KR20220143261A - Method for screening therapeutic agents of cancer by interaction THRAP3 and DDX5 - Google Patents

Method for screening therapeutic agents of cancer by interaction THRAP3 and DDX5 Download PDF

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KR20220143261A
KR20220143261A KR1020210049552A KR20210049552A KR20220143261A KR 20220143261 A KR20220143261 A KR 20220143261A KR 1020210049552 A KR1020210049552 A KR 1020210049552A KR 20210049552 A KR20210049552 A KR 20210049552A KR 20220143261 A KR20220143261 A KR 20220143261A
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cancer
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loop
cells
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KR102505355B1 (en
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최장현
권혁무
강현제
엄혜진
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울산과학기술원
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    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6845Methods of identifying protein-protein interactions in protein mixtures
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    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14Hydrolases (3)
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    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00Screening for compounds of potential therapeutic value
    • G01N2500/04Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)

Abstract

The present invention relates to a method for screening cancer therapeutics using the binding of THRAP3 and DDX5. More particularly, the present invention is to provide a method for screening, as cancer therapeutics, candidate substances which can induce apoptosis by reducing the binding of THRAP3 and DDX5 in cancer cells, as it is confirmed that the accumulation of R-loops is suppressed and DNA damage of cells is inhibited as THRAP3 and methylated DDX5 bind in a cellular R-loop (DNA:RNA hybrid), and XRN2, an exonuclease, is brought to degrade the RNA of the R-loop through the binding.

Description

THRAP3 및 DDX5의 결합을 이용한 암 치료제 스크리닝 방법{Method for screening therapeutic agents of cancer by interaction THRAP3 and DDX5}Method for screening therapeutic agents of cancer by interaction THRAP3 and DDX5

본 발명은 THRAP3 (Thyroid hormone receptor-associated protein 3) 및 DDX5 (DEAD box RNA helicase DDX5) 결합을 이용한 암 치료제 스크리닝 방법에 관한 것이다.The present invention relates to a cancer therapeutic screening method using THRAP3 (Thyroid hormone receptor-associated protein 3) and DDX5 (DEAD box RNA helicase DDX5) binding.

모든 생명체는 자신의 유전 정보를 DNA라는 형태로 저장하고 있다. 유전체(genome)를 보존하는 것은 모든 생명체의 생존과 원활한 기능 유지에 있어서 필수적이다. 하지만 세포는 정상적인 대사 중에 발생하는 활성산소종(reactive oxygen species; ROS) 또는 자외선과 같이 외부 환경에서 오는 스트레스 등에 의해 지속적으로 위험에 노출된다. 내부 및 외부의 다양한 위험 요인들은 DNA 염기 서열에 돌연변이(mutation)를 일으켜 유전체(genome)의 불안전성을 초래한다. 다행히도 세포 내에는 DNA 수선 기작(DNA repair system)이 존재하여 일상적으로 발생하는 돌연변이를 교정할 수 있지만, 때로는 손상 정도가 심하여 세포 내 시스템 만으로는 복구할 수 없는 상황이 발생한다. 이렇게 물리적, 화학적 원인에 의해 DNA 자가복제시 복원되지 않는 기초 구조의 변화가 발생한 것을 DNA 손상(damage)이라고 정의한다.All living things store their genetic information in the form of DNA. Preserving the genome is essential for the survival and smooth functioning of all living things. However, cells are continuously exposed to risks due to stress from the external environment such as reactive oxygen species (ROS) or ultraviolet rays generated during normal metabolism. Various internal and external risk factors cause mutations in DNA nucleotide sequences, resulting in genome instability. Fortunately, there is a DNA repair system in the cell that can correct the mutations that occur on a daily basis, but sometimes the damage is so severe that the intracellular system alone cannot repair it. A change in the basic structure that is not restored during DNA self-replication due to physical and chemical causes is defined as DNA damage.

DNA-RNA 잡종 (DNA:RNA hybrid, R-loop)은 DNA 사슬과 염기순서가 그것에 상보적인 RNA 사슬로 구성된 핵산분자로, A형 DNA 및 2중 사슬 RNA와 유사한 2중 나선구조이다. RNA-DNA잡종과 그 형성반응은 역전사효소에 의한 cDNA합성을 비롯하여 노던흡입법, S1 지도작성법 등 유전자해석기술에 이용되고 있으며, 생체에서는 전사반응이나 DNA 복제에서 시발체 합성 등으로 짧은 RNA-DNA 잡종을 형성한다.A DNA-RNA hybrid (DNA:RNA hybrid, R-loop) is a nucleic acid molecule composed of a DNA chain and an RNA chain whose nucleotide sequence is complementary thereto, and has a double helix structure similar to type A DNA and double-stranded RNA. RNA-DNA hybrids and their formation reactions are used in gene analysis technologies such as cDNA synthesis by reverse transcriptase, Northern aspiration, and S1 mapping. to form

그러나 DNA 전사-복제 과정에서 형성된 R-loop (DNA:RNA hybrid)가 해소되지 않을 경우 DNA 손상이 나타나며, 이러한 DNA 손상은 암 질환 발생의 원인이 되므로, DNA 전사-복제 과정 후 형성된 R-loop의 분해가 암 질환 치료에 주요 타겟이 될 수 있다.However, if the R-loop (DNA:RNA hybrid) formed during the DNA transcription-replication process is not resolved, DNA damage occurs, and this DNA damage causes cancer disease. Therefore, the R-loop formed after the DNA transcription-replication process Degradation could be a major target for the treatment of cancer diseases.

대한민국 공개특허 제10-2017-0088462호 (2017.08.02. 공개)Republic of Korea Patent Publication No. 10-2017-0088462 (published on Aug. 2, 2017)

본 발명은 THRAP3 및 DDX5 결합을 억제하여 암 세포의 DNA 손상을 유도시키는 후보약물을 선별하기 위한 암 치료제 스크리닝 방법에 관한 것이다.The present invention relates to a cancer therapeutic screening method for selecting a candidate drug that induces DNA damage in cancer cells by inhibiting THRAP3 and DDX5 binding.

본 발명은 암세포에 시험물질을 접촉시키는 단계; The present invention comprises the steps of contacting a test substance to cancer cells;

상기 시험물질을 접촉한 암세포에서 THRAP3 및 DDX5의 결합 수준을 확인하는 단계; 및checking the binding level of THRAP3 and DDX5 in cancer cells contacted with the test substance; and

대조구 시료와 비교하여 상기 THRAP3 및 DDX5의 결합 수준이 감소된 시험물질을 선별하는 단계를 포함하는 암 치료제 스크리닝 방법을 제공한다.Provided is a method for screening a cancer therapeutic agent, comprising selecting a test substance having a reduced binding level of THRAP3 and DDX5 compared to a control sample.

또한, 본 발명은 시험관 내에서(in vitro) 암세포의 THRAP3 및 DDX5 결합 수준을 감소시키는 단계를 포함하는 암세포의 DNA 손상을 유도하는 방법을 제공한다.In addition, the present invention provides a method of inducing DNA damage in cancer cells, comprising reducing the THRAP3 and DDX5 binding levels of the cancer cells in vitro.

