Radiogenomics in personalized management of lung cancer patients: Where are we?

With the rise of artificial intelligence, radiomics has emerged as a field of translational research based on the extraction of mineable high-dimensional data from radiological images to create "big data" datasets for the purpose of identifying distinct sub-visual imaging patterns. The integrated analysis of radiomic data and genomic data is termed radiogenomics, a promising strategy to identify potential imaging biomarkers for predicting driver mutations and other genomic parameters. In lung cancer, recent advances in whole-genome sequencing and the identification of actionable molecular alterations have led to an increased interest in understanding the complex relationships between imaging and genomic data, with the potential of guiding therapeutic strategies and predicting clinical outcomes. Although the integration of the radiogenomics data into lung cancer management may represent a new paradigm in the field, the use of this technique as a clinical biomarker remains investigational and still necessitates standardization and robustness to be effectively translated into the clinical practice. This review summarizes the basic concepts, potential contributions, challenges, and opportunities of radiogenomics in the management of patients with lung cancer.

Silicon and Nitrate Differentially Modulate the Symbiotic Performances of Healthy and Virus-Infected Bradyrhizobium-nodulated Cowpea (Vigna unguiculata), Yardlong Bean (V. unguiculata subsp. sesquipedalis) and Mung Bean (V. radiata).

The effects of 2 mM silicon (Si) and 10 mM KNO3 (N)-prime signals for plant resistance to pathogens-were analyzed in healthy and Cowpea chlorotic mottle virus (CCMV) or Cowpea mild mottle virus (CMMV)-infected Bradyrhizobium-nodulated cowpea, yardlong bean and mung bean plants. In healthy plants of the three Vigna taxa, nodulation and growth were promoted in the order of Si + N > N > Si > controls. In the case of healthy cowpea and yardlong bean, the addition of Si and N decreased ureide and α-amino acids (AA) contents in the nodules and leaves in the order of Si + N> N > Si > controls. On the other hand, the addition of N arrested the deleterious effects of CCMV or CMMV infections on growth and nodulation in the three Vigna taxa. However, the addition of Si or Si + N hindered growth and nodulation in the CCMV- or CMMV-infected cowpea and yardlong bean, causing a massive accumulation of ureides in the leaves and nodules. Nevertheless, the AA content in leaves and nodules of CCMV- or CMMV-infected cowpea and yardlong bean was promoted by Si but reduced to minimum by Si + N. These results contrasted to the counteracting effects of Si or Si + N in the CCMV- and CMMV-infected mung bean via enhanced growth, nodulation and levels of ureide and AA in the leaves and nodules. Together, these observations suggest the fertilization with Si + N exclusively in virus-free cowpea and yardlong bean crops. However, Si + N fertilization must be encouraged in virus-endangered mung bean crops to enhance growth, nodulation and N-metabolism. It is noteworthy to see the enhanced nodulation of the three Vigna taxa in the presence of 10 mM KNO3.

The seed-borne Southern bean mosaic virus hinders the early events of nodulation and growth in Rhizobium-inoculated Phaseolus vulgaris L.

To simulate seed-borne virus transmission, a noninvasive protocol was designed to infect the radicle of germinating seeds, with 100% effectiveness. Preinfection of 24-h-old black bean (Phaseolus vulgaris L.) radicles by Southern bean mosaic virus (SBMV) followed by Rhizobium inoculation 48h later caused a drastic reduction in root nodulation. Results were attributed to active virus replication within the elongating zone of the radicle at least 32h before Rhizobium inoculation, which elicited severe anatomical malformations; an abnormal accumulation of apoplastic reactive oxygen species in the rhizodermis, cortex, inner cortical and endodermic root cells; the formation of atypical root hair tips and the collapse of 94% of the root hairs in the SBMV-preinfected radicles. Adult SBMV-preinfected plants showed exacerbated virus symptoms and 80% growth reduction ascribed to major virus-induced ultrastructural alterations in the nodules. The accumulation of ureides, α-amino acids and total reducing sugars in the leaves and nodules of SBMV-preinfected plants are indicators of the hindering effects of SBMV infection on N2 fixation and ureide catabolism, causing N starvation. The exogenous addition of 1 or 4µM naringenin, genistein or daidzein did not counteract the deleterious effects of SBMV preinfection on nodulation.

Irradiance regulates genotype-specific responses of Rhizobium-nodulated soybean to increasing iron and two manganese concentrations in solution culture.

The growth of soybean plants were examined when subjected to three contrasting irradiance levels and to various combinations of nutrient solution Fe and Mn concentrations. Two Rhizobium-nodulated soybean genotypes (PI 227557 and Biloxi), which had been previously found to differ in their growth response to various Fe and Mn solutions, were studied. Both genotypes displayed the poorest growth, nodulation and the lowest chlorophyll and nodule ureide concentration at high irradiance (HI), regardless of the solution Fe and Mn concentrations. However, the genotypes differed under HI in their accumulation of Fe. For solution concentrations greater than 13 microM, PI 227557 accumulated up to 1200 microg Feg(-1) leaf dry wt mainly in the form of ferritin crystals within chloroplasts. In contrast, leaf Fe concentrations in Biloxi only reached 300 microg Feg(-1) dry wt and there were no ferritin crystals. Also, in PI 227557 HI induced more severe distortions in leaf cells and nodule ultrastructure than in Biloxi. Based on its poor growth under HI, PI 227557 could be categorized as an Fe-inefficient genotype prone to undergo photoinhibition at HI, in spite of the ferritin crystals in the chloroplasts. Enhanced growth, nodulation, chlorophyll and ureide concentrations in nodules as well as leaf ureide catabolism occurred in both genotypes grown at moderate irradiance (MI) in Fe solutions from 13 to 60 microM supplied with 20 microM Mn. At low irradiance (LI), plant growth and nodulation were lower than at MI values, but higher than those of plants at HI. Irradiance and solution Fe concentration did not alter leaf Cu and Zn concentration in either genotype, with the higher concentrations of these two elements detected in Biloxi. Solutions with Fe concentrations greater than 100 microM were deleterious for both genotypes at all irradiances. Low Fe and high Mn concentrations in leaves was bound to result in the best growth at HI.

Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands.

A well-resolved rhizobial species phylogeny with 51 haplotypes was inferred from a combined atpD + recA data set using Bayesian inference with best-fit, gene-specific substitution models. Relatively dense taxon sampling for the genera Rhizobium and Mesorhizobium was achieved by generating atpD and recA sequences for six type and 24 reference strains not previously available in GenBank. This phylogeny was used to classify nine nodule isolates from Sesbania exasperata, S. punicea and S. sericea plants native to seasonally flooded areas of Venezuela, and compared with a PCR-RFLP analysis of rrs plus rrl genes and large maximum likelihood rrs and nifH phylogenies. We show that rrs phylogenies are particularly sensitive to strain choice due to the high levels of sequence mosaicism found at this locus. All analyses consistently identified the Sesbania isolates as Mesorhizobium plurifarium or Rhizobium huautlense. Host range experiments on ten legume species coupled with plasmid profiling uncovered potential novel biovarieties of both species. This study demonstrates the wide geographic and environmental distribution of M. plurifarium, that R. galegae and R. huautlense are sister lineages, and the synonymy of R. gallicum, R. mongolense and R. yanglingense. Complex and diverse phylogeographic, inheritance and host-association patterns were found for the symbiotic nifH locus. The results and the analytical approaches used herein are discussed in the context of rhizobial taxonomy and molecular systematics.