403,851 results match your criteria genomic mutations

Prognostic Immunity and Therapeutic Sensitivity Analyses Based on Differential Genomic Instability-Associated LncRNAs in Left- and Right-Sided Colon Adenocarcinoma.

Front Mol Biosci 2021 31;8:668888. Epub 2021 Aug 31.

Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.

The purpose of our study was to develop a prognostic risk model based on differential genomic instability-associated (DGIA) long non-coding RNAs (lncRNAs) of left-sided and right-sided colon cancers (LCCs and RCCs); therefore, the prognostic key lncRNAs could be identified. We adopted two independent gene datasets, corresponding somatic mutation and clinical information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Identification of differential DGIA lncRNAs from LCCs and RCCs was conducted with the appliance of "Limma" analysis. Read More

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N6-methyladenosine (m6A) regulatory gene divides hepatocellular carcinoma into three subtypes.

J Gastrointest Oncol 2021 Aug;12(4):1860-1872

Department of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nannning, China.

Background: The N6-methyladenosine (m6A) plays an important role in epigenetic modification and tumor progression, but the modulations of m6A in hepatocellular carcinoma (HCC) have not been determined while the relationship between m6A regulation and immune cell infiltration remains unclear.

Methods: This study investigated the modification patterns of m6A by analyzing HCC samples from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) dataset, and performed molecular typing based on the characteristics of immune cell infiltration. The m6Ascore was also constructed to quantify m6A modifications and predict the immunotherapy response and prognosis of HCC patients. Read More

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The effect of the and mutations on the survival of hepatocellular carcinoma patients with different racial backgrounds.

J Gastrointest Oncol 2021 Aug;12(4):1786-1796

Department of Hepatobiliary Surgery/Research Laboratory of Hepatobiliary Tumor, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China.

Background: Racial disparities in the survival of patients with hepatocellular carcinoma (HCC) exist. Gene mutations have a profound effect on carcinogenesis, are easily affected by environment and etiology factors, and may result in survival divergences among patients with different racial backgrounds. This report explores the effects of gene mutations on the survival of American Caucasians and Asian patients. Read More

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Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites.

Virus Evol 2021 4;7(2):veab054. Epub 2021 Jun 4.

Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.

(CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity, and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Read More

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Pan-Cancer Analysis of PARP1 Alterations as Biomarkers in the Prediction of Immunotherapeutic Effects and the Association of Its Expression Levels and Immunotherapy Signatures.

Front Immunol 2021 31;12:721030. Epub 2021 Aug 31.

State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.

Background: Poly (ADP-ribose) polymerases-1 (PARP1) alterations are associated with PARP1 inhibitor resistance, regulating the function of Treg cells and PDL1 expression in tumor cells, and high PARP1 expression is significantly associated with aggressive behavior and chemotherapeutic resistance in several tumors. However, a comprehensive analysis of the predictive values of PARP1 alteration for immune checkpoint inhibitor (ICI) effectiveness in tumors remains unclear, and the associations between its expression and immunotherapy signatures also needs to be explored further.

Methods: We performed some analyses with the cBioPortal online database (https://www. Read More

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Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea.

Front Microbiol 2021 31;12:736915. Epub 2021 Aug 31.

College of Plant Protection, Agricultural University of Hebei, Baoding, China.

Since hyperthermophilic Archaea (HA) thrive in high-temperature environments, which accelerate the rates of deamination of base in DNA, their genomic stability is facing a severe challenge. Hypoxanthine (Hx) is one of the common deaminated bases in DNA. Generally, replication of Hx in DNA before repaired causes AT → GC mutation. Read More

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Whole-Genome Sequencing of Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials.

Front Microbiol 2021 31;12:713233. Epub 2021 Aug 31.

Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom.

Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published. Read More

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Absence of Biomarker-Driven Treatment Options in Small Cell Lung Cancer, and Selected Preclinical Candidates for Next Generation Combination Therapies.

Front Pharmacol 2021 31;12:747180. Epub 2021 Aug 31.

Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.

Lung cancer is the second most common cancer in the United States, and small cell lung cancer (SCLC) accounts for about 15% of all lung cancers. In SCLC, more than other malignancies, the standard of care is based on clinical demonstration of efficacy, and less on a mechanistic understanding of why certain treatments work better than others. This is in large part due to the virulence of the disease, and lack of clinically or biologically relevant biomarkers beyond routine histopathology. Read More

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Highly efficient CRISPR/Cas9 system in Plasmodium falciparum using Cas9-expressing parasites and a linear donor template.