본 발명에 따르면 THRAP3의 발현이 억제된 암 세포에서 THRAP3과 DDX5의 결합이 감소되었으며, THRAP3과 DDX5의 결합 감소에 의해 RNA 분해 효소인 XRN2의 발현이 감소되고, 이에 따라 R-loop 축적과 DNA 손상이 유도되어 암세포 증식이 억제되는 효과를 확인함에 따라, 상기 THRAP3과 DDX5의 결합 수준을 저해할 경우 암 세포 내 R-loop 축적이 유도되어 DNA가 손상되고, 이를 통하여 암 세포사멸을 증가시킬 수 있으므로, 상기 THRAP3 및 DDX5 결합을 조절하여 암세포 사멸을 유도할 수 있는 후보물질을 암 치료제로 제공하기 위한 스크리닝 방법을 제공하고자 한다.According to the present invention, the binding of THRAP3 and DDX5 was reduced in cancer cells in which the expression of THRAP3 was suppressed, and the expression of XRN2, an RNA degrading enzyme, was reduced due to the decrease in the binding of THRAP3 and DDX5. Accordingly, R-loop accumulation and DNA damage were reduced. As this induction confirms the effect of inhibiting cancer cell proliferation, when the binding level of THRAP3 and DDX5 is inhibited, R-loop accumulation in cancer cells is induced, DNA is damaged, and thus cancer cell death can be increased. , to provide a screening method for providing a candidate substance capable of inducing cancer cell death by regulating the THRAP3 and DDX5 binding as a cancer therapeutic agent.

도 1은 THRAP3과 R-loop의 공동 국소부위화 및 THRAP3 결핍에 따른 R-loop 축적을 확인한 결과로, 도 1a는 THRAP3가 핵 내에서 R-loop과 동일한 위치에 존재하는 것을 확인한 결과이며, 도 1b는 R-loop 항체를 이용한 면역 침강을 통해서 THRAP3가 R-loop과 결합하고 있다는 것과 siRNA 형질 주입으로 인해 THRAP3가 결핍된 상황에서 R-loop의 형성이 증가해있는 것을 확인한 결과이다.
도 2는 THRAP3 결핍에 따른 DNA 복제 억제 및 DSB 유도를 확인한 결과로, 도 1a는 DNA 중합효소의 보조 인자로서, 전사-복제 충돌로 인한 R-loop 생성 과정에서 축적된다고 알려진 PCNA 단백질이 THRAP3가 결핍된 상황에서 핵에 증가되어있는 것을 통해 R-loop의 형성 증가를 확인한 것이며, 도 2b 및 도 2c는 EdU를 혼성시켜 새롭게 복제된 DNA들을 보았을 때, 비교군에 비해 THRAP3가 결핍된 세포에서 수가 감소해있는 것을 확인결과이며, 도 2d 및 도 2e는 R-loop으로 유도될 수 있는 DNA 이중가닥 손상을 확인하기 위해 대표적인 지표인 γH2AX와 53BP1을 핵에서 형광으로 표지하여 THRAP3 결핍으로 증가하는 것을 확인한 결과로, 상기 결과들로부터 R-loop을 풀어주는 RNaseH1의 과발현을 통해 정상으로 회복되는 것을 확인할 수 있었다.
도 3은 THRAP3과 DDX5 및 XRN2의 결합을 확인한 결과로, 도 3a는 질량 분석법을 통해 찾은 250여개의 THRAP3와 결합하는 단백질들 중 R-loop의 해소와 관련된 단백질을 분류해내어 가장 유의미한 단백질인 DDX5, RNA helicase를 확인한 결과이며, 도 3b, 도 3c, 도 3d, 도 3e 및 도 3f는 THRAP3 항체를 이용한 면역침강법을 통해서 THRAP3가 DDX5 뿐만 아니라 DDX5와 결합하여 R-loop을 구성하고 있는 RNA를 잘라내어 직접적인 R-loop제거 기능을 담당하는 XRN2과도 결합해 있는 것을 확인한 결과로, R-loop을 해소하기 위해 DDX5와 XRN2가 결합체를 이룰 때, DDX5의 메틸화가 중요한 역할을 한다. 따라서 메틸화 억제제(g)와 메틸화가 이루어지는 arginie 잔기를 lysine으로 치환한 DDX5를 이용해 THRAP3와의 결합정도를 확인한 결과(h, i), DDX5의 메틸화는 THRAP3와의 결합도 매개하며, 메틸화를 방해하였을 때 결합이 감소하는 것을 확인한 결과이다.
도 4는 DDX5가 THRAP3 N 말단과 상호작용하는 것을 확인한 결과로, THRAP3 단백질을 부위별로 잘라낸 구조들을 세포에 발현시켜 면역침강법을 이용해 DDX5와의 결합을 확인하였을 때 THRAP3의 N 말단 부위와 결합하는 것을 확인한 결과이다.
도 5는 R-loop 분해를 위한 THRAP3의 하위 타겟으로 XRN2를 확인한 결과로, THRAP3의 결핍으로 인한 R-loop의 형성 증가를 일으키는 직접적인 하위 요인을 찾기 위해 위의 도면3에서 결합을 확인하였던 XRN2를 THRAP3가 결핍된 상태에서 현상을 확인하였을 때, R-loop으로의 접근이 감소해있는 것을 확인한 결과이다.
도 6은 THRAP3이 유방암 세포에서 R-loop를 분해시키는 효과를 확인한 결과로, 도 6a는 THRAP3를 통한 R-loop 분해 효과를 유방암세포주인 MCF7 세포에서 확인하기 위해 THRAP3의 siRNA 형질주입을 하였으며, THRAP3 넉다운 세포에서 DNA 복제가 감소하는 것을 확인한 결과이며, 도 6b는 THRAP3가 결핍된 세포에서 R-loop이 증가된 것을 확인한 결과로, 그로 인해 DNA 이중가닥 손상이 유도되는 것을 γH2AX, 53BP1 형광 염색의 증가로 확인하였으며, 또한 THAP3가 결핍된 상태로 선별화 된 MCF7 세포에서 세포의 증식이 감소하고, R-loop을 해소시키는 RNaseH1의 과발현으로 세포증식이 회복되는 것을 확인함으로써, THRAP3의 감소로 인한 R-loop의 조절이 암세포의 증식을 조절하는 것에 영향을 미친다는 것을 확인한 결과이다.
도 7은 R-loop 분해에 있어서, THRAP3 작용을 나타내는 모식도로, THRAP3는 R-loop의 RNA 부위에 결합하여 메틸화된 DDX5와 결합체를 구성하고, RNA를 잘라내는 XRN2의 동원을 유도함으로써 R-loop을 해소시키는 역할을 하는 것을 나타낸다.
1 is a result of confirming the co-localization of THRAP3 and R-loop and R-loop accumulation according to THRAP3 deficiency. Figure 1b is the result of confirming that THRAP3 binds to R-loop through immunoprecipitation using R-loop antibody and that R-loop formation is increased in a THRAP3 deficient situation due to siRNA transfection.
Figure 2 is the result of confirming the inhibition of DNA replication and DSB induction according to THRAP3 deficiency. It was confirmed that the increase in the formation of R-loop through the increase in the nucleus under the current situation, and FIGS. 2b and 2c show that when looking at newly replicated DNA by hybridizing EdU, the number decreased in THRAP3 deficient cells compared to the control group. 2d and 2e show that γH2AX and 53BP1, which are representative indicators, are fluorescently labeled in the nucleus to confirm the DNA double-stranded damage that can be induced by R-loop, and it is confirmed that the increase due to THRAP3 deficiency As a result, it was confirmed that normal recovery was achieved through overexpression of RNaseH1 that releases R-loop from the above results.
Figure 3 is the result of confirming the binding of THRAP3 to DDX5 and XRN2, Figure 3a is the most significant protein DDX5 by classifying the protein related to the resolution of R-loop among the 250 THRAP3-binding proteins found through mass spectrometry. , are the results of confirming the RNA helicase, and FIGS. 3b, 3c, 3d, 3e and 3f show that THRAP3 binds to DDX5 as well as DDX5 and RNA constituting the R-loop through immunoprecipitation using the THRAP3 antibody. As a result of confirming that it is also bound to XRN2, which is responsible for the direct R-loop removal function after cutting, DDX5 methylation plays an important role when DDX5 and XRN2 form a bond to resolve R-loop. Therefore, as a result of confirming the degree of binding to THRAP3 using DDX5 in which the methylation inhibitor (g) and the methylation arginie residue were substituted with lysine (h, i), DDX5 methylation also mediates binding to THRAP3, and binding when methylation is disturbed It is the result of confirming that this decrease.
4 is a result confirming that DDX5 interacts with the N-terminal of THRAP3. When the THRAP3 protein is expressed in cells and the binding to DDX5 is confirmed using the immunoprecipitation method, the binding to the N-terminal site of THRAP3 is shown. This is the confirmed result.
5 is a result of confirming XRN2 as a sub-target of THRAP3 for R-loop degradation, XRN2, which was confirmed binding in FIG. It is the result of confirming that the access to the R-loop is decreased when the phenomenon is confirmed in the state of THRAP3 deficiency.
6 is a result of confirming the effect of THRAP3 to degrade R-loop in breast cancer cells. It is a result of confirming that DNA replication is decreased in knockdown cells, and FIG. 6b is a result of confirming that R-loop is increased in THRAP3-deficient cells, thereby inducing DNA double-stranded damage. Increase in γH2AX, 53BP1 fluorescence staining In addition, by confirming that cell proliferation was reduced in MCF7 cells selected in a THAP3-deficient state, and cell proliferation was restored by overexpression of RNaseH1 that resolves R-loop, R- caused by a decrease in THRAP3 This is the result of confirming that the control of the loop affects the regulation of the proliferation of cancer cells.
7 is a schematic diagram showing the action of THRAP3 in R-loop degradation. THRAP3 binds to the RNA site of R-loop to form a conjugate with methylated DDX5, and induces the recruitment of RNA-cleaving XRN2 to R-loop. indicates that it plays a role in resolving

