JPWO2020197659A5

JPWO2020197659A5 -

Info

Publication number: JPWO2020197659A5
Application number: JP2021557068A
Authority: JP
Publication date: 2023-02-15

Description

本開示は、以下の［１］から［１５］を含む。
［１］試料を分析する方法であって、
（ａ）対象からＲＮＡの試料を得る工程と、
（ｂ）上記試料中のＪＵＰ、ＳＵＣＬＧ２、ＩＦＩ２７、ＦＣＥＲ１Ａ、ＨＥＳＸ１、ＳＭＡＲＣＤ３、ＩＣＡＭ１、及びＥＢＩ３によってコードされるＲＮＡ転写物の量を測定して、遺伝子発現データを生成する工程と、を含む、方法。
［２］上記測定工程が、ＲＴ－ＰＣＲによって行われる、上記［１］に記載の方法。
［３］上記測定工程が、定量的等温増幅法を使用して行われる、上記［１］に記載の方法。
［４］上記測定工程が、配列決定によって行われる、上記［１］に記載の方法。
［５］上記測定工程が、上記ＲＮＡ又は上記ＲＮＡから調製されたｃＤＮＡを標識し、上記標識されたＲＮＡ又はｃＤＮＡを支持体にハイブリダイズさせることによって行われる、上記［１］に記載の方法。
［６］上記試料が、全血、白血球、好中球、末梢血単核球（ＰＢＭＣ）、又はバフィーコートから単離されたＲＮＡを含む、上記［１］から［５］のいずれか一項に記載の方法。
［７］（ｃ）上記遺伝子発現データに基づいて、上記対象がウイルス感染を有するか細菌感染を有するかを示す報告を提供する工程であって、
（ｉ）ＪＵＰ、ＳＵＣＬＧ２、ＩＦＩ２７、ＦＣＥＲ１Ａ、ＨＥＳＸ１発現の増加は、上記対象がウイルス感染を有することを示し、
（ｉｉ）ＳＭＡＲＣＤ３、ＩＣＡＭ１、ＥＢＩ３の増加は、上記対象が細菌感染を有することを示す工程を更に含む、上記［１］から［６］のいずれか一項に記載の方法。
［８］対象を治療する方法であって、
（ａ）上記対象がウイルス感染を有するか細菌感染を有するかを示す報告を受け取る工程であって、上記報告が、ＪＵＰ、ＳＵＣＬＧ２、ＩＦＩ２７、ＦＣＥＲ１Ａ、ＨＥＳＸ１、ＳＭＡＲＣＤ３、ＩＣＡＭ１、及びＥＢＩ３によってコードされるＲＮＡ転写物の量を測定することによって得られた遺伝子発現データに基づく、工程と、
（ｂ）ＪＵＰ、ＳＵＣＬＧ２、ＩＦＩ２７、及びＦＣＥＲ１Ａ、並びにＨＥＳＸ１発現が増加したとして上記患者を同定する工程と、
上記対象を抗ウイルス療法で治療する工程、又は
（ｃ）ＳＭＡＲＣＤ３、ＩＣＡＭ１、ＥＢＩ３の発現が増加したとして上記患者を同定する工程と、
上記対象を抗菌療法で治療する工程と、を含む、方法。
［９］工程（ｂ）が、抗ウイルス剤を上記対象に投与するステップを含む、上記［８］に記載の方法。
［１０］工程（ｃ）が、抗生物質を上記対象に投与するステップを含む、上記［８］に記載の方法。
［１１］ＪＵＰ、ＳＵＣＬＧ２、ＩＦＩ２７、ＦＣＥＲ１Ａ、ＨＥＳＸ１、ＳＭＡＲＣＤ３、ＩＣＡＭ１及びＥＢＩ３によってコードされる上記ＲＮＡ転写物の量を測定する試薬を含むキット。
［１２］上記試薬が、各ＲＮＡ転写物について、上記転写物にハイブリダイズする配列特異的オリゴヌクレオチドを含む、上記［１１］に記載のキット。
［１３］配列特異的オリゴヌクレオチドがビオチン化され、及び／又は光学的に検出可能な部分で標識されている、上記［１２］に記載のキット。
［１４］上記試薬が、各ＲＮＡ転写物について、上記ＲＮＡ転写物からの配列又は上記ＲＮＡ転写物から調製されたｃＤＮＡを増幅する一対のＰＣＲプライマーを含む、上記［１１］に記載のキット。
［１５］上記試薬が、複数の反応容器を含み、それぞれが、上記転写物又は上記転写物から調製されたｃＤＮＡにハイブリダイズする少なくとも１つの配列特異的等温増幅プライマーを含む、上記［１１］に記載のキット。
ＪＵＰ、ＳＵＣＬＧ２、ＩＦＩ２７、ＦＣＥＲ１Ａ、ＨＥＳＸ１、ＳＭＡＲＣＤ３、ＩＣＡＭ１、及びＥＢＩ３の８つの遺伝子の発現に基づいて、患者をウイルス感染又は細菌感染を有すると分類することができる。ＪＵＰ、ＳＵＣＬＧ２、ＩＦＩ２７、ＦＣＥＲ１Ａ、ＨＥＳＸ１発現の増加は、対象がウイルス感染を有することを示し、ＳＭＡＲＣＤ３、ＩＣＡＭ１、ＥＢＩ３の増加は、対象が細菌感染を有することを示す。
The present disclosure includes the following [1] to [15].
[1] A method of analyzing a sample, comprising:
(a) obtaining a sample of RNA from a subject;
(b) measuring the amount of RNA transcripts encoded by JUP, SUCLG2, IFI27, FCER1A, HESX1, SMARCD3, ICAM1, and EBI3 in said sample to generate gene expression data. .
[2] The method according to [1] above, wherein the measuring step is performed by RT-PCR.
[3] The method according to [1] above, wherein the measuring step is performed using a quantitative isothermal amplification method.
[4] The method according to [1] above, wherein the measuring step is performed by sequencing.
[5] The method according to [1] above, wherein the measuring step is performed by labeling the RNA or cDNA prepared from the RNA, and hybridizing the labeled RNA or cDNA to a support.