Sci Rep 2021 Sep 16;11(1):18501. Epub 2021 Sep 16.

Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.

The CRISPR/Cas9 system is a powerful genetic engineering technology for Plasmodium falciparum. We here report further improvement of the CRISPR/Cas9 system by combining the Cas9-expressing parasite with a liner donor template DNA. The Cas9-expressing parasite was generated by inserting the cas9 gene in the genome by double crossover recombination. Read More

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September 2021

USP21 deubiquitinase elevates macropinocytosis to enable oncogenic KRAS bypass in pancreatic cancer.

Genes Dev 2021 Sep 16. Epub 2021 Sep 16.

Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.

Activating mutations in KRAS (KRAS*) are present in nearly all pancreatic ductal adenocarcinoma (PDAC) cases and critical for tumor maintenance. By using an inducible KRAS* PDAC mouse model, we identified a deubiquitinase USP21-driven resistance mechanism to anti-KRAS* therapy. USP21 promotes KRAS*-independent tumor growth via its regulation of MARK3-induced macropinocytosis, which serves to maintain intracellular amino acid levels for anabolic growth. Read More

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September 2021

SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia.

Cancer Discov 2021 Sep 16. Epub 2021 Sep 16.

Cold Spring Harbor Laboratory

An enhanced requirement for nutrients is a hallmark property of cancer cells. Here, we optimized an in vivo genetic screening strategy in acute myeloid leukemia (AML), which led to the identification of the myo-inositol transporter SLC5A3 as a dependency in this disease. We demonstrate that SLC5A3 is essential to support a myo-inositol auxotrophy in AML. Read More

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September 2021

Prognostic impact of IDH mutations in chondrosarcoma.

J Orthop Sci 2021 Sep 13. Epub 2021 Sep 13.

Department of Musculoskeletal Oncology and Rehabilitation, National Cancer Center Hospital, Tokyo, Japan. Electronic address:

Background: Mutant isocitrate dehydrogenase (IDH) in chondrosarcoma produces the oncometabolite 2-hydroxyglutarate (2-HG) and contributes to malignant progression, and is therefore a potential therapeutic target for chondrosarcoma. Robust historical control data are important in clinical trials of rare cancers such as chondrosarcoma in order to show a clear benefit of new drugs. However, it remains controversial whether IDH mutation status is associated with the clinical outcome of chondrosarcoma, and this hinders the development of mutant IDH inhibitors in clinical trials. Read More

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September 2021

A TP53 mutation model for the prediction of prognosis and therapeutic responses in head and neck squamous cell carcinoma.

BMC Cancer 2021 Sep 16;21(1):1035. Epub 2021 Sep 16.

State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of General and Emergency Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China.

Background: Tumor protein p53 (TP53) is the most frequently mutated gene in head and neck squamous cell carcinoma (HNSC), and TP53 mutations are associated with inhibited immune signatures and poor prognosis. We established a TP53 mutation associated risk score model to evaluate the prognosis and therapeutic responses of patients with HNSC.

Methods: Differentially expressed genes between patients with and without TP53 mutations were determined by using data from the HNSC cohort in The Cancer Genome Atlas database. Read More

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September 2021

Genetic counseling as preventive intervention: toward individual specification of transgenerational autism risk.

J Neurodev Disord 2021 Sep 16;13(1):39. Epub 2021 Sep 16.

Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA.

Background: Although autism spectrum disorders (ASD) are among the most heritable of all neuropsychiatric syndromes, most affected children are born to unaffected parents. Recently, we reported an average increase of 3-5% over general population risk of ASD among offspring of adults who have first-degree relatives with ASD in a large epidemiologic family sample. A next essential step is to investigate whether there are measurable characteristics of individual parents placing them at higher or lower recurrence risk, as this information could allow more personalized genetic counseling. Read More

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September 2021

Germline and Somatic Variants Convergently Promote Endothelial-to-Mesenchymal Transition in Simplex Brain Arteriovenous Malformation.

Circ Res 2021 Sep 17. Epub 2021 Sep 17.

Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, CHINA.

