Gene expression‐based in vivo and in vitro prediction of liver toxicity allows compound selection at an early stage of drug development

Abstract

We have analyzed gene expression and histopathology of rat liver treated with a histamine-3 receptor inverse agonist under development for the treatment of obesity 24 h after a single acute administration. While histopathology did not identify a clear liver toxicity, analysis of gene changes strongly suggested the development of toxicity. This prediction was confirmed in a 2-week repeat-dose rat study where prominent liver pathology occurred, while gene changes that lead to the prediction persisted. A subset of these genes was analyzed in vitro in both rat and human hepatocytes to reveal the potential relevancy of the findings for the situation in humans. This comprehensive analysis of the development compound at the gene expression level allowed interpretation of findings of the follow-up compound in a frontloaded 24-h single-dose acute study that was initiated before regular 2-week repeat-dose studies started. The high similarity of the follow-up compound to the lead compound based on gene expression lead to the immediate termination of the development program for this compound series. Our data demonstrate the value of genomics-based early toxicity prediction in short-term in vivo studies for the characterization of compounds to allow prioritization and selection of suited candidates before compound-, animal-, and cost-intensive longer term studies are undertaken.

Decoding mechanisms by which silent codon changes influence protein biogenesis and function

“…In addition to the original approach of applying the most frequently used codons by the host (Richardson et al, 2006, Villalobos et al, 2006), other programs incorporate criteria such as natural codon distribution (Gao et al, 2004, Gaspar et al, 2012, Jayaraj et al, 2005, Raab et al, 2010, Roth et al, 2011, Wu et al, 2006), host tRNA concentrations (Fuglsang, 2003, Qian et al, 2012), or slow translating regions thought to be important for protein folding (Angov et al, 2008). A recent approach termed the “preferred human codon-optimized method” integrates the preferred human codons, with >60% GC content (Inouye et al, 2015).…”

A Decade of Toxicogenomic Research and Its Contribution to Toxicological Science

“…Ruepp et al (2005) claimed to find several examples in their study indicating an earlier detection of toxicological events by transcript profiling, which precedes pathology. For example, in the study of tacrine hepatotoxicity, the 6h transcript profiles flagged 4 out of 5 animals to have liver damage (cholestasis), but histological analysis did not find changes until 24 h. Roth et al (2011) reported gene expressions changes in rat liver treated with a histamine-3 receptor agonist after a single acute administration. Their analysis of gene expression changes strongly suggested the development of toxicity while histopathology did not identify a clear liver toxicity; the toxicogenomics findings were confirmed in a 2-week repeated-dose rat study where prominent liver pathology occurred.…”

Microfluidics nucleic acid testing for point-of-care liver assessment

“…For completeness, further to our aforesaid contributions, our contributions include the initiation of a preliminary selection process by performing a statistical analysis on a database repository of microarray gene expression profiling experiments from comprehensive animal studies [23,[28][29][30][31]. This preliminary selection process is imperative for the identification and selection of the critical GOIs (Specific Objectives (A-v)) to be used in using microfluidics NAT for liver assessment.…”

“…The first microarray dataset (GEO accession reference number: GSE17388) was based on a reported analysis [30] of gene expression changes performed using the Affymetrix ® chip and the aforementioned U34 array. Said reported work was strongly correlated to hepatotoxicity in the presence of 24-h (short duration) and 336-h (long duration) drug toxicity study using two different drug compounds (i.e.…”

“…At this juncture, we have initiated a preliminary selection process (delineated in Chapter 2) by performing a statistical analysis on a database repository of extensive microarray gene expression profiling experiments [23,[28][29][30][31] from comprehensive animal studies. This preliminary selection process is crucial for a comprehensive liver assessment, and complements our aforementioned proposed "Lab-in-a-Needle" concept device for practical POCT liver assessment.…”