# US 2014/0194309 A1 · In vitro method for predicting in vivo genotoxicity of chemical compounds

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2014/0194309 A1
- Document ID: US20140194309A1
- Status: Published application
- Kind: A1
- Application number: 14/117,731
- Filed: 2012-05-19
- Published: 2014-07-10
- Earliest claimed: 2011-05-19
- Assignees: Academisch Ziekenhuis Maastricht; Universiteit Maastricht
- Inventors: Joseph Henri Marie van Delft; Joseph Catharina Stephanus Kleinjans; Christina Magkoufopoulu; Danyel Gerardus Jacobus Jennen
- Web page: https://patentgrep.com/patent/US20140194309A1

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- G01N 33/5014: {for testing toxicity}
- G01N 33/5017: {for testing neoplastic activity}
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

The invention is in the field of genomics and it provides an in vitro method for predicting whether a compound is genotoxic in vivo. In particular, the invention provides a method for predicting the in vivo genotoxicity of a compound comprising the steps of performing an Ames test on the compound and determining if the result is positive or negative, followed by a step wherein the gene expression of at least 3 genes is determined in a HepG2 cell, compared to a reference value and predicting that the compound is in vivo genotoxic if the expression level of more than 2 of the genes is above a reference value.

## Claims

### Claim 1

A method for predicting the in vivo genotoxicity of a compound, the method comprising:
exposing a HepG2 cell to the compound for a period of time between 12 and 48 hours,
determining, for a HepG2 cell exposed to an Ames positive compound, the level of expression of a first gene set comprising at least genes NR0B2, PWWP2B and LOC100131914,
determining, for a HepG2 cell exposed to an Ames negative compound, the level of expression of a second gene set, comprising at least genes SLC40A1, PNMA6A and C10orf65,
comparing the level of expression of the first gene set or the second gene set to a set of predetermined reference values, and
predicting the compound to be in vivo genotoxic where the expression level of at least 2 genes of the first or second gene set are above their predetermined reference values.

### Claim 2 (depends on 1)

The method according to claim 1, wherein the first gene set comprises at least one gene selected from the group consisting of genes CEACAM1, SLC27A1, TTR, UBE2E2, NAT8, GMFG, RBPMS, C10orf10, PROSC, TBC1D9, OR10H1, APOM, C1orf128, AVEN, ZNRF3 and SNORD8.

### Claim 3 (depends on 1)

The method according to claim 1, wherein the second gene set comprises at least one gene selected from the group consisting of genes SGK1, SLC64A, ANXA6, BTD, FGA, NDUFA10, NFATC3, MTMR15, ANAPC5, ZNF767, SCRN2 and GSTK1.

### Claim 4 (depends on 1)

The method according to claim 1, wherein the predetermined reference value for a particular gene is calculated as the mean of the log 2 of the ratios of the expression level said gene in the presence and absence of at least one genotoxic compound and at least one non-genotoxic reference compound.

### Claim 5 (depends on 1)

The method according to claim 1, wherein the predetermined reference value for the gene is −0.099 for NR0B2, is −0.071 for PWWP2B, is −0.054 for LOC100131914, is 0.1795 for CEACAM1, is −0.014 for CLCN4, is −0.1825 for EML1, is 0.006 for UBE2E2, is 0.046 for USP13, is −0.0125 for GMFG, is −0.0445 for PROSC, is −0.2465 for TTR, is −0.267 for NAT8, is −0.0495 for RBPMS, is 0.0355 for C10orf10, is −0.163 for TBC1D9, is −0.0575 for SNX11, is 0.104 for ROBO4, is −0.1415 for BCOR, is 0.081 for ROBO2, is −0.0775 for SRMS, is 0.0455 for OR10H1, is 0 for TPK1, is 0.0405 for C10orf54, is −0.0105 for SNORD8, is 0.0655 for FAM116B, is −0.163 for APOM, is 0.0465 for NRIP3, is 0.1155 for C1orf128/PITHD1, is 0.148 for AVEN, is 0.086 for BRUNOL6, is −0.3185 for ZNRF3, is 0.119 for BEAN, is −0.037 for SLC27A1 is 0.329 for SLC40A1, is 0.251 for PNMA6A, is 0.146 for C10orf65, is 0.1655 for ANXA6, is 0 for APOA4, is 0.037 for BTD, is 0.0275 for LGTN, is −0.086 for AGFG1, is 0.038 for NDUFA10, is 0.159 for NFATC3, is −0.057 for PLAA, is 0.0755 for MTMR15, is 0.0265 for ANAPC5, is 0.0845 for MRPS5, is 0.0985 for ZNF767, is 0.0355 for GSTK1, is −0.0205 for FGA, is 0.1975 for SGK1, is 0.0535 for SLC6A4, is 0.0405 for SCRN2, is 0.0165 for CC2D1B, or is −0.048 for LOC648921/LOC283693.

### Claim 6 (depends on 1)

The method according to claim 1, wherein said period of time is about 24 hours.

### Claim 7 (depends on 1)

The method according to claim 1, wherein the compound is predicted to be in vivo genotoxic if the expression level of more than half of the genes in the first or second gene set are above their predetermined reference values after exposure to the compound.

### Claim 8 (depends on 1)

The method according to claim 1, wherein comparing the level of expression of the first gene set or the second gene set to a set of predetermined reference values is performed by a computer program.

### Claim 9 (depends on 8)

The method according to claim 8, wherein the computer program is PAM (Prediction Analysis for Microarrays) or Support Vector Machines (SVM).