for calibrating variant-induced spliceogenicity and estimating thresholds for BRCA2 haploinsufficiency. Read More

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http://dx.doi.org/10.1158/0008-5472.CAN-20-0895DOI Listing

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability.

Clin Epigenetics 2020 Jul 8;12(1):102. Epub 2020 Jul 8.

Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.

Both colorectal (CRC, 15%) and endometrial cancers (EC, 30%) exhibit microsatellite instability (MSI) due to MLH1 hypermethylation and silencing. The MLH1 promoter polymorphism, rs1800734 is associated with MSI CRC risk, increased methylation and reduced MLH1 expression. In EC samples, we investigated rs1800734 risk using MSI and MSS cases and controls. Read More

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http://dx.doi.org/10.1186/s13148-020-00889-3DOI Listing

The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations.

J Clin Med 2020 Jul 6;9(7). Epub 2020 Jul 6.

Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA.

Recent public policy, governmental regulatory and economic trends have motivated the establishment and deepening of community health and academic medical center alliances. Accordingly, community oncology practices now deliver a significant portion of their oncology care in association with academic cancer centers. In the age of precision medicine, this alliance has acquired critical importance; novel advances in nucleic acid sequencing, the generation and analysis of immense data sets, the changing clinical landscape of hereditary cancer predisposition and ongoing discovery of novel, targeted therapies challenge community-based oncologists to deliver molecularly-informed health care. Read More

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http://dx.doi.org/10.3390/jcm9072125DOI Listing

Variations in the Referral Pattern for Genetic Counseling of Patients with Early-Onset Breast Cancer: A Population-Based Study in Southern Sweden.

Public Health Genomics 2020 Jul 8:1-10. Epub 2020 Jul 8.

Department of Laboratory Medicine in Lund, Clinical Genetics, Lund University, Lund, Sweden.

Swedish national breast cancer guidelines recommend that all women diagnosed with breast cancer (BC) at the age of 35 years or younger should be referred to their regional oncogenetic clinic for genetic counseling and testing, regardless of family history of cancer. The main objective of this study was to evaluate whether place of residence at BC diagnosis and treating hospital were associated with the fact that not all BC patients diagnosed at ≤35 years in the southern part of Sweden have attended genetic counseling and testing. Between 2000 and 2013, 279 women in the South Swedish Health Care Region were diagnosed with BC at ≤35 years. Read More

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http://dx.doi.org/10.1159/000508684DOI Listing

Mining therapeutic and prognostic significance of STATs in renal cell carcinoma with bioinformatics analysis.

Genomics 2020 Jul 5. Epub 2020 Jul 5.

Department of Ophthalmology, Shantou University Medical college, Shantou 515041, China.

Renal cell carcinoma is one of the most common malignancies with high morbidity and mortality. STAT proteins play a significant role in cell biological behavior and immune response associated with cancer progression. In our study, the datasets analyzed for the expression and potential functions can be found in several bioinformatics analysis tools. Read More

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http://dx.doi.org/10.1016/j.ygeno.2020.06.032DOI Listing

Single-cell genomics reveals the genetic and molecular bases for escape from mutational epistasis in myeloid neoplasms.

Blood 2020 Jul 8. Epub 2020 Jul 8.

Memorial Sloan Kettering Cancer Center, New York, New York, United States.

Large-scale sequencing studies of hematologic malignancies have revealed notable epistasis among high-frequency mutations. One of the most striking examples of epistasis occurs for mutations in RNA splicing factors. These lesions are amongst the most common alterations in myeloid neoplasms and generally occur in a mutually exclusive manner, a finding attributed to their synthetic lethal interactions and/or convergent effects. Read More

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http://dx.doi.org/10.1182/blood.2020006868DOI Listing

Kinome capture sequencing of high-grade serous ovarian carcinoma reveals novel mutations in the JAK3 gene.

PLoS One 2020 8;15(7):e0235766. Epub 2020 Jul 8.

Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

High-grade serous ovarian carcinoma (HGSOC) remains the deadliest form of epithelial ovarian cancer and despite major efforts little improvement in overall survival has been achieved. Identification of recurring "driver" genetic lesions has the potential to enable design of novel therapies for cancer. Here, we report on a study to find such new therapeutic targets for HGSOC using exome-capture sequencing approach targeting all kinase genes in 127 patient samples. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235766PLOS

The report of the use of patient-derived xenograft models in the development of anticancer drugs in Japan.

Cancer Sci 2020 Jul 8. Epub 2020 Jul 8.

Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, 277-8577, Japan.

