Diagnostic methods for infectious disease using endogenous gene expression

Abstract

Disclosed are methods of diagnosis of a pathogen-associated disease. These methods comprise: providing a biological sample from a human subject; determining presence, absence and/or quantity of a bacterial pathogen, a viral pathogen, or a combination thereof, by a pathogen culture, a serum antibody detection test, a pathogen antigen detection test, a pathogen DNA and/or RNA detection test, or a combination thereof; determining in the sample, expression levels of at least one endogenous gene in which aberrant expression levels are associated with infection with a pathogen, by a microarray hybridization assay, RNA-seq assay, polymerase chain reaction assay, a LAMP assay, a ligase chain reaction assay, a Southern, Northern, or Western blot assay, an ELISA or a combination thereof. The subject can be diagnosed with the disease if the subject comprises the pathogen and an aberrant level of expression of an endogenous gene.

What is claimed is: 
     
         1 . A method of deterinining etiology of a pathogen-associated disease in a human subject, comprising:
 a) providing at least one biological sample from a human subject;   b) detecting in the sample the presence, absence and/or quantity of a bacterial pathogen, a viral pathogen, or a combination thereof, by a pathogen culture, a serum antibody detection test, a pathogen antigen detection test, a pathogen DNA detection test, a pathogen RNA detection test, or a combination thereof;   c) detecting in the sample expression levels of at least one endogenous gene in which aberrant expression levels are associated with infection with a bacterial pathogen, a viral pathogen or a combination thereof by a microarray hybridization assay, an RNA-seq assay, a polymerase chain reaction assay, a LAMP assay, a ligase chain reaction assay, a Southern blot assay, a Northern blot assay, a Western blot assay, an enzyme-linked immunosorbent assay (ELISA) or as combination thereof, wherein the etiology of the pathogen-associated disease is determined to be bacterial if the sample a) comprises a bacterial pathogen and b) exhibits an aberrant level of expression of at least 1.5 fold increase or decrease of at least one endogenous gene associated with bacterial infection, and wherein the etiology of the pathogen-associated disease is determined to be viral if the sample a) comprises a viral pathogen and b) exhibits an aberrant level of expression of at least 1.5 fold increase or decrease of at least one endogenous gene associated with viral infection.   
     
     
         2 . A method in accordance with  claim 1 , wherein the pathogen-associated disease is Fever Without an Apparent Source (FWS). 
     
     
         3 . A method in accordance with  claim 1 , wherein the detecting expression levels of at least one endogenous gene comprises performing a detection assay comprising labeled cDNA probes. 
     
     
         4 . A method in accordance with  claim 3 , wherein the labeled cDNA probes comprise fluorescently labeled cDNA probes. 
     
     
         5 . A method in accordance with  claim 4 , wherein the labeled cDNA probes comprise dual color fluorescently labeled cDNA probes. 
     
     
         6 . A method in accordance with  claim 1 , wherein the at least one biological sample is selected from the group consisting of a blood sample, a nasopharyngeal sample, a urine sample, a lumbar puncture sample, a biopsy sample, a tissue sample and a combination thereof. 
     
     
         7 . A method in accordance with  claim 1 , wherein the at least one biological sample is a peripheral blood sample. 
     
     
         8 . A method in accordance with  claim 1 , wherein the detecting the expression levels of at least one endogenous gene comprises performing a detection assay selected from the group consisting of a microarray hybridization assay, an RNA-seq assay, a polymerase chain reaction assay, a LAMP assay, a ligase chain reaction assay, a Southern blot assay, a Northern blot assay and a combination thereof. 
     
     
         9 . A method in accordance with  claim 1 , wherein the detecting the expression levels of at least one endogenous gene comprises performing a microarray hybridization assay. 
     
     
         10 . A method in accordance with  claim 1 , wherein the at least one endogenous gene in which aberrant expression levels are associated with infection with a bacterial pathogen, a viral pathogen or a combination thereof is selected from the group consisting of a TREM1 Signaling Pathway gene, a Toll-like Receptor Signaling Pathway gene, a Natural Killer Cell Signaling Pathway gene, an Interferon Signaling Pathway gene, an Integrin Signaling Pathway gene and a combination thereof. 
     