이하, 본 발명을 보다 상세하게 설명한다.Hereinafter, the present invention will be described in more detail.

본 발명은 세포의 R-loop (DNA:RNA hybrid)에서 THRAP3과 메틸화된 DDX5가 결합하며, 상기 결합을 통하여 핵산외부가수분해효소 (exonuclease)인 XRN2가 동원되어 R-loop의 RNA를 분해시킴으로써 R-loop의 축적을 억제시켜 세포의 DNA 손상을 저해시키는 것을 확인함에 따라, 암 세포에서 THRAP3과 DDX5의 결합을 조절하여 세포 사멸을 유도할 수 있는 후보물질을 암 치료제로 스크리닝하는 방법을 제공하고자 한다.In the present invention, THRAP3 and methylated DDX5 are bound in R-loop (DNA:RNA hybrid) of cells, and XRN2, an exonuclease, is mobilized through the binding to degrade R-loop RNA. By inhibiting the accumulation of -loop and confirming that it inhibits cell DNA damage, it is intended to provide a method for screening candidate substances capable of inducing apoptosis as a cancer treatment agent by regulating the binding of THRAP3 and DDX5 in cancer cells. .

본 발명은 암세포에 시험물질을 접촉시키는 단계; The present invention comprises the steps of contacting a test substance to cancer cells;

상기 시험물질을 접촉한 암세포에서 THRAP3 및 DDX5의 결합 수준을 확인하는 단계; 및 대조구 시료와 비교하여 상기 THRAP3 및 DDX5의 결합 수준이 감소된 시험물질을 선별하는 단계를 포함하는 암 치료제 스크리닝 방법을 제공할 수 있다.checking the binding level of THRAP3 and DDX5 in cancer cells contacted with the test substance; and selecting a test substance having a reduced binding level of THRAP3 and DDX5 as compared to a control sample.

상기 암 치료제 스크리닝 방법은 시험물질을 접촉한 암세포에서 THRAP3 및 XRN2 결합 수준 감소를 추가로 더 확인하는 단계를 포함하는 것일 수 있다.The cancer therapeutic agent screening method may further include further confirming a decrease in THRAP3 and XRN2 binding levels in cancer cells contacted with a test substance.

상기 THRAP3은 R-loop (DNA:RNA hybrid) 내에서 DDX5와 결합하여 핵산외부가수분해효소 (exonuclease)를 동원시켜 R-loop를 분해시키는 것일 수 있다.The THRAP3 may bind to DDX5 in R-loop (DNA: RNA hybrid) and mobilize exonuclease to degrade R-loop.

상기 DDX5는 PRMT5에 의해 아르기닌이 메틸화되고, 메틸화된 DDX5가 THRAP3의 N 말단에 결합하는 것일 수 있다.The DDX5 may be one in which arginine is methylated by PRMT5, and the methylated DDX5 binds to the N-terminus of THRAP3.

상기 THRAP3 및 DDX5의 결합 수준 감소는 암세포 내 R-loop (DNA:RNA hybrid) 분해를 억제시킴으로써, DNA 손상을 유도하여 암세포를 사멸시키는 것일 수 있다.The decrease in the binding level of THRAP3 and DDX5 may be to inhibit R-loop (DNA:RNA hybrid) degradation in cancer cells, thereby inducing DNA damage and killing cancer cells.

상기 암은 골육종, 유방암, 대장암, 폐암, 간암, 신장암, 위암, 뇌암, 전립선암 및 췌장암으로 이루어진 군에서 선택되는 것일 수 있다.The cancer may be selected from the group consisting of osteosarcoma, breast cancer, colon cancer, lung cancer, liver cancer, kidney cancer, stomach cancer, brain cancer, prostate cancer and pancreatic cancer.

또한, 본 발명은 시험관 내에서(in vitro) 암세포의 THRAP3 및 DDX5 결합 수준을 감소시키는 단계를 포함하는 암세포의 DNA 손상을 유도하는 방법을 제공할 수 있다.In addition, the present invention may provide a method for inducing DNA damage in cancer cells, comprising reducing the THRAP3 and DDX5 binding levels of the cancer cells in vitro.

상기 THRAP3 및 DDX5 결합 수준은 면역침전법(Immunoprecipitation) 및 면역블랏팅(Immunoblotting)으로 확인될 수 있지만, 이에 제한되지 않는다.The THRAP3 and DDX5 binding level may be confirmed by immunoprecipitation (Immunoprecipitation) and immunoblotting (Immunoblotting), but is not limited thereto.

본 발명의 "THRAP3"은 NCBI accession no. 9967 일 수 있으며, "DDX5"는 NCBI accession no. 1655 일 수 있으며, "XRN2"는 NCBI accession no. 22803일 수 있으나, 이에 제한되지 않는다."THRAP3" of the present invention is NCBI accession no. 9967, "DDX5" is the NCBI accession no. 1655, "XRN2" is the NCBI accession no. 22803, but is not limited thereto.

본 발명의 스크리닝 방법을 언급하면서 사용되는 용어 "시험물질"은 유전자의 발현량에 영향을 미치거나, 단백질의 발현 또는 활성에 영향을 미치거나 또는 단백질 사이의 결합에 영향을 미치는지 여부를 검사하기 위하여 스크리닝에서 이용되는 미지의 후보 물질을 의미한다. 상기 시료는 화학물질, 뉴클레오타이드, 안티센스-RNA, siRNA(small interference RNA) 및 천연물 추출물을 포함하나, 이에 제한되는 것은 아니다.The term "test substance" used while referring to the screening method of the present invention affects the expression level of a gene, affects the expression or activity of a protein, or affects the binding between proteins. It refers to an unknown candidate substance used in screening. The sample includes, but is not limited to, chemicals, nucleotides, antisense-RNA, small interference RNA (siRNA), and natural product extracts.

이하, 본 발명의 이해를 돕기 위하여 실시예를 들어 상세하게 설명하기로 한다. 다만 하기의 실시예는 본 발명의 내용을 예시하는 것일 뿐 본 발명의 범위가 하기 실시예에 한정되는 것은 아니다. 본 발명의 실시예는 당업계에서 평균적인 지식을 가진 자에게 본 발명을 보다 완전하게 설명하기 위해 제공되는 것이다.Hereinafter, to help the understanding of the present invention, examples will be described in detail. However, the following examples are merely illustrative of the content of the present invention, and the scope of the present invention is not limited to the following examples. The embodiments of the present invention are provided to more completely explain the present invention to those of ordinary skill in the art.