Cell line-derived xenograft (CDX) models created by implanting cancer cell lines into immunodeficient mice have been largely contributed to develop cancer drug therapies. However, cell lines often lose their original biological characteristics through many passages and cancer tissues in CDX models have many cancer cells and few cancer stromal cells, therefore, CDX models are currently considered not suitable for predicting the results of clinical studies. On the other hand, patient-derived xenograft (PDX) models are gaining importance, in which human cancer biological characteristics and microenvironments are recreated by implanting tumor tissue into immunodeficient mice. Read More

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http://dx.doi.org/10.1111/cas.14564DOI Listing

Mutations in the exocyst component EXOC2 cause severe defects in human brain development.

J Exp Med 2020 Oct;217(10)

Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.

The exocyst, an octameric protein complex, is an essential component of the membrane transport machinery required for tethering and fusion of vesicles at the plasma membrane. We report pathogenic variants in an exocyst subunit, EXOC2 (Sec5). Affected individuals have severe developmental delay, dysmorphism, and brain abnormalities; variability associated with epilepsy; and poor motor skills. Read More

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http://dx.doi.org/10.1084/jem.20192040DOI Listing
October 2020

High expression levels of pyrimidine metabolic rate-limiting enzymes are adverse prognostic factors in lung adenocarcinoma: a study based on The Cancer Genome Atlas and Gene Expression Omnibus datasets.

Purinergic Signal 2020 Jul 8. Epub 2020 Jul 8.

Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital,, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.

Reprogramming of metabolism is described in many types of cancer and is associated with the clinical outcomes. However, the prognostic significance of pyrimidine metabolism signaling pathway in lung adenocarcinoma (LUAD) is unclear. Using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, we found that the pyrimidine metabolism signaling pathway was significantly enriched in LUAD. Read More

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http://dx.doi.org/10.1007/s11302-020-09711-4DOI Listing

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST).

Bioinformatics 2020 Jul 8. Epub 2020 Jul 8.

Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.

Motivation: A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called 'causal interaction' takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. Read More

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http://dx.doi.org/10.1093/bioinformatics/btaa622DOI Listing

Synoviocyte-targeted therapy synergizes with TNF inhibition in arthritis reversal.

Sci Adv 2020 Jun 26;6(26):eaba4353. Epub 2020 Jun 26.

Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, La Jolla, CA 92093, USA.

Fibroblast-like synoviocytes (FLS) are joint-lining cells that promote rheumatoid arthritis (RA) pathology. Current disease-modifying antirheumatic agents (DMARDs) operate through systemic immunosuppression. FLS-targeted approaches could potentially be combined with DMARDs to improve control of RA without increasing immunosuppression. Read More

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http://dx.doi.org/10.1126/sciadv.aba4353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319753PMC

Human endogenous retrovirus-K mRNA expression and genomic alignment data in hepatoblastoma.

Data Brief 2020 Aug 18;31:105895. Epub 2020 Jun 18.

Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, United States.

Human Endogenous Retroviruses are a class of genomic elements that are the result of ancient retroviral infection of the human germline. Many are biologically active elements that have been implicated in multiple diseases including cancer. The most recent class to invade the human genome is the HERV-K(HML-2) (HERV-K) family. Read More

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http://dx.doi.org/10.1016/j.dib.2020.105895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7330144PMC

Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data.

Data Brief 2020 Aug 16;31:105860. Epub 2020 Jun 16.

Department of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, Sweden.

Patient-derived scaffolds (PDSs) generated from primary breast cancer tumors can be used to model the tumor microenvironment . Patient-derived scaffolds are generated by repeated detergent washing, removing all cells. Here, we analyzed the protein composition of 15 decellularized PDSs using liquid chromatography-mass spectrometry/mass spectrometry. Read More

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http://dx.doi.org/10.1016/j.dib.2020.105860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327418PMC

Genomics of Peripheral T-Cell Lymphoma and Its Implications for Personalized Medicine.

Front Oncol 2020 19;10:898. Epub 2020 Jun 19.

Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.

Peripheral T-cell lymphoma (PTCL) is a rare, heterogenous group of mature T-cell neoplasms that comprise 10-15% of non-Hodgkin lymphoma cases in the United States. All subtypes of PTCL, except for ALK anaplastic T-cell lymphoma, are associated with poor prognosis, with median overall survival (OS) rates of 1-3 years. The diagnosis of PTCL is mainly based on clinical presentation, morphologic features, and immunophenotypes. Read More

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http://dx.doi.org/10.3389/fonc.2020.00898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317006PMC

Comparison of unsupervised machine-learning methods to identify metabolomic signatures in patients with localized breast cancer.

Comput Struct Biotechnol J 2020 3;18:1509-1524. Epub 2020 Jun 3.

University Côte d'Azur, Epidemiology and Biostatistics Department, Centre Antoine Lacassagne, Nice F-06189, France.