Brain arteriovenous malformations (bAVMs) are abnormal entanglement of blood vessels in brain, with direct connections from arteries to veins, lacking functional capillary bed. Although several somatic mutations were reported, the molecular mechanism and genetic disposition of bAVM remain poorly understood. We aim to identify transcriptional anomalies and critical functional pathways in bAVM lesions, and explore their association with key de novo germline and somatic variants in bAVM patients. Read More

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September 2021

Swine as reservoirs of zoonotic borderline oxacillin-resistant Staphylococcus aureus ST398.

Comp Immunol Microbiol Infect Dis 2021 Aug 28;79:101697. Epub 2021 Aug 28.

Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (UFPB), Rod. PB079 Km12, s/n, 58397-000, Areia, PB, Brazil; Global One Health Initiative (GOHi), The Ohio State University, 43210, Columbus, OH, USA. Electronic address:

Methicillin resistance mediated by the mecA gene in Staphylococcus aureus, also known as "true MRSA", is typically associated with high oxacillin MIC values (≥8 mg/L). Because non-mecA-mediated oxacillin resistant S. aureus phenotypes can also cause hard-to-treat diseases in humans, their misidentification as methicillin-susceptible S. Read More

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DNA polymerase delta Exo domain stabilizes mononucleotide microsatellites in human cells.

DNA Repair (Amst) 2021 Sep 3;108:103216. Epub 2021 Sep 3.

Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Japan. Electronic address:

In prokaryotes and yeasts, DNA polymerase proofreading (PPR) and DNA mismatch repair (MMR) cooperatively counteracts replication errors leading to repeat sequence destabilization (i.e. insertions/deletions of repeat units). Read More

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September 2021

Construction and verification of a prognostic risk model based on immunogenomic landscape analysis of bladder caner.

Gene 2021 Sep 13:145966. Epub 2021 Sep 13.

Department of Urology, Affiliated Wuxi No.2 Hospital of Nanjing Medical University, Wuxi, China; Medical College of Nantong University, Nantong, China. Electronic address:

This study was designed to construct a prognostic risk model to predict prognosis and immunotherapy response of bladder cancer (BCa) patinets. 350 differential expressed immune-related genes (DEIRGs) were obtained according to the transcriptome profiling and immune-related genes from the Cancer Genome Atlas (TCGA) database and ImmPort database, respectively. A prognostic risk model was constructed based on 15 hub genes through univariate, multivariate, and LASSO Cox regression analyses. Read More

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September 2021

The medaka fish transposable element is in an early stage of decay: identification of a nonautonomous copy.

Genome 2021 Sep 16. Epub 2021 Sep 16.

Kyoto University, 12918, Primate Research Institute, Inuyama, Japan;

The majority of DNA-based transposable elements comprise autonomous and nonautonomous copies, or only nonautonomous copies, where the autonomous copy contains an intact gene for a transposase protein and the nonautonomous copy does not. Even if autonomous copies coexist, they are generally less frequent. The element of medaka fish is one of the few elements for which a nonautonomous copy has not yet been found. Read More

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September 2021

A genomic snapshot of Salmonella enterica serovar Typhi in Colombia.

PLoS Negl Trop Dis 2021 Sep 16;15(9):e0009755. Epub 2021 Sep 16.

University of Cambridge School of Clinical Medicine Department of Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.

Little is known about the genetic diversity of Salmonella enterica serovar Typhi (S. Typhi) circulating in Latin America. It has been observed that typhoid fever is still endemic in this part of the world; however, a lack of standardized blood culture surveillance across Latin American makes estimating the true disease burden problematic. Read More

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September 2021

Translating genetic and functional data into clinical practice: a series of 223 families with myotonia.

Brain 2021 Sep 16. Epub 2021 Sep 16.

MRC International Centre for Genomic Medicine in Neuromuscular Diseases, Department of Neuromuscular disease, UCL Queen Square Institute of Neurology, London, UK.

High throughput DNA sequencing is increasingly employed to diagnose single gene neurological and neuromuscular disorders. Large volumes of data present new challenges in data interpretation and its useful translation into clinical and genetic counselling for families. Even when a plausible gene is identified with confidence, interpretation of the clinical significance and inheritance pattern of variants can be challenging. Read More

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September 2021

Adjuvant therapy in non-small cell lung cancer: is targeted therapy joining the standard of care?

Expert Rev Anticancer Ther 2021 Sep 16. Epub 2021 Sep 16.

Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai System & Icahn School of Medicine, Mount Sinai, New York, NY, USA.

