TCGA-TCIA Impact on Radiogenomics Cancer Research: A Systematic Review.

Abstract:

:In the last decade, the development of radiogenomics research has produced a significant amount of papers describing relations between imaging features and several molecular 'omic signatures arising from next-generation sequencing technology and their potential role in the integrated diagnostic field. The most vulnerable point of many of these studies lies in the poor number of involved patients. In this scenario, a leading role is played by The Cancer Genome Atlas (TCGA) and The Cancer Imaging Archive (TCIA), which make available, respectively, molecular 'omic data and linked imaging data. In this review, we systematically collected and analyzed radiogenomic studies based on TCGA-TCIA data. We organized literature per tumor type and molecular 'omic data in order to discuss salient imaging genomic associations and limitations of each study. Finally, we outlined the potential clinical impact of radiogenomics to improve the accuracy of diagnosis and the prediction of patient outcomes in oncology.

journal_name

Int J Mol Sci

authors

Zanfardino M,Pane K,Mirabelli P,Salvatore M,Franzese M

doi

10.3390/ijms20236033

subject

Has Abstract

pub_date

2019-11-29 00:00:00

issue

23

issn

1422-0067

pii

ijms20236033

journal_volume

20

pub_type

杂志文章
  • Retrospective Study of Metastatic Melanoma and Renal Cell Carcinoma to the Brain with Multivariate Analysis of Prognostic Pre-Treatment Clinical Factors.

    abstract::Patients with brain metastasis from renal cell carcinoma (RCC) or melanoma have historically had very poor prognoses of less than one year. Stereotactic radiosurgery (SRS) can be an effective treatment for patients with these tumors. This study analyzes the effect of pretreatment prognostic factors on overall survival...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms17030400

    authors: Ferrel EA,Roehrig AT,Kaya EA,Carlson JD,Ling BC,Wagner A,MacKay AR,Call JA,Demakas JJ,Lamoreaux WT,Fairbanks RK,Cooke BS,Peressini B,Lee CM

    更新日期:2016-03-18 00:00:00

  • Redox Components: Key Regulators of Epigenetic Modifications in Plants.

    abstract::Epigenetic modifications including DNA methylation, histone modifications, and chromatin remodeling are crucial regulators of chromatin architecture and gene expression in plants. Their dynamics are significantly influenced by oxidants, such as reactive oxygen species (ROS) and nitric oxide (NO), and antioxidants, lik...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21041419

    authors: R M SK,Wang Y,Zhang X,Cheng H,Sun L,He S,Hao F

    更新日期:2020-02-19 00:00:00

  • Comparative Solid-State Stability of Perindopril Active Substance vs. Pharmaceutical Formulation.

    abstract::This paper presents the results obtained after studying the thermal stability and decomposition kinetics of perindopril erbumine as a pure active pharmaceutical ingredient as well as a solid pharmaceutical formulation containing the same active pharmaceutical ingredient (API). Since no data were found in the literatur...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms18010164

    authors: Buda V,Andor M,Ledeti A,Ledeti I,Vlase G,Vlase T,Cristescu C,Voicu M,Suciu L,Tomescu MC

    更新日期:2017-01-15 00:00:00

  • Neuroinflammation and Oxidative Stress in Psychosis and Psychosis Risk.

    abstract::Although our understanding of psychotic disorders has advanced substantially in the past few decades, very little has changed in the standard of care for these illnesses since the development of atypical anti-psychotics in the 1990s. Here, we integrate new insights into the pathophysiology with the increasing interest...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms18030651

    authors: Barron H,Hafizi S,Andreazza AC,Mizrahi R

    更新日期:2017-03-17 00:00:00

  • Functional Heterologous Expression of Mature Lipase LipA from Pseudomonas aeruginosa PSA01 in Escherichia coli SHuffle and BL21 (DE3): Effect of the Expression Host on Thermal Stability and Solvent Tolerance of the Enzyme Produced.

    abstract::This study aimed to express heterologously the lipase LipA from Pseudomonas aeruginosa PSA01 obtained from palm fruit residues. In previous approaches, LipA was expressed in Escherichia coli fused with its signal peptide and without its disulfide bond, displaying low activity. We cloned the mature LipA with its trunca...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21113925

    authors: Pulido IY,Prieto E,Pieffet GP,Méndez L,Jiménez-Junca CA

    更新日期:2020-05-30 00:00:00

  • Laser induced C(60) cage opening studied by semiclassical dynamics simulation.

    abstract::Laser induced opening of the C(60) cage is studied by a semiclassical electron-radiation-ion dynamics technique. The simulation results indicate that the C(60) cage is abruptly opened immediately after laser excitation. The opening of the C(60) cage induces a quick increase in kinetic energy and a sharp decrease in el...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms12010353

    authors: Tang H,Li H,Dou Y

    更新日期:2011-01-13 00:00:00

  • Expression of Hypoxia-Inducible Factor 1α (HIF-1α) and Genes of Related Pathways in Altered Gravity.