<실험예><Experimental example>

하기의 실험예들은 본 발명에 따른 각각의 실시예에 공통적으로 적용되는 실험예를 제공하기 위한 것이다.The following experimental examples are intended to provide experimental examples commonly applied to each embodiment according to the present invention.

1. 세포 배양1. Cell Culture

U2OS 세포 및 MDA-MB-231 세포를 American Type Culture Collection (ATCC)에서 구입하여 10% 태아소혈청(FBS)이 포함된 DMEM (Dulbecco’s modified Eagle’s medium) 배지에서 배양하였으며, 세포를 37℃ 및 5% CO2 배양기에서 유지시켰다. U2OS cells and MDA-MB-231 cells were purchased from the American Type Culture Collection (ATCC) and cultured in DMEM (Dulbecco's modified Eagle's medium) medium containing 10% fetal bovine serum (FBS). It was maintained in a CO 2 incubator.

MDA-MB-231의 증식 능력을 확인하기 위해, 105 세포를 분주하고 매일 계수하였다. 렌티바이러스 shRNA 형질주입을 통하여 THRAP3 넉다운 MDA-MB-231 세포를 준비하였다. 렌티바이스 생산을 위해, HEK-293T 세포 (ATCC)에 4 μg의 렌티바이러스 pLKO.1 shRNA, packaging 및 엔빌로프 (envelope) 벡터를 형질주입하였다. To confirm the proliferative ability of MDA-MB-231, 10 5 cells were aliquoted and counted daily. THRAP3 knockdown MDA-MB-231 cells were prepared through lentiviral shRNA transfection. For lentivis production, HEK-293T cells (ATCC) were transfected with 4 μg of lentiviral pLKO.1 shRNA, packaging and envelope vectors.

형질주입된 세포 배양배지를 수집하여 MDA-MB-231에 감염시키고, 감염 후 퓨로마이신 (VWR Chemicals) 2 μg/mL으로 세포를 선택하였다.The transfected cell culture medium was collected, infected with MDA-MB-231, and cells were selected with 2 μg/mL of puromycin (VWR Chemicals) after infection.

2. 플라스미드 및 siRNA 형질주입2. Plasmid and siRNA transfection

RNaseH1-V5, Flag/Myc-DDX5, HA-THRAP3 플라스미드 및 하기 siRNA 20 nM 형질주입은 각각 Lipofectamine 2000 및 RNAiMAX transfection reagent (Invitrogen)으로 제조사 설명서의 형질감염 과정에 따라 수행되었다.Transfections of RNaseH1-V5, Flag/Myc-DDX5, HA-THRAP3 plasmids and the following siRNA at 20 nM were performed with Lipofectamine 2000 and RNAiMAX transfection reagent (Invitrogen), respectively, according to the transfection procedure of the manufacturer's instructions.

1) siRNA1) siRNA

Negative control siRNA: 5'-UUC UCC GAA CGU GUC ACG UTT-3'Negative control siRNA: 5'-UUC UCC GAA CGU GUC ACG UTT-3'

human THRAP3 siRNA: 5'-GGU AUA AGC UCC GAG AUG A-3'human THRAP3 siRNA: 5'-GGU AUA AGC UCC GAG AUG A-3'

2) shRNA2) shRNA

human THRAP3 MISSION shRNA, human THRAP3 MISSION shRNA,

shTHRAP3 #1 sequence: CCG GAG TAT ATC AGA ATC GGG ATT TCT CGA GAA ATC CCG ATT CTG ATA TAC TTT TTT GshTHRAP3 #1 sequence: CCG GAG TAT ATC AGA ATC GGG ATT TCT CGA GAA ATC CCG ATT CTG ATA TAC TTT TTT G

shTHRAP3 #2 sequence: CCG GGC CTT GAT ATT GAA CGT CGT ACT CGA GTA CGA CGT TCA ATA TCA AGG CTT TTT GshTHRAP3 #2 sequence: CCG GGC CTT GAT ATT GAA CGT CGT ACT CGA GTA CGA CGT TCA ATA TCA AGG CTT TTT G

shTHRAP3 #3 sequence: CCG GAG ATC TCG TTC TCG TTC ATT TCT CGA GAA ATG AAC GAG AAC GAG ATC TTT TTT GshTHRAP3 #3 sequence: CCG GAG ATC TCG TTC TCG TTC ATT TCT CGA GAA ATG AAC GAG AAC GAG ATC TTT TTT G

shTHRAP3 #4 sequence: CCG GTG GAG CTA AGA TGA CTA ATT TCT CGA GAA ATT AGT CAT CTT AGC TCC ATT TTT GshTHRAP3 #4 sequence: CCG GTG GAG CTA AGA TGA CTA ATT TCT CGA GAA ATT AGT CAT CTT AGC TCC ATT TTT G

3. 세포 용해, 웨스턴 블로팅 및 면역침강 분석3. Cell Lysis, Western Blotting and Immunoprecipitation Analysis

차가운 PBS로 세척된 세포에 1% 디옥시콜레이트염, 단백질분해효소 억제제 (Roche) 및 인산가수분해효소 억제제 칵테일(Sigma Aldrich)이 포함된 RIPA 용해 버퍼를 처리하여 전체 세포 용해물을 준비하였다.Whole cell lysates were prepared by treating cells washed with cold PBS with RIPA lysis buffer containing 1% deoxycholate salt, protease inhibitor (Roche) and phosphatase inhibitor cocktail (Sigma Aldrich).

수집된 세포 현탁액을 강하게 와류시키고 15000rpm, 4℃에서 15분간 원심분리하였다. 제거된 세포 단백질 추출물의 농도를 Pierce BCA Protein Assay Kit로 확인하였다. The collected cell suspension was vortexed vigorously and centrifuged at 15000 rpm, 4° C. for 15 minutes. The concentration of the removed cell protein extract was confirmed with the Pierce BCA Protein Assay Kit.

동량의 단백질을 SDS-PAGE에 로딩하고 니트로셀룰로스 막 (GE healthcare)으로 옮겼다. 5% 탈지유로 막을 블로킹하고 각각의 1차 항체를 4℃에서 하룻밤동안 인큐베이션하였다.Equal amounts of protein were loaded onto SDS-PAGE and transferred to a nitrocellulose membrane (GE healthcare). The membranes were blocked with 5% skim milk and each primary antibody was incubated overnight at 4°C.

TBST 버퍼로 30분간 막을 세척하고 1:10000으로 희석된 HRP가 결합된 이차 항체와 실온에서 1시간 동안 인큐베이션하였다. chemiluminescent HRP substrate solutions (Advansta)으로 단백질 발현을 확인하였다. The membrane was washed with TBST buffer for 30 minutes and incubated with HRP-conjugated secondary antibody diluted at 1:10000 for 1 hour at room temperature. Protein expression was confirmed with chemiluminescent HRP substrate solutions (Advansta).

면역침강분석을 위해, 세포 단백질 추출물을 특이적인 항체와 4℃에서 하룻밤동안 회전 인큐베이션하였다. 이후 단백질-항체 시료를 단백질 A/G 아가로스 비드와 4℃에서 1시간동안 혼합하여 침강시켰다. For immunoprecipitation assays, cellular protein extracts were spin-incubated with specific antibodies overnight at 4°C. Thereafter, the protein-antibody sample was mixed with protein A/G agarose beads at 4° C. for 1 hour for sedimentation.

4. 면역형광 분석4. Immunofluorescence Assay

U2OS 세포를 챔버 슬라이드에 분주하였다. 분주 1일 후 세포를 두번 세척하고 어름 위에서 0.5% 트리톤 X-100로 5분간 추출한 후 실온에서 15분간 3% 파라포름알데하이드로 고정하였다. U2OS cells were seeded on chamber slides. After 1 day of dispensing, the cells were washed twice, extracted with 0.5% Triton X-100 on ice for 5 minutes, and fixed with 3% paraformaldehyde for 15 minutes at room temperature.