Genomics and transcriptomics have led to the widely-used molecular classification of breast cancer (BC). However, heterogeneous biological behaviors persist within breast cancer subtypes. Metabolomics is a rapidly-expanding field of study dedicated to cellular metabolisms affected by the environment. Read More

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http://dx.doi.org/10.1016/j.csbj.2020.05.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327012PMC

Germline Sequencing Identifies Rare Variants in Finnish Subjects with Familial Germ Cell Tumors.

Appl Clin Genet 2020 30;13:127-137. Epub 2020 Jun 30.

Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO, USA.

Purpose: Pediatric germ cell tumors are rare, representing about 3% of childhood malignancies in children less than 15 years of age, presenting in neonates or adolescents with a greater incidence noted in older adolescents. Aberrations in primordial germ cell proliferation/differentiation can lead to a variety of neoplasms, including teratomas, embryonal carcinoma, choriocarcinoma, and yolk sac tumors.

Patients And Methods: Three Finnish families with varying familial germ cell tumors were identified, and whole-genome sequencing was performed using an Illumina sequencing platform. Read More

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http://dx.doi.org/10.2147/TACG.S245093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335280PMC

In vivo functional screening for systems-level integrative cancer genomics.

Nat Rev Cancer 2020 Jul 7. Epub 2020 Jul 7.

Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.

With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Read More

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http://dx.doi.org/10.1038/s41568-020-0275-9DOI Listing

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery.

NPJ Syst Biol Appl 2019 Jul 9;5(1):22. Epub 2019 Jul 9.

Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.

Computational tools for multiomics data integration have usually been designed for unsupervised detection of multiomics features explaining large phenotypic variations. To achieve this, some approaches extract latent signals in heterogeneous data sets from a joint statistical error model, while others use biological networks to propagate differential expression signals and find consensus signatures. However, few approaches directly consider molecular interaction as a data feature, the essential linker between different omics data sets. Read More

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http://dx.doi.org/10.1038/s41540-019-0099-yDOI Listing

A user guide for the online exploration and visualization of PCAWG data.

Nat Commun 2020 Jul 7;11(1):3400. Epub 2020 Jul 7.

European Molecular Biology Laboratory, 69117, Heidelberg, Germany.

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user's guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout. Read More

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http://dx.doi.org/10.1038/s41467-020-16785-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7340791PMC

Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies.

mSystems 2020 Jul 7;5(4). Epub 2020 Jul 7.

Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA.

Epidemiologic studies use various biosample collection methods to study associations between human oral microbiota and health outcomes. However, the agreement between the different methods is unclear. We compared a commercially available OMNIgene ORAL kit to three alternative collection methods: Saccomanno's fixative, Scope mouthwash, and nonethanol mouthwash. Read More

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http://dx.doi.org/10.1128/mSystems.00156-20DOI Listing

A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily.

Sci Signal 2020 Jul 7;13(639). Epub 2020 Jul 7.

Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

Aberrant regulation of metabolic kinases by altered redox homeostasis substantially contributes to aging and various diseases, such as diabetes. We found that the catalytic activity of a conserved family of fructosamine-3-kinases (FN3Ks), which are evolutionarily related to eukaryotic protein kinases, is regulated by redox-sensitive cysteine residues in the kinase domain. The crystal structure of the FN3K homolog from revealed that it forms an unexpected strand-exchange dimer in which the ATP-binding P-loop and adjoining β strands are swapped between two chains in the dimer. Read More

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http://dx.doi.org/10.1126/scisignal.aax6313DOI Listing

A frameshift variant in specificity protein 1 triggers superactivation of Sp1-mediated transcription in familial bone marrow failure.

Proc Natl Acad Sci U S A 2020 Jul 7. Epub 2020 Jul 7.

Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT London, United Kingdom.

Inherited bone marrow failure (BMF) syndromes are a heterogeneous group of diseases characterized by defective hematopoiesis and often predisposing to myelodysplastic syndrome (MDS) and acute myelogenous leukemia. We have studied a large family consisting of several affected individuals with hematologic abnormalities, including one family member who died of acute leukemia. By whole-exome sequencing, we identified a novel frameshift variant in the ubiquitously expressed transcription factor specificity protein 1 (). Read More

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http://dx.doi.org/10.1073/pnas.2002857117DOI Listing

Upregulation of fibronectin following loss of p53 function is a poor prognostic factor in ovarian carcinoma with a unique immunophenotype.

Cell Commun Signal 2020 Jul 7;18(1):103. Epub 2020 Jul 7.

Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan.

Background: We previously demonstrated that ovarian high grade serous carcinomas (OHGSeCa) and ovarian clear cell carcinomas (OCCCa) with an HNF-1β+/p53+/ARID1A+ immunophenotype were associated with the worst unfavorable prognosis. To clarify the molecular mechanisms underlying this finding, we focused on alterations in the p53 signaling pathway in these tumors.