    abstract::Immune system deterioration in space represents a major risk, which has to be mitigated for exploration-class missions into the solar system. Altered gravitational forces have been shown to regulate adaptation processes in cells of the immune system, which are important for appropriate risk management, monitoring and ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20020436

    authors: Vogel J,Thiel CS,Tauber S,Stockmann C,Gassmann M,Ullrich O

    更新日期:2019-01-20 00:00:00

  • Effects of dietary conjugated linoleic acid and biopolymer encapsulation on lipid metabolism in mice.

    abstract::Forty mice were randomly divided into four groups on the basis of the diet to be fed as follows: 5% (low) fat diet (T1: LF); 20% (high) fat diet (T2: HF); 20% fat containing 1% conjugated linoleic acid (CLA) (T3: HFC); and 20% fat containing 1% CLA with 0.5% biopolymers (T4: HFCB). The high-fat with CLA diet groups (H...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms14046848

    authors: Hur SJ,Kim DH,Chun SC,Lee SK

    更新日期:2013-03-26 00:00:00

  • Genetics and Extracellular Vesicles of Pediatrics Sleep Disordered Breathing and Epilepsy.

    abstract::Sleep remains one of the least understood phenomena in biology, and sleep disturbances are one of the most common behavioral problems in childhood. The etiology of sleep disorders is complex and involves both genetic and environmental factors. Epilepsy is the most popular childhood neurological condition and is charac...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20215483

    authors: Khalyfa A,Sanz-Rubio D

    更新日期:2019-11-04 00:00:00

  • Dietary polyphenols in prevention and treatment of prostate cancer.

    abstract::Prostate cancer is the most prevalent disease affecting males in many Western countries, with an estimated 29,480 deaths in 2014 in the US alone. Incidence rates for prostate cancer deaths have been decreasing since the early 1990s in men of all races/ethnicities, though they remain about 60% higher in African America...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms16023350

    authors: Lall RK,Syed DN,Adhami VM,Khan MI,Mukhtar H

    更新日期:2015-02-03 00:00:00

  • Microglial Pro-Inflammatory and Anti-Inflammatory Phenotypes Are Modulated by Translocator Protein Activation.

    abstract::A key role of the mitochondrial Translocator Protein 18 KDa (TSPO) in neuroinflammation has been recently proposed. However, little is known about TSPO-activated pathways underlying the modulation of reactive microglia. In the present work, the TSPO activation was explored in an in vitro human primary microglia model ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20184467

    authors: Pozzo ED,Tremolanti C,Costa B,Giacomelli C,Milenkovic VM,Bader S,Wetzel CH,Rupprecht R,Taliani S,Settimo FD,Martini C

    更新日期:2019-09-10 00:00:00

  • Fluence Rate Differences in Photodynamic Therapy Efficacy and Activation of Epidermal Growth Factor Receptor after Treatment of the Tumor-Involved Murine Thoracic Cavity.

    abstract::Photodynamic therapy (PDT) of the thoracic cavity can be performed in conjunction with surgery to treat cancers of the lung and its pleura. However, illumination of the cavity results in tissue exposure to a broad range of fluence rates. In a murine model of intrathoracic PDT, we studied the efficacy of 2-(1-hexyloxye...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms17010101

    authors: Grossman CE,Carter SL,Czupryna J,Wang L,Putt ME,Busch TM

    更新日期:2016-01-14 00:00:00

  • Fragment C of tetanus toxin: new insights into its neuronal signaling pathway.

    abstract::When Clostridium tetani was discovered and identified as a Gram-positive anaerobic bacterium of the genus Clostridium, the possibility of turning its toxin into a valuable biological carrier to ameliorate neurodegenerative processes was inconceivable. However, the non-toxic carboxy-terminal fragment of the tetanus tox...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms13066883

    authors: Calvo AC,Oliván S,Manzano R,Zaragoza P,Aguilera J,Osta R

    更新日期:2012-01-01 00:00:00

  • Polysaccharides from the Edible Mushroom Agaricus bitorquis (Quél.) Sacc. Chaidam Show Anti-hypoxia Activities in Pulmonary Artery Smooth Muscle Cells.

    abstract::Three kinds of new water-soluble polysaccharides (FA, FB and FC) were isolated from wild mushroom Agaricus bitorquis (Quél.) Sacc. Chaidam by the classical method "water extraction and alcohol precipitation" and purified by column chromatography. The Mw of FA, FB and FC ranged from 5690 Da to 38,340 Da. The three poly...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20030637

    authors: Jiao Y,Kuang H,Wu J,Chen Q

    更新日期:2019-02-01 00:00:00

  • 1-benzyl-2-phenylbenzimidazole (BPB), a benzimidazole derivative, induces cell apoptosis in human chondrosarcoma through intrinsic and extrinsic pathways.