PBS로 두번 세척한 후 0.5% 트리톤 X-100를 첨가하여 세포를 투과시켰다.After washing twice with PBS, 0.5% Triton X-100 was added to permeabilize the cells.

특히 크로마틴 결합 단백질의 경우, 0.5 % 트리톤 X-100으로 2분간 추출하고 100% 메탄올로 -20℃에서 30분간 고정하는 단계로 변경되었다.In particular, in the case of chromatin-binding protein, extraction was performed with 0.5% Triton X-100 for 2 minutes and fixed with 100% methanol at -20°C for 30 minutes.

이후, 세포에 블로킹 버퍼를 1시간 동안 처리하고 1:1000으로 희석된 1차 항체와 4℃에서 하룻밤동안 인큐베이션하였다. Thereafter, the cells were treated with blocking buffer for 1 hour and incubated overnight at 4° C. with the primary antibody diluted 1:1000.

항체 세척 후, Alexa Fluor 결합된 2차 항체를 처리하고 1시간 동안 인큐베이션하고, PBS로 세척된 세포의 형광 현미경 이미지를 얻었다.After antibody washing, Alexa Fluor-conjugated secondary antibody was treated and incubated for 1 hour, and a fluorescence microscope image of cells washed with PBS was obtained.

5. 근접 접합 분석 (Proximity Ligation Assay)5. Proximity Ligation Assay

Duolink® PLA fluorescence kit (Sigma Aldrich)를 이용하여 표준 프로토콜에 따라 근접 접합 분석을 수행하였다. Proximity junction analysis was performed according to standard protocols using a Duolink® PLA fluorescence kit (Sigma Aldrich).

간략하게, 슬라이드에 분주된 U2OS 세포의 추출, 고정 및 투과 단계 후 세포를 PBS가 첨가된 2% BSA로 실온에서 1시간 동안 블로킹하였다.Briefly, after extraction, fixation, and permeabilization of U2OS cells seeded on slides, cells were blocked with PBS-added 2% BSA at room temperature for 1 hour.

희석된 1차 항체를 세포에 첨가하여 4℃에서 하룻밤동안 인큐베이션하였다. Diluted primary antibody was added to the cells and incubated overnight at 4°C.

PBS로 3회 항체를 세척하고 premixed PLUS 및 MINUS PLA 프로브와 37℃에서 1시간 동안 인큐베이션하였다. 이후 시료를 37℃ 항온 항습기에서 형광 결합 용액 (ligation solution) 및 증폭 용액 (amplification solution)과 각각 30분 및 100분간 인큐베이션하였다. Antibodies were washed three times with PBS and incubated with premixed PLUS and MINUS PLA probes at 37° C. for 1 hour. Thereafter, the samples were incubated with a fluorescence ligation solution and an amplification solution for 30 minutes and 100 minutes, respectively, in a constant temperature and humidity chamber at 37°C.

키트에 제공되는 세척 버퍼로 최종 세척 후 DAPI와 슬라이드에 올려놓고 63× 오일 액침 대물렌즈를 이용한 공초점 현미경 분석을 수행하여 얻어진 이미지에서 핵 PLA foci 수를 정량하였다.After final washing with the washing buffer provided in the kit, the number of nuclear PLA foci was quantified in the images obtained by placing on slides with DAPI and performing confocal microscopy analysis using a 63× oil immersion objective.

6. DRIP (S9.6 DNA:RNA immunoprecipitation) 분석6. DRIP (S9.6 DNA:RNA immunoprecipitation) analysis

세포를 얼음 위에서 85mM KCl, 5mM PIPES(pH8.0) 및 0.5% NP-40이 포함된 용해 버퍼에서 10분간 인큐베이션하였다. 용해된 세포를 수집하고 4℃, 3000g으로 5분간 원심분리하였다.Cells were incubated for 10 min in lysis buffer containing 85 mM KCl, 5 mM PIPES (pH 8.0) and 0.5% NP-40 on ice. Lysed cells were collected and centrifuged at 4° C., 3000 g for 5 minutes.

핵 펠렛을 사용 직전에 0.2% 데옥시콜레이트염, 0.1% SDS 및 0.5% 트리톤 X-100 및 단백질분해효소 억제제 칵테일을 첨가한 RSB 버퍼 (10mM Tris-HCl (pH7.5), 200mM NaCl, 2.5mM MgCl2)에 재현탁시켰다.Prior to use, nuclear pellets were prepared in RSB buffer (10 mM Tris-HCl (pH7.5), 200 mM NaCl, 2.5 mM) with 0.2% deoxycholate salt, 0.1% SDS and 0.5% Triton X-100 and protease inhibitor cocktail added MgCl 2 ) was resuspended.

Diagenode bioruptor를 이용하여 10분간 핵을 초음파 처리한 후 추출물을 0.5% Triton X-100이 포함된 RSB 버퍼에 희석하고 S9.6 항체로 면역침강하였다.After sonicating the nucleus for 10 minutes using a diagenode bioruptor, the extract was diluted in RSB buffer containing 0.5% Triton X-100 and immunoprecipitated with S9.6 antibody.

7. EdU 혼성화된 DNA 복제 분석7. EdU Hybridized DNA Replication Analysis

Click-iT™ EdU Cell Proliferation Kit (Invitrogen) 및 Alexa Fluor™ 488 dye를 이용한 EdU (5-ethynyl-2’-deoxyurinidine) 혼성을 통하여 DNA 복제를 확인하였다.DNA replication was confirmed through EdU (5-ethynyl-2’-deoxyurinidine) hybridization using Click-iT™ EdU Cell Proliferation Kit (Invitrogen) and Alexa Fluor™ 488 dye.

THRAP3 넉다운, RNaseH1 과발현된 U2OS 세포를 15분간 EdU working 용액으로 라벨링하였다. 인큐베이션 후 배지를 즉시 제거하고, 실온에선 15분간 4% 포름알데하이드가 포함된 PBS로 세포를 고정한 후 0.5% Triton X-100가 포함된 PBS로 20분 동안 투과시켰다.THRAP3 knockdown, RNaseH1 overexpressed U2OS cells were labeled with EdU working solution for 15 minutes. After incubation, the medium was removed immediately, and cells were fixed with PBS containing 4% formaldehyde for 15 minutes at room temperature, and then permeabilized with PBS containing 0.5% Triton X-100 for 20 minutes.

세포에서 투과 버퍼를 제거하고 세포를 두번 세척하였다. CuSO4와 Alexa Fluror azide가 포함된 Click-iT™ 반응 칵테일이 포함된 반응 버퍼를 세포에 첨가하고 실온에서 30분간 빛을 차단하여 인큐베이션하였다.The permeation buffer was removed from the cells and the cells were washed twice. A reaction buffer containing a Click-iT™ reaction cocktail containing CuSO 4 and Alexa Fluror azide was added to the cells and incubated at room temperature for 30 minutes while blocking light.

핵 시각화를 위해, 15분간 DAPI 염색 하였다. 형광 현미경으로 EdU 혼성을 확인하고 EdU 양성 세포 및 형광 강도를 분석하였다.For nuclear visualization, DAPI staining was performed for 15 min. EdU hybridization was confirmed by fluorescence microscopy, and EdU-positive cells and fluorescence intensity were analyzed.

8. 정제 및 질량 분석8. Purification and Mass Spectrometry

HEK293 세포를 FLAG/Myc 태그된 THRAP3을 이소성 형질주입시키고 용해물을 준비하여 고정된 항-FLAG M2 아가로스 (Sigma Aldrich)와 혼합하였다.HEK293 cells were ectopic transfected with FLAG/Myc tagged THRAP3 and lysates were prepared and mixed with immobilized anti-FLAG M2 agarose (Sigma Aldrich).