[6] Any one of [1] to [5] above, wherein the sample comprises RNA isolated from whole blood, leukocytes, neutrophils, peripheral blood mononuclear cells (PBMC), or buffy coat The method described in .
[7] (c) providing a report indicating whether the subject has a viral infection or a bacterial infection based on the gene expression data, comprising:
(i) increased expression of JUP, SUCLG2, IFI27, FCER1A, HESX1 indicates that said subject has a viral infection;
(ii) The method of any one of [1] to [6] above, wherein an increase in SMARCD3, ICAM1, EBI3 indicates that the subject has a bacterial infection.
[8] A method of treating a subject, comprising:
(a) receiving a report indicating whether the subject has a viral infection or a bacterial infection, wherein the report is encoded by JUP, SUCLG2, IFI27, FCER1A, HESX1, SMARCD3, ICAM1, and EBI3; based on gene expression data obtained by measuring the amount of RNA transcripts;
(b) identifying the patient as having increased JUP, SUCLG2, IFI27, and FCER1A, and HESX1 expression;
treating the subject with antiviral therapy, or
(c) identifying the patient as having increased expression of SMARCD3, ICAM1, EBI3;
and C. treating said subject with antimicrobial therapy.
[9] The method according to [8] above, wherein step (b) comprises administering an antiviral agent to the subject.
[10] The method of [8] above, wherein step (c) comprises administering an antibiotic to the subject.
[11] A kit comprising reagents for measuring the amount of the above RNA transcripts encoded by JUP, SUCLG2, IFI27, FCER1A, HESX1, SMARCD3, ICAM1 and EBI3.
[12] The kit of [11] above, wherein the reagent comprises, for each RNA transcript, a sequence-specific oligonucleotide that hybridizes to the transcript.
[13] The kit of [12] above, wherein the sequence-specific oligonucleotide is biotinylated and/or labeled with an optically detectable moiety.
[14] The kit of [11] above, wherein the reagent comprises, for each RNA transcript, a pair of PCR primers that amplify a sequence from the RNA transcript or a cDNA prepared from the RNA transcript.
[15] The above [11], wherein the reagent comprises a plurality of reaction vessels, each containing at least one sequence-specific isothermal amplification primer that hybridizes to the transcript or cDNA prepared from the transcript. Kit as described.
Patients can be classified as having viral or bacterial infections based on the expression of eight genes: JUP, SUCLG2, IFI27, FCER1A, HESX1, SMARCD3, ICAM1, and EBI3. An increase in JUP, SUCLG2, IFI27, FCER1A, HESX1 expression indicates that the subject has a viral infection and an increase in SMARCD3, ICAM1, EBI3 indicates that the subject has a bacterial infection.