    abstract::In this study, we investigated the anticancer effects of a new benzimidazole derivative, 1-benzyl-2-phenyl -benzimidazole (BPB), in human chondrosarcoma cells. BPB-mediated apoptosis was assessed by the MTT assay and flow cytometry analysis. The in vivo efficacy was examined in a JJ012 xenograft model. Here we found t...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms131216472

    authors: Liu JF,Huang YL,Yang WH,Chang CS,Tang CH

    更新日期:2012-12-04 00:00:00

  • A Potential Lock-Type Mechanism for Unconventional Secretion in Fungi.

    abstract::Protein export in eukaryotes can either occur via the classical pathway traversing the endomembrane system or exploit alternative routes summarized as unconventional secretion. Besides multiple examples in higher eukaryotes, unconventional secretion has also been described for fungal proteins with diverse functions in...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20030460

    authors: Reindl M,Hänsch S,Weidtkamp-Peters S,Schipper K

    更新日期:2019-01-22 00:00:00

  • Cladieunicellins K and L, new eunicellin-based diterpenoids from an octocoral Cladiella sp.

    abstract::Two new eunicellin-based diterpenoids, cladieunicellins K (1) and L (2), were isolated from an octocoral Cladiella sp. The structures of 1 and 2 were elucidated by spectroscopic methods and 2 exhibited moderate cytotoxicity towards the MOLT-4 human leukemia. ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms141121781

    authors: Shih FY,Chen TH,Lu MC,Chen WF,Wen ZH,Kuo YH,Sung PJ

    更新日期:2013-11-04 00:00:00

  • Characteristics and Cryopreservation of Semen of Sex-Reversed Females of Salmonid Fish.

    abstract::Sex reversal has been used as a breeding strategy by salmonid fish to produce genetically and phenotypically single sex populations. Production of all-female fish has great importance for the creation of monosex female triploids of salmonid fish, which are valued for their sterility, lack of female maturation, and lar...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms22020964

    authors: Judycka S,Nynca J,Hliwa P,Ciereszko A

    更新日期:2021-01-19 00:00:00

  • Impact of PPAR-Alpha Polymorphisms-The Case of Metabolic Disorders and Atherosclerosis.

    abstract::Peroxisome proliferator activated receptor α (PPARα) has the most relevant biological functions among PPARs. Activation by drugs and dietary components lead to major metabolic changes, from reduced triglyceridemia to improvement in the metabolic syndrome. Polymorphisms of PPARα are of interest in order to improve our ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20184378

    authors: Ruscica M,Busnelli M,Runfola E,Corsini A,Sirtori CR

    更新日期:2019-09-06 00:00:00

  • Plant MicroRNAs in Cross-Kingdom Regulation of Gene Expression.

    abstract::MicroRNAs (miRNAs) are a class of noncoding small RNAs, which play a crucial role in post-transcriptional gene regulation. Recently, various reports revealed that miRNAs could be transmitted between species to mediate cross-kingdom regulation by integrating into a specific target gene-mediated regulatory pathway to ex...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms19072007

    authors: Wang W,Liu D,Zhang X,Chen D,Cheng Y,Shen F

    更新日期:2018-07-10 00:00:00

  • Increase in Toxicity of Anticancer Drugs by PMTPV, a Claudin-1-Binding Peptide, Mediated via Down-Regulation of Claudin-1 in Human Lung Adenocarcinoma A549 Cells.

    abstract::Claudin-1 (CLDN1), a tight junctional protein, is highly expressed in lung cancer cells and may contribute to chemoresistance. A drug which decreases CLDN1 expression could be a chemosensitizer for enhancing the efficacy of anticancer drugs, but there is no such drug known. We found that PMTPV, a short peptide, which ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21165909

    authors: Nasako H,Takashina Y,Eguchi H,Ito A,Ishikawa Y,Matsunaga T,Endo S,Ikari A

    更新日期:2020-08-17 00:00:00

  • Seasonal variation in the hepatoproteome of the dehydration and freeze-tolerant wood frog, Rana sylvatica.

    abstract::Winter's advent invokes physiological adjustments that permit temperate ectotherms to cope with stresses such as food shortage, water deprivation, hypoxia, and hypothermia. We used liquid chromatography (LC) in combination with tandem mass spectrometry (MS/MS) quantitative isobaric (iTRAQ™) peptide mapping to assess v...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms12128406

    authors: Kiss AJ,Muir TJ,Lee RE Jr,Costanzo JP

    更新日期:2011-01-01 00:00:00

  • Metformin Restores Parkin-Mediated Mitophagy, Suppressed by Cytosolic p53.