인큐베이션 후, FLAG 태그된 THRAP3 및 상호작용 단백질을 결합 버퍼로 세척하고 3× FLAG 펩타이드 (Sigma Aldrich)로 용리하였다.After incubation, FLAG tagged THRAP3 and interacting proteins were washed with binding buffer and eluted with 3× FLAG peptide (Sigma Aldrich).

용리된 단백질을 SDS-PAGE에 분리시키고, 분자 특징을 고분해능 혼성 질량 분광계 (LTQ-Orbitrap, Thermo Fisher Scientific)를 이용한 reverse-phase LC-MS/MS을 수행하여 분석하였다.The eluted proteins were separated by SDS-PAGE, and molecular characteristics were analyzed by reverse-phase LC-MS/MS using a high-resolution hybrid mass spectrometer (LTQ-Orbitrap, Thermo Fisher Scientific).

<실시예 1> THRAP3과 DNA:RNA hybrid (R-loop)의 연관성 확인<Example 1> Confirmation of association between THRAP3 and DNA:RNA hybrid (R-loop)

THRAP3은 RNA 결합 단백질이며, RNA 대사작용 관여를 통한 DNA 손상 반응과 관련있기 때문에 THRAP3이 R-loop 구조의 RNA와 연관성이 있다고 가정하였다.Since THRAP3 is an RNA-binding protein and is involved in DNA damage response through RNA metabolism, it was hypothesized that THRAP3 is related to R-loop-structured RNA.

이를 확인하기 위해, R-loop와 THRAP3 항체를 탐지할 수 있는 S9.6 항체를 이용하여 근접 접합 분석 (Proximity Ligation Assay; PLA)을 수행하였다. To confirm this, Proximity Ligation Assay (PLA) was performed using the S9.6 antibody capable of detecting R-loop and THRAP3 antibody.

그 결과, 도 1A와 같이 핵 영역에서 공동 국소화를 확인하였으며, siRNA를 이용한 THRAP3 결핍에 따른 결찰 신호 감소가 확인되었다.As a result, co-localization was confirmed in the nuclear region as shown in FIG. 1A, and a decrease in the ligation signal according to THRAP3 deficiency using siRNA was confirmed.

또한, U2OS 세포에서 S9.6 및 THRAP3 항체를 이용한 DNA-RNA 면역침강 분석을 수행한 결과, 도 1B와 같이 R-loops 및 THRAP3 간의 연관성을 확인할 수 있었다.In addition, as a result of performing DNA-RNA immunoprecipitation analysis using S9.6 and THRAP3 antibodies in U2OS cells, the association between R-loops and THRAP3 was confirmed as shown in FIG. 1B.

다음으로, THRAP3가 R-loop 수준을 조절할 수 있는 지 여부를 확인하였다.Next, it was checked whether THRAP3 could regulate the R-loop level.

그 결과, 도 1C와 같은 면역형광 이미지에서 siRNA에 의해 THRAP3 발현이 억제된 경우, R-loops 량이 현저하게 증가되는 것을 확인할 수 있었다.As a result, when THRAP3 expression was suppressed by siRNA in the immunofluorescence image as shown in FIG. 1C, it was confirmed that the amount of R-loops was significantly increased.

상기 결과로부터 THRAP3이 R-loop와 상호작용하고 R-loop를 조절하는 것이 확인되었다.From the above results, it was confirmed that THRAP3 interacts with R-loop and regulates R-loop.

<실시예 2> THRAP3 결핍에 의한 복제 억제 및 DSB (double-strand break) 유도 확인<Example 2> Confirmation of replication inhibition and DSB (double-strand break) induction by THRAP3 deficiency

앞선 실험에서 THRAP3 감소에 의해 R-loop가 축적되는 것을 확인하였으며, TRC (Transcription replication collision) 영역의 복제분기점에서 증식세포 핵항원 (PCNA)이 증가하고 TRC로 유도된 R-loop가 PCNA의 축적을 유도하는 것으로 보고되어 짐에 따라, THRAP3이 결핍되었을 때, R-loop 가닥 내 PCNA 수준을 확인하였다. 도 2A의 PLA 결과를 참고하면, R-loop에서 PCNA가 현저하게 증가한 것을 확인할 수 있었다. In the previous experiment, it was confirmed that the R-loop was accumulated due to the decrease in THRAP3, and the proliferation cell nuclear antigen (PCNA) increased at the replication fork in the transcription replication collision (TRC) region, and the TRC-induced R-loop decreased the accumulation of PCNA. As reported to induce induction, the level of PCNA in the R-loop strand was confirmed when THRAP3 was deficient. Referring to the PLA results of FIG. 2A, it was confirmed that PCNA was significantly increased in R-loop.

또한, 분리되지 않은 R-loop가 DNA 가닥 절단을 촉진시켜 DNA 손상을 유도하는 것으로 보고됨에 따라, DNA 복제 평가를 위해 대조군 및 THRAP3 넉다운 조건에서 U2OS 세포에 대한 EdU 혼성화를 확인하였다.In addition, as it is reported that unseparated R-loop promotes DNA strand breakage and induces DNA damage, EdU hybridization to U2OS cells was confirmed under control and THRAP3 knockdown conditions for DNA replication evaluation.

그 결과, 도 2B 및 도 2C와 같이 THRAP3의 감소 수준은 DNA 복제를 억제하였으나, R-loop 분해를 유도하는 리보뉴클레아제인 RNaseH1의 과발현은 복제능을 회복시켰다.As a result, as shown in FIGS. 2B and 2C , the decreased level of THRAP3 inhibited DNA replication, but overexpression of RNaseH1, a ribonuclease that induces R-loop degradation, restored the replication ability.

한편, 도 2D 및 도 2E와 같이 THRAP3 넉다운은 DSB (double-strand break)의 대표적 마커인 핵 당 γH2AX 및 53BP1 foci를 증가시켰다. 또한, RNaseH1 과발현은 THRAP3 결핍에 의해 유도된 DNA 이중가닥 절단을 감소시켰다.Meanwhile, as shown in FIGS. 2D and 2E , THRAP3 knockdown increased γH2AX and 53BP1 foci per nucleus, which are representative markers of double-strand break (DSB). In addition, RNaseH1 overexpression reduced DNA double-strand breaks induced by THRAP3 deficiency.

또한, 도 2F와 같이 THRAP3 siRNA가 형질주입된 세포에서 감소된 DNA 복제 및 심각한 DNA 손상은 세포 증식을 지연시키는 것을 확인할 수 있었다.In addition, as shown in FIG. 2F , it was confirmed that reduced DNA replication and severe DNA damage in cells transfected with THRAP3 siRNA delayed cell proliferation.

<실시예 3> THRAP3와 DDX5 및 XRN2의 결합 확인<Example 3> Confirmation of binding of THRAP3 with DDX5 and XRN2

THRAP3이 R-loop 수준과 게놈 안정성을 조절하는 메커니즘을 이해하기 위해, THRAP3과 상호작용하는 단백질 확인을 위한 질량분석을 수행하였다.To understand the mechanism by which THRAP3 regulates R-loop levels and genomic stability, mass spectrometry was performed to identify proteins that interact with THRAP3.

도 3A와 같이 THRAP3 발현과 함께 2배 이상의 유의한 발현 변화를 나타내는 단백질을 분리한 후 7개의 RNA 헬리카제 및 5개의 DNA 손상 관련 단백질로 분류하였으며, 이중 주요 THRAP3 상호작용 단백질로 DDX5를 확인하였다. 또한, 실제로 U2OS 세포에서 THRAP3 및 DDX5 간의 내인성 상호작용을 확인하였다.As shown in FIG. 3A, after separating the protein showing a two-fold or more significant expression change along with THRAP3 expression, it was classified into 7 RNA helicases and 5 DNA damage-related proteins, and DDX5 was identified as a major THRAP3 interacting protein. In addition, we confirmed the endogenous interaction between THRAP3 and DDX5 in U2OS cells.

