Risk stratification for hepatocellular cancer among patients with cirrhosis using a hepatic fat polygenic risk score.

BackgroundPolygenic risk scores (PRS) hold the promise to refine prognostication in hepatocellular cancer (HCC). The few available HCC PRS include germline risk variants identified among individuals of mostly European ancestry, but data are lacking on the transportability of these PRS in multiethnic U.S patients with cirrhosis from multiple etiologies.MethodsWe used data from 1644 patients with cirrhosis enrolled in two prospective cohort studies in the U.S. Patients were followed until HCC diagnosis, death, liver transplantation, or last study visit through June 30, 2021. The high-risk variants in PNPLA3-MBOAT7-TM6SF2-GCKR were combined in a PRS and we evaluated its association with HCC. Discriminatory accuracy was assessed using the C-statistic.ResultsDuring 4,759 person-years of follow-up, 93 patients developed HCC. Mean age was 59.8 years, 68.6% were male, 27.2% Hispanic, 25.1% non-Hispanic Black, 25.7% had NAFLD, 42.1% had heavy alcohol use, and 19.5% had active HCV. HCC risk increased by 134% per unit increase in PRS (HR = 2.30; 95% CI, 1.35-3.92). Compared to cirrhosis patients in the lowest tertile of the PRS, those in the highest tertile had 2-fold higher risk of HCC (HR = 2.05; 95% CI, 1.22-3.44). The PRS alone had modest discriminatory ability (C-statistic = 0.58; 95% CI, 0.52-0.63); however, adding PRS to a predictive model with traditional HCC risk factors had a C-statistic of 0.70 (95% CI, 0.64-0.76), increasing from 0.68 without the PRS (p = 0.0012).ConclusionsOur findings suggest that PRS may enhance risk prediction for HCC in contemporary U.S. cirrhosis patients

Whole genome sequence of two <i>Rathayibacter toxicus</i> strains reveals a tunicamycin biosynthetic cluster similar to <i>Streptomyces chartreusis</i>

<div><p><i>Rathayibacter toxicus</i> is a forage grass associated Gram-positive bacterium of major concern to food safety and agriculture. This species is listed by USDA-APHIS as a plant pathogen select agent because it produces a tunicamycin-like toxin that is lethal to livestock and may be vectored by nematode species native to the U.S. The complete genomes of two strains of <i>R</i>. <i>toxicus</i>, including the type strain FH-79, were sequenced and analyzed in comparison with all available, complete <i>R</i>. <i>toxicus</i> genomes. Genome sizes ranged from 2,343,780 to 2,394,755 nucleotides, with 2079 to 2137 predicted open reading frames; all four strains showed remarkable synteny over nearly the entire genome, with only a small transposed region. A cluster of genes with similarity to the tunicamycin biosynthetic cluster from <i>Streptomyces chartreusis</i> was identified. The tunicamycin gene cluster (TGC) in <i>R</i>. <i>toxicus</i> contained 14 genes in two transcriptional units, with all of the functional elements for tunicamycin biosynthesis present. The TGC had a significantly lower GC content (52%) than the rest of the genome (61.5%), suggesting that the TGC may have originated from a horizontal transfer event. Further analysis indicated numerous remnants of other potential horizontal transfer events are present in the genome. In addition to the TGC, genes potentially associated with carotenoid and exopolysaccharide production, bacteriocins and secondary metabolites were identified. A CRISPR array is evident. There were relatively few plant-associated cell-wall hydrolyzing enzymes, but there were numerous secreted serine proteases that share sequence homology to the pathogenicity-associated protein Pat-1 of <i>Clavibacter michiganensis</i>. Overall, the genome provides clear insight into the possible mechanisms for toxin production in <i>R</i>. <i>toxicus</i>, providing a basis for future genetic approaches.</p></div

<i>R</i>. <i>toxicus</i> CRISPR locus.

<p>Coding regions are depicted with black arrows and the non-coding CRISPR is in green. Scale bar ticks correspond to 5 kb.</p

Genome comparisons of sequenced <i>Rathayibacter toxicus</i> strains.

<p>Genome comparisons of sequenced <i>Rathayibacter toxicus</i> strains.</p

Maximum likelihood phylogenetic tree of putatively secreted serine proteases for <i>R</i>. <i>toxicus</i> FH-79 and <i>C</i>. <i>michiganensis</i> subsp. <i>michiganensis</i> NCPPB382.

<p>Percentage of trees in which the associated taxa clustered together is shown next to the branches; values less than 70 have been omitted. <i>R</i>. <i>toxicus</i> FH-79 is designated with black diamonds; gene name and accession numbers are displayed in parentheses.</p

<i>R</i>. <i>toxicus</i> groups with the <i>Microbacteriaceae</i>.

<p>Maximum likelihood bootstrap phylogram of representative Actinobacteria showing strong support for placement of <i>R</i>. <i>toxicus</i> FH-79 in the <i>Microbacteriaceae</i>. Phylogeny based on concatenated 16S, <i>gyrB</i>, and <i>secA1</i> sequences.</p

Pigment and menaquinone biosynthetic clusters.

<p>Gene clusters from <i>R</i>. <i>toxicus</i> FH-79 appearing to encode a carotenoid pigment (A) and menaquinone MK-10 (B). Scale bar ticks correspond to 1 kb.</p

Collinearity of four complete <i>R</i>. <i>toxicus</i> genomes.

<p>A Mauve alignment shows two large locally collinear blocks separated by short transpositions. Green line connects short transposed region. A) <i>R</i>. <i>toxicus</i> FH-79; B) <i>R</i>. <i>toxicus</i> FH-232; C) <i>R</i>. <i>toxicus</i> FH-145 (NZ_CP010848.1); D) <i>R</i>. <i>toxicus</i> WAC3373 (NZ_CP013292.1).</p