     
         11 . A method in accordance with  claim 1 , wherein the at least one endogenous gene in which aberrant expression levels are associated with infection with a bacterial pathogen is selected from the group consisting of FYN, CD247, EITPR3, CD3, ZAP70, PLCG1, PRKCH, LCK, LAT, PRKCQ, ITK, RHOU, GNA3, PPP1R12A, RHOT1, FCER1G, LYN, RALB, GNAQ, MARCKS, TGM2, ARHGEF11, MYL12A, EP300, MYL9, CREB5, FCGR2A, GNG10, GNG11, C1QB, NOD2, TLR2, TLR1, RNASEL, C5AR1, TLR4, MYD88, PIK3CB, C3AR1, TLR6, CASP1, TLR5, NLRC4, TLR8, IL1B, ITGB7, TSPAN4, PPP1R1, ZYX, VASP, ITGA2B, ITGB5, VCL, ITGB3, MYLK, ASAP1, ITGAM, ITGAX, KLRD1, KIR2DL3, KIR2DL4, KIR3DL3, KIR3DL1, HCST, CD247, NCR3, FCGR3B, SIGLEC9, FCER1G, JAK2, CASP5 and a combination thereof. 
     
     
         12 . A method in accordance with  claim 1 , wherein the at least one endogenous gene in which aberrant expression levels are associated with infection with a bacterial pathogen is selected from the group consisting of RHOU, GNA13, PPP1R12A, RHOT1, FCER1G, LYN, RALB, GNAQ, MARCKS, TGM2, ARHGEF11, MYL12A, EP300, MYL9, CREB5, FCGR2A, GNG10, GNG11, C1QB, NOD2, TLR2, TLR1, RNASEL, C5AR1, TLR4, MYD88, PIK3CB, C3AR1, TLR6, CASP1, TLR5, NLRC4, TLR8, IL1B, PPP1R1, ZYX, MYL12A, VASP, ITGA2B, ITGB5, VCL, ITGB3, MYLK, ASAP1, ITGAM, ITGAX, FCGR3B, SIGLEC9, FCER1G, JAK2, CASP5 and a combination thereof, and wherein the at least one gene has an aberrant level of expression of at least a 1.5 fold increase compared to a control level. 
     
     
         13 . A method in accordance with  claim 1 , wherein the at least one endogenous gene in which aberrant expression levels are associated with infection with a bacterial pathogen is selected from the group consisting of FYN, CD247, EITPR3, CD3, ZAP70, PLCG1, PRKCH, LCK, LAT, PRKCQ, ITK, ITGB7, TSPAN4, KLRD1, KIR2DL3, KIR2DL4, KIR3DL3, KIR3DL1, HCST, CD247, NCR3 and a combination thereof, wherein the at least one gene has an aberrant level of expression of at least a 1.5 fold decrease compared to a control level. 
     
     
         14 . A method in accordance with  claim 1 , wherein the at least one endogenous gene is associated with a viral infection and is selected from the group consisting of CDKN1C, MT2A, SPATS2L, IRF7, ZBP1, OAS2, OAS1, ISG15, IFI6, HERC5, OAS3, RSAD2, OASL, IFIT3, OFOT and IFI27, and wherein the at least one gene has an aberrant level of expression of at least a 1.5 fold increase compared to a bacterium-infected control level. 
     
     
         15 . A method in accordance with  claim 1 , wherein the at least one endogenous gene is associated with a viral infection and is selected from the group consisting of MYH9 and ARAP3, wherein the at least one gene has an aberrant level of expression of at least a 1.5 fold decrease compared to a bacterium-infected control level. 
     
     
         16 . A method in accordance with  claim 1 , wherein the at least one endogenous gene is associated with a viral infection and is selected from the group consisting of BAK1, IFNGR1, STAT2, IFI35, MX1, IFIT1 and IFIT3, wherein the at least one gene has an aberrant level of expression of at least a 1.5 fold increase compared to a bacterium-infected control level. 
     