Claims

A method of analyzing a sample, comprising:
(a) obtaining a sample of RNA from a subject;
(b) measuring the amount of RNA transcripts encoded by JUP, SUCLG2, IFI27, FCER1A, HESX1, SMARCD3, ICAM1, and EBI3 in said sample to generate gene expression data. .

2. The method of claim 1, wherein said measuring step is performed by RT-PCR.

2. The method of claim 1, wherein said measuring step is performed using a quantitative isothermal amplification method.

2. The method of claim 1, wherein said measuring step is performed by sequencing.

2. The method of claim 1, wherein the measuring step is performed by labeling the RNA or cDNA prepared from the RNA and hybridizing the labeled RNA or cDNA to a support.

6. The method of any one of claims 1-5, wherein the sample comprises RNA isolated from whole blood, leukocytes, neutrophils, peripheral blood mononuclear cells (PBMC), or buffy coat.

(c) providing a report indicating whether the subject has a viral or bacterial infection based on the gene expression data, comprising:
(i) increased expression of JUP, SUCLG2, IFI27, FCER1A, HESX1 indicates that said subject has a viral infection;
7. The method of any one of claims 1-6, further comprising (ii) an increase in SMARCD3, ICAMl, EBI3 is indicative that the subject has a bacterial infection.

A drug, including an antiviral or antibacterial agent, for treating a subject,
(a) a report indicating whether the subject has a viral or bacterial infection , the amount of RNA transcripts encoded by JUP , SUCLG2, IFI27, FCER1A, HESX1, SMARCD3, ICAM1, and EBI3; There are reports based on gene expression data obtained by measuring
(b) said subject is a subject identified as having increased JUP, SUCLG2, IFI27, and FCER1A, and HESX1 expression and is treated with an antiviral therapy, or (c) said An agent wherein the subject is identified as having increased expression of SMARCD3, ICAM1, EBI3 and is being treated with antimicrobial therapy.

9. The medicament according to claim 8, wherein in the case of ( b), it comprises an antiviral agent.

9. The drug according to claim 8, wherein in the case of ( c), it contains an antibiotic.

A kit containing reagents for measuring the amount of said RNA transcripts encoded by JUP, SUCLG2, IFI27, FCER1A, HESX1, SMARCD3, ICAM1 and EBI3.

12. The kit of Claim 11, wherein said reagent comprises, for each RNA transcript, a sequence-specific oligonucleotide that hybridizes to said transcript.

13. The kit of claim 12, wherein the sequence-specific oligonucleotide is biotinylated and/or labeled with an optically detectable moiety.

12. The kit of claim 11, wherein said reagents comprise, for each RNA transcript, a pair of PCR primers that amplify a sequence from said RNA transcript or a cDNA prepared from said RNA transcript.

12. The kit of claim 11, wherein said reagent comprises a plurality of reaction vessels, each containing at least one sequence-specific isothermal amplification primer that hybridizes to said transcript or cDNA prepared from said transcript.