    abstract::Metformin is known to alleviate hepatosteatosis by inducing 5' adenosine monophosphate (AMP)-kinase-independent, sirtuin 1 (SIRT1)-mediated autophagy. Dysfunctional mitophagy in response to glucolipotoxicities might play an important role in hepatosteatosis. Here, we investigated the mechanism by which metformin induc...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms17010122

    authors: Song YM,Lee WK,Lee YH,Kang ES,Cha BS,Lee BW

    更新日期:2016-01-16 00:00:00

  • 3D-Reconstructed Retinal Pigment Epithelial Cells Provide Insights into the Anatomy of the Outer Retina.

    abstract::The retinal pigment epithelium (RPE) is located between the neuroretina and the choroid, and plays a critical role in vision. RPE cells internalise outer segments (OS) from overlying photoreceptors in the daily photoreceptor renewal. Changes to RPE structure are linked with age and retinopathy, which has been describe...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21218408

    authors: Keeling E,Chatelet DS,Tan NYT,Khan F,Richards R,Thisainathan T,Goggin P,Page A,Tumbarello DA,Lotery AJ,Ratnayaka JA

    更新日期:2020-11-09 00:00:00

  • Identification of RNA-Binding Proteins as Targetable Putative Oncogenes in Neuroblastoma.

    abstract::Neuroblastoma is a common childhood cancer with almost a third of those affected still dying, thus new therapeutic strategies need to be explored. Current experimental therapies focus mostly on inhibiting oncogenic transcription factor signalling. Although LIN28B, DICER and other RNA-binding proteins (RBPs) have repor...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21145098

    authors: Bell JL,Hagemann S,Holien JK,Liu T,Nagy Z,Schulte JH,Misiak D,Hüttelmaier S

    更新日期:2020-07-19 00:00:00

  • Hepatitis C Virus and Hepatocellular Carcinoma: When the Host Loses Its Grip.

    abstract::Chronic infection with hepatitis C virus (HCV) is a major cause of hepatocellular carcinoma (HCC). Novel treatments with direct-acting antivirals achieve high rates of sustained virologic response; however, the HCC risk remains elevated in cured patients, especially those with advanced liver disease. Long-term HCV inf...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21093057

    authors: Goto K,Roca Suarez AA,Wrensch F,Baumert TF,Lupberger J

    更新日期:2020-04-26 00:00:00

  • Blockade of the Adenosine A3 Receptor Attenuates Caspase 1 Activation in Renal Tubule Epithelial Cells and Decreases Interleukins IL-1β and IL-18 in Diabetic Rats.

    abstract::Diabetic nephropathy (DN) is the main cause of end-stage renal disease, which remains incurable. The progression of DN is associated with progressive and irreversible renal fibrosis and also high levels of adenosine. Our aim was to evaluate the effects of ADORA3 antagonism on renal injury in streptozotocin-induced dia...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20184531

    authors: Garrido W,Jara C,Torres A,Suarez R,Cappelli C,Oyarzún C,Quezada C,San Martín R

    更新日期:2019-09-13 00:00:00

  • Effect of Gelation Temperature on the Molecular Structure and Physicochemical Properties of the Curdlan Matrix: Spectroscopic and Microscopic Analyses.

    abstract::In order to determine the effect of different gelation temperatures (80 °C and 90 °C) on the structural arrangements in 1,3-β-d-glucan (curdlan) matrices, spectroscopic and microscopic approaches were chosen. Attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR) and Raman spectroscopy are wel...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21176154

    authors: Gieroba B,Sroka-Bartnicka A,Kazimierczak P,Kalisz G,Pieta IS,Nowakowski R,Pisarek M,Przekora A

    更新日期:2020-08-26 00:00:00

  • Functional Mechanisms of Mitochondrial Respiratory Chain Supercomplex Assembly Factors and Their Involvement in Muscle Quality.

    abstract::Impairment of skeletal muscle function causes disabilities in elderly people. Therefore, in an aged society, prevention and treatment of sarcopenia are important for expanding healthy life expectancy. In addition to aging, adipose tissue disfunction and inflammation also contribute to the pathogenesis of sarcopenia by...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21093182

    authors: Azuma K,Ikeda K,Inoue S

    更新日期:2020-04-30 00:00:00

  • Regulation of Akt/FoxO3a/Skp2 Axis Is Critically Involved in Berberine-Induced Cell Cycle Arrest in Hepatocellular Carcinoma Cells.

    abstract::The maintenance of ordinal cell cycle phases is a critical biological process in cancer genesis, which is a crucial target for anti-cancer drugs. As an important natural isoquinoline alkaloid from Chinese herbal medicine, Berberine (BBR) has been reported to possess anti-cancer potentiality to induce cell cycle arrest...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms19020327

    authors: Li F,Dong X,Lin P,Jiang J

    更新日期:2018-01-23 00:00:00