Methods: Changes in cell phenotype and function following knockdown of wild-type p53 (p53-KD) were assessed using OCCCa cells expressing endogenous HNF-1β and ARID1A. Read More

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http://dx.doi.org/10.1186/s12964-020-00580-3DOI Listing

Mitochondrial GWAS and association of nuclear - mitochondrial epistasis with BMI in T1DM patients.

BMC Med Genomics 2020 Jul 7;13(1):97. Epub 2020 Jul 7.

Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland.

Background: BMI is a strong indicator of complications from type I diabetes, especially under intensive treatment.

Methods: We have genotyped 435 type 1 diabetics using Illumina Infinium Omni Express Exome-8 v1.4 arrays and performed mitoGWAS on BMI. Read More

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http://dx.doi.org/10.1186/s12920-020-00752-7DOI Listing

Validation of a Circulating Tumor-Derived DNA Blood Test for Detection of Methylated BCAT1 and IKZF1 DNA.

J Appl Lab Med 2017 Sep;2(2):165-175

Clinical Genomics Pty Ltd, North Ryde, New South Wales, Australia.

Background: Colvera™ is a test that detects circulating tumor-derived DNA in patients with colorectal cancer by assaying for the presence of methylated BCAT1 and IKZF1 in blood. This study describes the analytical and clinical performance characteristics of the test.

Methods: Validation was performed in accordance with ISO15189 and National Pathology Accreditation Advisory Council requirements. Read More

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http://dx.doi.org/10.1373/jalm.2017.023135DOI Listing
September 2017

Effect of dose-dense adjuvant chemotherapy in hormone receptor positive/HER2-negative early breast cancer patients according to immunohistochemically defined luminal subtype: an exploratory analysis of the GIM2 trial.

Eur J Cancer 2020 Jul 4;136:43-51. Epub 2020 Jul 4.

Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Viale Benedetto XV, 10, 16132, Genoa, GE, Italy; Breast Unit, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genoa, GE, Italy. Electronic address:

Background: Luminal A-like and luminal B-like subtypes have different sensitivity to (neo)adjuvant chemotherapy, but their role in predicting dose-dense (DD) efficacy in the high-risk setting is unknown. In this exploratory analysis of the Gruppo Italiano Mammella 2 (GIM2) trial, we investigated DD efficacy according to luminal-like subtypes.

Methods: Patients with node-positive early breast cancer were randomised to receive either DD or standard-interval (SI) anthracycline-based chemotherapy followed by paclitaxel. Read More

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http://dx.doi.org/10.1016/j.ejca.2020.05.007DOI Listing

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program.

Cell Syst 2020 Jun 29. Epub 2020 Jun 29.

Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Centre for Trophoblast Research University of Cambridge, Cambridge CB2 3EG, UK. Electronic address:

Zygotic genome activation (ZGA) is an essential transcriptional event in embryonic development that coincides with extensive epigenetic reprogramming. Complex manipulation techniques and maternal stores of proteins preclude large-scale functional screens for ZGA regulators within early embryos. Here, we combined pooled CRISPR activation (CRISPRa) with single-cell transcriptomics to identify regulators of ZGA-like transcription in mouse embryonic stem cells, which serve as a tractable, in vitro proxy of early mouse embryos. Read More

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http://dx.doi.org/10.1016/j.cels.2020.06.004DOI Listing

Core regulatory circuitries in defining cancer cell identity across the malignant spectrum.

Open Biol 2020 07 8;10(7):200121. Epub 2020 Jul 8.

Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA.

Gene expression programmes driving cell identity are established by tightly regulated transcription factors that auto- and cross-regulate in a feed-forward manner, forming core regulatory circuitries (CRCs). CRC transcription factors create and engage super-enhancers by recruiting acetylation writers depositing permissive H3K27ac chromatin marks. These super-enhancers are largely associated with BET proteins, including BRD4, that influence higher-order chromatin structure. Read More

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http://dx.doi.org/10.1098/rsob.200121DOI Listing

SOLTI-1503 PROMETEO TRIAL: combination of talimogene laherparepvec with atezolizumab in early breast cancer.

Future Oncol 2020 Jul 7. Epub 2020 Jul 7.

Scientific Department, SOLTI Breast Cancer Research Group, Barcelona, Spain.

New treatment strategies such as immune checkpoint inhibitors and oncolytic viruses are opening new possibilities in cancer therapy. Preliminary results in melanoma and other tumors showed that the combination of talimogene laherparepvec with an anti-PD-1/PD-L1 or anti-CTLA4 has greater efficacy than either therapy alone, without additional safety concerns beyond those expected for each agent. The presence of residual cancer after neoadjuvant chemotherapy in early breast cancer patients is an unmet medical need. Read More

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http://dx.doi.org/10.2217/fon-2020-0246DOI Listing