     
         17 . A method of treatment of a Fever without an Apparent Source (FWS) in a human subject, comprising:
 determining a bacterial etiology by providing at least one blood sample from the human subject, detecting in the sample the presence, absence and/or quantity of a bacterial pathogen, by a pathogen culture, a serum antibody detection test, a pathogen antigen detection test, a pathogen DNA detection test, a pathogen RNA detection test, or a combination thereof, detecting in the sample expression levels of at least one endogenous gene in which aberrant expression levels are associated with infection with a bacterial pathogen by a microarray hybridization assay, an RNA-seq assay, a polymerase chain reaction assay, a LAMP assay, a ligase chain reaction assay, a Southern blot assay, a Northern blot assay, a Western blot assay, an enzyme-linked immunosorbent assay or a combination thereof, wherein the etiology of the FWS is determined to be bacterial if the sample a) comprises a bacterial pathogen and b) exhibits an aberrant level of expression of at least 1.5 fold increase or decrease of at least one endogenous gene associated with bacterial infection; and   administering an antibiotic.   
     
     
         18 . A method of treatment of as Fever without an Apparent Source (FWS) in accordance with  claim 17 , wherein the detecting expression levels of at least one endogenous gene in which aberrant expression levels are associated with infection with a bacterial pathogen comprises performing a microarray hybridization assay with labeled cDNA probes, and wherein the etiology of the disease is determined to be bacterial if a gene selected from the group consisting of RHOU, GNA13, PPP1R12A, RHOT1, FCER1G, LYN, RALB, GNAQ, MARCKS, TGM2, ARHGEF11, MYL12A, EP300, MYL9, CREB5, FCGR2A, GNG10, GNG11, C1QB, NOD2, TLR2, TLR1, RNASEL, C5AR1, TLR4, MYD88, PIK3CB, C3AR1, TLR6, CASP1, TLR5, NLRC4, TLR8, IL1B, PPP1R1, ZYX, MYL12A, VASP, ITGA2B, ITGB5, VCL, ITGB3, MYLK, ASAP1, ITGAM, ITGAX, FCGR3B, SIGLEC9, FCER1G, JAK2, CASP5 and a combination thereof has an aberrant level of expression of at least as 1.5 fold increase compared to a control level, or if a gene selected from the group consisting of FYN, CD247, EITPR3, CD3, ZAP70, PLCG1, PRKCH, LCK, LAT, PRKCQ, ITK, ITGB7, TSPAN4, KLRD1, KIR2DL3, KIR2DL4, KIR3DL3, KIR3DL1, HCST, CD247, NCR3 and a combination thereof has an aberrant level of expression of at least a 1.5 fold decrease compared to a control level. 
     
     
         19 . A method of treatment of a Fever without an Apparent Source (FWS) in a human subject, comprising:
 determining a viral etiology by providing at least one blood sample from the human subject, detecting in the sample the presence, absence and/or quantity of a viral pathogen, by a pathogen culture, a serum antibody detection test, a pathogen antigen detection test, a pathogen DNA detection test, a pathogen RNA detection test, or a combination thereof, detecting in the sample expression levels of at least one endogenous gene in which aberrant expression levels are associated with infection with a viral pathogen by a microarray hybridization assay, an RNA-seq assay, a polymerase chain reaction assay, a LAMP assay, a ligase chain reaction assay, a Southern blot assay, a Northern blot assay, a Western blot assay, an enzyme-linked immunosorbent assay or a combination thereof, wherein the etiology of the FWS is determined to be viral if the sample a) comprises a viral pathogen and b) exhibits an aberrant level of expression of at least 1.5 fold increase or decrease of at least one endogenous gene associated with viral infection; and   administering an anti-viral drug.   
     
     
         20 . A method of treatment of a Fever without an Apparent Source (FWS) in accordance with  claim 19 , wherein the detecting expression levels of at least one endogenous gene in which aberrant expression levels are associated with infection with a viral pathogen comprises performing a microarray hybridization assay with labeled cDNA probes, and wherein the etiology of the disease is determined to be viral if a gene selected from the group consisting of CDKN1C, MT2A, SPATS2L, IRF7, ZBP1, OAS2, OAS1, ISG15, IFI6, HERC5, OAS3, RSAD2, OASL, IFIT3, OTOF and IFI27, and a combination thereof has an aberrant level of expression of at least a 1.5 fold increase compared to a bacterium-infected control level, or if a gene selected from the group consisting of MYH9 and ARAP3 has an aberrant level of expression of at least a 1.5 fold decrease compared to a bacterium-infected control level.