그 결과, 도 3B와 같이 THRAP3 항체 및 대조군 IgG 항체와 인큐베이션된 용해 세포에서 DDX5는 THRAP3과 함께 공동 면역침강되었다. 또한, 엑소뉴클레아제 기능에 의한 R-loop 분해에 관여하는 XRN2도 THRAP3과 내인성 결합하는 것을 확인하였다.As a result, DDX5 co-immunoprecipitated with THRAP3 in lysed cells incubated with THRAP3 antibody and control IgG antibody as shown in FIG. 3B. In addition, it was confirmed that XRN2, which is involved in R-loop degradation by exonuclease function, also endogenously binds with THRAP3.

한편, 도 3C와 같이 RNaseH1을 과발현시킨 경우, DDX5 및 XRN2 와의 단백질 결합이 약화되는 것을 확인할 수 있었으며, 도 3D와 같이 THRAP3에 의한 XRN2 모집 또한 현저하게 감소되는 것을 확인할 수 있었다.On the other hand, when RNaseH1 was overexpressed as shown in FIG. 3C, it was confirmed that the protein binding to DDX5 and XRN2 was weakened, and XRN2 recruitment by THRAP3 was also significantly reduced as shown in FIG. 3D.

반면, R-loop 형성을 증가시킬 수 있은 국소이성질화효소 (topoisomerase)로 알려진 camptothecin (CPT)으로 세포를 자극할 경우, THRAP3은 CPT 처리 후 시간 의존적으로 DDX5 및 XRN2와 동적으로 결합하는 것을 확인할 수 있었다. 도 3E를 참고하면 DDX5는 CPT 처리 후 30분만에 THRAP3과 매우 강하게 결합하였으며 XRN2는 처리 후 약 3시간 후에 뒤 따르는 것이 확인되었다.On the other hand, when cells were stimulated with camptothecin (CPT), known as a topoisomerase, which could increase R-loop formation, it was confirmed that THRAP3 dynamically binds to DDX5 and XRN2 in a time-dependent manner after CPT treatment. there was. Referring to FIG. 3E , it was confirmed that DDX5 was strongly bound to THRAP3 30 minutes after CPT treatment, and XRN2 followed approximately 3 hours after treatment.

다음으로, THRAP3가 DDX5 및 XRN2 간의 연관성에 영향을 미치는 지를 확인하 하였다. THRAP3 siRNA 및 대조군 스크럼블 siRNA 형질주입된 U2OS 세포를 용해시키고 DDX5로 면역침강시켰다. Next, it was checked whether THRAP3 affects the association between DDX5 and XRN2. THRAP3 siRNA and control scrambled siRNA transfected U2OS cells were lysed and immunoprecipitated with DDX5.

그 결과, 도 3F와 같이 DDX5와 상호작용하는 XRN2가 THRAP3 결핍 조건에서 감소된 것을 확인할 수 있었다.As a result, as shown in FIG. 3F, it was confirmed that XRN2 interacting with DDX5 was reduced in the THRAP3-deficient condition.

DDX5는 PRMT5에 의해 메틸화된 아르기닌-구아닌 모티프에서 뉴클레아제를 동원하여 R-loop를 해결하고 R-loop의 축적을 저해한다.DDX5 recruits nucleases from arginine-guanine motifs methylated by PRMT5 to resolve R-loops and inhibit R-loop accumulation.

이에 따라, DDX5 메틸화 변화에 의해 THRAP3과 DDX5의 결합이 변화되는 지를 확인하기 위해, PRMT5에 의해 유도되는 메틸화를 억제하기 위해 U2OS 세포에 EPZ015666 (PRMT5 inhibitor, Sigma Aldrich, Cat# 1421) 20μM을 72시간 동안 처리하였다.Accordingly, in order to check whether the binding of THRAP3 and DDX5 is changed by the change in DDX5 methylation, 20 μM of EPZ015666 (PRMT5 inhibitor, Sigma Aldrich, Cat# 1421) was administered to U2OS cells to suppress PRMT5 induced methylation for 72 hours. treated during

그 결과, 도 3G와 같이 DDX5 아르기닌 메틸화의 억제는 THRAP3과의 단백질 상호작용 역시 억제시키는 것을 확인하였다. As a result, it was confirmed that inhibition of DDX5 arginine methylation also inhibited protein interaction with THRAP3 as shown in FIG. 3G.

EPZ015666의 영향을 추가로 확인하기 위해, 야생형 Flag/Myc-DDX5와 PRMT5에 의해 메틸화되는 것으로 알려진 5개의 아르기닌 서열을 라이신 잔기로 변경한 RK 돌연변이체를 발생시켰다.To further confirm the effect of EPZ015666, wild-type Flag/Myc-DDX5 and RK mutants were generated in which five arginine sequences known to be methylated by PRMT5 were replaced with lysine residues.

그 결과, 도 3G와 같이 CPT 조건에서 RK 돌연변이체 DDX5와 THRAP3간의 상호작용이 감소된 것을 확인할 수 있었다. As a result, it was confirmed that the interaction between the RK mutant DDX5 and THRAP3 was reduced in the CPT condition as shown in FIG. 3G.

상기 결과로부터 THRAP3은 R-loop 분해에 필요한 RNA 헬리카제 DDX5 및 엑소뉴클라아제 XRN2와 물리적으로 상호작용하는 것이 확인되었다.From the above results, it was confirmed that THRAP3 physically interacts with RNA helicase DDX5 and exonuclease XRN2 required for R-loop degradation.

<실시예 4> THRAP3의 N 말단에서 DDX5와의 상호작용 확인<Example 4> Confirmation of interaction with DDX5 at the N-terminus of THRAP3

다음으로 THRAP3의 어떤 도메인이 DDX5 상호작용에 필수적인지를 확인하기 위해, 도 4A와 같이 Flag/Myc tagged DDX5와 5 종류의 HA-tagged THRAP3 도메인 절단 돌연변이체를 세포에 공동 형질주입하고 Flag 항체로 면역침강을 수행하였다.Next, to confirm which domain of THRAP3 is essential for DDX5 interaction, as shown in FIG. 4A, Flag/Myc tagged DDX5 and 5 types of HA-tagged THRAP3 domain truncated mutants were co-transfected into cells and immunoprecipitated with Flag antibody. was performed.

그 결과, 도 4B와 같이 △N 및 △NC THRAP3은 DDX5와 상호작용하지 못하였다. As a result, as shown in FIG. 4B, ΔN and ΔNC THRAP3 did not interact with DDX5.

상기 결과로부터 N 말단 도메인이 THRAP3과 DDX5 단백질 결합에 기여하는 것이 확인되었다.From the above results, it was confirmed that the N-terminal domain contributes to the binding of THRAP3 and DDX5 proteins.

<실시예 5> R-loop 분해능에서 있어 XRN2 역할 확인<Example 5> Confirm the role of XRN2 in R-loop resolution

앞선 실험에서 THRAP3과 R-loop 분해 단백질 DDX5 및 XRN2의 상호작용을 확인하였으나, THRAP3에 의해 매개되는 R-loop 분해능에 대한 기본 메커니즘은 명확하게 확인되지 않았다. 이에 따라, 상기 THRAP3, DDX5 및 XRN 간의 각 상호작용 결과로부터 THRAP3이 R-loop 분해능 단백질의 모집을 조절할 수 있을 것이라 가설을 세우고, 이를 확인하기 위해 THRAP3 넉다운 조건에서 DRIP 분석을 수행하였다.In the previous experiment, the interaction between THRAP3 and the R-loop degradation proteins DDX5 and XRN2 was confirmed, but the basic mechanism for the R-loop degradation mediated by THRAP3 was not clearly identified. Accordingly, from the results of each interaction between THRAP3, DDX5 and XRN, it was hypothesized that THRAP3 could regulate the recruitment of R-loop resolution proteins, and to confirm this, DRIP analysis was performed under THRAP3 knockdown conditions.

