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US 2026/0098299 A1Published application
Gene expression-based identification of early lyme disease
AssigneesThe Regents of the University of California, The Johns Hopkins University
InventorsCharles Y. CHIU, Jerome BOUQUET, Venice SERVELLITA, Mark J. SOLOSKI, John N. AUCOTT
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Abstract
The present disclosure relates to measuring gene expression of cells of a blood sample obtained from a mammalian subject suspected of having a tick-borne disease. In particular, the present disclosure provides tools for determining whether a human subject has acute Lyme disease by transcriptome profiling a peripheral blood mononuclear cell or a whole blood sample from the subject.
Claims53
A method for measuring gene expression, comprising the steps of:
- (a) measuring RNA expression of a plurality of genes of cells from a blood sample obtained from a mammalian subject suspected of having a tick-borne disease;
- (b) calculating a weighted RNA expression score for each of the plurality of genes;
- and
- (c) calculating a Lyme disease score by taking the sum of the weighted RNA expression scores, wherein the plurality of genes comprises at least 3, 4, 5, 6 or all 7 genes of the group consisting of IGSF6, JMJD6, NIF3L1, SHCBP1, SYTL1, TTK and ZNF384.
1 more element
A kit comprising:
- (a) a plurality of oligonucleotides which hybridize to a plurality of genes comprising at least 3, 4, 5, 6, or 7 genes of the group consisting of IGSF6, JMJD6, NIF3L1, SHCBP1, SYTL1, TTK and ZNF384;
- (b) instructions and/or an algorithm for:
- (i) use of the oligonucleotides for measuring RNA expression of the plurality of genes;
- (ii) calculating a weighted RNA expression score for each of the plurality of genes;
- and (iii) calculating a Lyme disease score by taking the sum of the weighted RNA expression scores.
2 more elements
An in vitro method for measuring RNA expression of a gene, comprising:
- i) obtaining RNA extracted from a peripheral blood mononuclear cell (PBMC) sample of a human subject suspected of having a tick-borne disease;
- and
- ii) performing targeted RNA expression resequencing comprising hybridization of an upstream oligonucleotide and a downstream oligonucleotide to the extracted RNA to measure RNA expression of the gene,
- wherein the gene comprises one or more of the group consisting of IGSF6, JMJD6, NIF3L1, SHCBP1, SYTL1, TTK and ZNF384.
1 more element
A kit comprising:
- (a) a plurality of upstream oligonucleotides and a plurality of downstream oligonucleotides, which hybridize to one of a plurality of genes comprising at least 3, 4, 5, 6, or 7 of the group consisting of IGSF6, JMJD6, NIF3L1, SHCBP1, SYTL1, TTK and ZNF384;
- (b) instructions for:
- (i) use of the oligonucleotides for measuring RNA expression of the plurality of genes by performing targeted RNA expression resequencing comprising hybridization of the plurality of upstream oligonucleotides and the plurality of a downstream oligonucleotides to RNA extracted from a peripheral blood mononuclear cell (PBMC) sample of a human subject suspected of having a tick-bome disease to measure RNA expression of the plurality of genes,
- wherein when the plurality of genes comprises:
- IGSF6, one of the plurality of upstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:25 and one of the plurality of downstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:26;
- JMJD6, one of the plurality of upstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:29 and one of the plurality of downstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:30;
- NIF3L1, one of the plurality of upstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:37 and one of the plurality of downstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:38;
- SHCBP1, one of the plurality of upstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:41 and one of the plurality of downstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:42;
- SYTL1, one of the plurality of upstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:51 and one of the plurality of downstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:52;
- TTK, one of the plurality of upstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:57 and one of the plurality of downstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:58;
- and/or
- ZNF384, one of the plurality of upstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:61 and one of the plurality of downstream oligonucleotides comprises the nucleotide sequence of SEQ ID NO:62.
9 more elements
Dependencies are inferred from the claim text.