Introduction: Surgical resection is the standard of care in non-small cell lung cancer (NSCLC) for early stage disease (stage I-IIIA). Despite the use of adjuvant chemotherapy, the 5- year overall survival (OS) rates remain low. In NSCLC with advanced stages (stage IV), tailored strategies have become the gold standard approach applying precision medicine thanks to the introduction of genomic analysis with next generation sequencing (NGS) and the development of targeted therapy and immunotherapy. Read More

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September 2021

Novel compound heterozygous mutations in identified in a Chinese family with developmental glaucoma.

Mol Med Rep 2021 Nov 16;24(5). Epub 2021 Sep 16.

Xiamen Eye Center, Xiamen University, Xiamen, Fujian 361000, P.R. China.

Developmental glaucoma, a subset of glaucoma, is associated with trabeculodysgenesis and/or anterior segment dysgenesis. It is one of the major causes of childhood blindness. Understanding its genetic background is important to diagnose, and identify potential therapeutic targets, of this disease. Read More

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November 2021

TP53 lacks tetramerization and N-terminal domains due to novel inactivating mutations detected in leukemia patients.

J Cancer Res Ther 2021 Jul-Sep;17(4):931-937

Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.

Background: TP53 is a highly conserved tumor suppressor gene present on chromosome 17 and comprised 11 exons and 12 introns. The TP53 protein maintained the genomic integrity of the cell by regulating different pathways. The association of TP53 with leukemia and the increasing prevalence of leukemia in Pakistan instigated us to initiate the current study. Read More

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September 2021

Cancer immunotherapy: Recent advances and challenges.

J Cancer Res Ther 2021 Jul-Sep;17(4):834-844

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

Immunotherapy is a treatment that uses specific components of a person's immune system to fight diseases. This is usually done by stimulating or assisting one's immune system is attacking the offending agent - for instance, in the case of cancer - the target of immunotherapy will be cancer cells. Some types of immunotherapy are also called biologic therapy or biotherapy. Read More

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September 2021

Circulating tumour DNA is a promising biomarker for risk stratification of central chondrosarcoma with IDH1/2 and GNAS mutations.

Mol Oncol 2021 Sep 15. Epub 2021 Sep 15.

Research Department of Pathology, University College London, UCL Cancer Institute, London, UK.

Chondrosarcoma (CS) is a rare tumour type and the most common primary malignant bone cancer in adults. The prognosis, currently based on tumour grade, imaging and anatomical location, is not reliable and more objective biomarkers are required. We aimed to determine whether the level of circulating tumour DNA (ctDNA) in the blood of CS patients could be used to predict outcome. Read More

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September 2021

APOBEC3C, a nucleolar protein induced by genotoxins, is excluded from DNA damage sites.

FEBS J 2021 Sep 16. Epub 2021 Sep 16.

Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.

The human genome contains 11 APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) cytidine deaminases classified into four families. These proteins function mainly in innate antiviral immunity and can also restrict endogenous retrotransposable element multiplication. The present study focuses on APOBEC3C (A3C), a member of the APOBEC3 sub-family. Read More

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September 2021

Plant Mitochondria - Past, present and future.

Plant J 2021 Sep 16. Epub 2021 Sep 16.

Department of Biology, Lund University, SE-22362, Lund, Sweden.

The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) The ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates. Read More

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September 2021

Transcriptomic Changes During Stage Progression of Mycosis Fungoides.

Br J Dermatol 2021 Sep 16. Epub 2021 Sep 16.

Division of Dermatology, University of Alberta, Edmonton, AB, Canada.

Background: Mycosis fungoides (MF) is the most common cutaneous T cell lymphoma, which in the early patch/plaque stages runs an indolent course. However, ~25% of MF patients develop skin tumors, a hallmark of progression to the advanced stage and is associated with high mortality. The mechanisms involved in stage progression are poorly elucidated. Read More

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September 2021

Case Report and Literature Review: Primary Pulmonary NUT-Midline Carcinoma.

Front Oncol 2021 30;11:700781. Epub 2021 Aug 30.

Thoracic Surgery Department, Weifang People's Hospital, Weifang, China.

Nuclear protein of the testis (NUT) carcinoma is a very rare and aggressive carcinoma characterized by chromosomal rearrangement. NUT-midline carcinoma (NMC) can occur anywhere in the body, but most of the tumors are found in the midline anatomic structure or mediastinum. Pulmonary-originated NMC is extremely rare and often difficult to be distinguished from other poorly differentiated tumors, making the diagnosis awfully challenged in clinical practice. Read More

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