그 결과, 도 5B와 같이 R-loop에서 THRAP3 결핍은 XRN2 결합을 감소시켰으나 DDX5 변화는 나타나지 않았다. 또한, 도 5C와 같이 THRAP3 넉아웃 세포에서 S9.6 및 XRN2 사이의 유의하게 낮은 PLA 신호가 확인되었다.As a result, as shown in FIG. 5B, THRAP3 deficiency in R-loop reduced XRN2 binding, but no change in DDX5. In addition, as shown in FIG. 5C , a significantly low PLA signal between S9.6 and XRN2 was confirmed in THRAP3 knockout cells.

상기 결과들로부터 THRAP3에 의해 유도되는 R-loop 축적은 부분적으로 XRN2 모집 감소에 의해 발생되는 것이 확인됨에 따라, R-loop 분해능에 있어 XRN2은 THRAP3의 하위 타겟임이 확인되었다.From the above results, it was confirmed that R-loop accumulation induced by THRAP3 was partially caused by a decrease in XRN2 recruitment. Therefore, it was confirmed that XRN2 is a sub-target of THRAP3 in R-loop resolution.

<실시예 6> 유방암 세포에서 THRAP3의 영향 확인<Example 6> Confirmation of the effect of THRAP3 in breast cancer cells

병리학적 조건에서 R-loop 분해능에 대한 THRAP3의 역할을 확인하였다.The role of THRAP3 on R-loop resolution in pathological conditions was confirmed.

도 6A를 참고하면 앞서 확인된 U2OS 세포에서와 같이 THRAP3 결핍은 MCF7 유방 선암 세포에서 EdU 혼성화 세포를 감소시켰으며, 이는 DNA 복제 감소를 의미한다.Referring to FIG. 6A , as in the previously identified U2OS cells, THRAP3 deficiency reduced EdU hybridization cells in MCF7 breast adenocarcinoma cells, which means reduced DNA replication.

또한, 도 6C 및 도 6D와 같이 MCF7 세포에서 THRAP3 넉다운은 핵 내 R-loop 축적을 유도하였으며, 도 6E 및 도 6F와 같이 THRAP3으로 매개된 R-loop 축적은 핵 내 γH2AX 및 53BP1 국소화를 유도하고, RNaseH1 과발현을 통한 R-loops 분해는 THRAP3 넉다운에 의한 DNA 이중 가닥 절단을 완화시켰다.In addition, as shown in FIGS. 6C and 6D , THRAP3 knockdown in MCF7 cells induced nuclear R-loop accumulation, and THRAP3-mediated R-loop accumulation induced nuclear γH2AX and 53BP1 localization as shown in FIGS. 6E and 6F , and , R-loops degradation via RNaseH1 overexpression mitigated DNA double-strand breaks caused by THRAP3 knockdown.

또한, 도 6G 및 도 6H와 같이 THRAP3이 넉다운된 MCF7 유방암 세포주의 세포 증식이 억제되는 것을 확인할 수 있었다.In addition, it was confirmed that the cell proliferation of the MCF7 breast cancer cell line in which THRAP3 is knocked down is inhibited as shown in FIGS. 6G and 6H.

이상으로 본 발명 내용의 특정한 부분을 상세히 기술하였는 바, 당업계의 통상의 지식을 가진 자에게 있어서, 이러한 구체적 기술은 단지 바람직한 실시양태일 뿐이며, 이에 의해 본 발명의 범위가 제한되는 것이 아닌 점은 명백할 것이다. 따라서 본 발명의 실질적인 범위는 첨부된 청구항들과 그것들의 등가물에 의하여 정의된다고 할 것이다.As described above in detail a specific part of the content of the present invention, for those of ordinary skill in the art, it is clear that this specific description is only a preferred embodiment, and the scope of the present invention is not limited thereby. something to do. Accordingly, the substantial scope of the present invention will be defined by the appended claims and their equivalents.

Claims (7)

암세포에 시험물질을 접촉시키는 단계;
상기 시험물질을 접촉한 암세포에서 THRAP3 및 DDX5의 결합 수준을 확인하는 단계; 및
대조구 시료와 비교하여 상기 THRAP3 및 DDX5의 결합 수준이 감소된 시험물질을 선별하는 단계를 포함하는 암 치료제 스크리닝 방법.
contacting the test substance to the cancer cells;
checking the binding level of THRAP3 and DDX5 in cancer cells contacted with the test substance; and
A cancer treatment screening method comprising the step of selecting a test substance having a reduced binding level of THRAP3 and DDX5 compared to a control sample.
청구항 1에 있어서, 상기 암 치료제 스크리닝 방법은 시험물질을 접촉한 암세포에서 THRAP3 및 XRN2 결합 수준 감소를 추가로 더 확인하는 단계를 포함하는 것을 특징으로 하는 암 치료제 스크리닝 방법.The method according to claim 1, wherein the screening method for a cancer treatment agent further comprises the step of further confirming a decrease in the binding level of THRAP3 and XRN2 in cancer cells contacted with the test substance. 청구항 1에 있어서, 상기 THRAP3은 R-loop (DNA:RNA hybrid) 내에서 DDX5와 결합하여 핵산외부가수분해효소 (exonuclease)를 동원시켜 R-loop를 분해시키는 것을 특징으로 하는 암 치료제 스크리닝 방법.The method according to claim 1, wherein the THRAP3 binds to DDX5 in an R-loop (DNA: RNA hybrid) and mobilizes an exonuclease to degrade the R-loop. 청구항 1에 있어서, 상기 DDX5는 PRMT5에 의해 아르기닌이 메틸화되고, 메틸화된 DDX5가 THRAP3의 N 말단에 결합하는 것을 특징으로 하는 암 치료제 스크리닝 방법.The method according to claim 1, wherein in DDX5, arginine is methylated by PRMT5, and the methylated DDX5 binds to the N-terminus of THRAP3. 청구항 1에 있어서, 상기 THRAP3 및 DDX5의 결합 수준 감소는 암세포 내 R-loop (DNA:RNA hybrid) 분해를 억제시킴으로써, DNA 손상을 유도하여 암세포를 사멸시키는 것을 특징으로 하는 암 치료제 스크리닝 방법.The method according to claim 1, wherein the reduction of the binding level of THRAP3 and DDX5 inhibits R-loop (DNA:RNA hybrid) degradation in cancer cells, thereby inducing DNA damage and killing cancer cells. 청구항 1에 있어서, 상기 암은 골육종, 유방암, 대장암, 폐암, 간암, 신장암, 위암, 뇌암, 전립선암 및 췌장암으로 이루어진 군에서 선택되는 것을 특징으로 하는 암 치료제 스크리닝 방법.The method according to claim 1, wherein the cancer is selected from the group consisting of osteosarcoma, breast cancer, colorectal cancer, lung cancer, liver cancer, kidney cancer, stomach cancer, brain cancer, prostate cancer and pancreatic cancer. 시험관 내에서(in vitro) 암세포의 THRAP3 및 DDX5 결합 수준을 감소시키는 단계를 포함하는 암세포의 DNA 손상을 유도하는 방법.A method of inducing DNA damage in cancer cells, comprising reducing the level of binding of THRAP3 and DDX5 in the cancer cells in vitro.
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Citations (2)

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US20100130527A1 (en) * 2008-11-18 2010-05-27 Lehrer Raphael Individualized cancer treatment
KR20170088462A (en) 2016-01-22 2017-08-02 중앙대학교 산학협력단 Method for screening therapeutic agents of hematological malignancies by interaction RE-IIBP with RNF20

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100130527A1 (en) * 2008-11-18 2010-05-27 Lehrer Raphael Individualized cancer treatment
KR20170088462A (en) 2016-01-22 2017-08-02 중앙대학교 산학협력단 Method for screening therapeutic agents of hematological malignancies by interaction RE-IIBP with RNF20

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