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20240722_184639

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  • ◆ RegulomeDB에는 약 30,000개 정도의 SNP들이 eQTL에 속하고, (조절딩하는) 후보유전자를 확인 할 수 있다
  • ■ These QTLs are often found on different chromosomes.
  • ■ plant height is controlled by many genes of small effect, or by a few genes of large effect.
  • ■ many QTLs are associated with a single trait.
  • ■ An eQTL is a possibly very large region of DNA with a SNP) that explains some difference in phenotype that you’re observing.
  • ■ 연구 Flow
⇨좁혀 김
넓은데부터The region for an eQTL can first be measured in centimorgans (roughly 1 million base pairs).Eventually, it might be narrowed down to a single SNP causing the phenotypic difference
어떤 유전자위치가 그 차이를 만들어내는지 확인한 뒤에,그 유전자위치에 들어있는 여러 유전자의 돌연변이를 확인
  • eQTL (Expression quantitative trait loci)
    • definition
      • ◆ genomic loci that explain variation in expression levels of mRNAs (and finally protein level).
    • 배경
      • ◆ eQTL의 개념은 그동안 유전자의 coding region에 집중되어 있던 변이 탐구의 영역을 non-coding region으로 확장시키고
      • ◆ 많은 GWAS 연구에서 발굴되었던 많은 non-coding region에 위치한 SNP들의 해석에 대한 한 가지 가능성을 제시해 줍니다: 즉, 그 동안의 많은 GWAS 연구들에서 발견된 많은 후보 유전자 영역들은 대부분 단백질을 코딩하는 영역이 아니라서 그 생물학적 역할에 대한 해석이 어려웠는데, 이 중 일부는 유전자 발현을 조절하는 eQTL일 가능성이 있다는 것
    • Mechanism that eQTL을 통한 유전자 발현 조절
Cis-effect C Local regulatory variation
Cis-regulatory
(allele-specific) 		인접 유전자의 promoter에 위치한 영역의 유전형의 차이가 직접적으로 유전자 발현량에 차이를 주는 경우를 말하며,
대부분은 cis의 형태로 작동해서 대립유전자 특이적 방법(allele-specific manner)으로 발현에 영향을 준다. 정의한 바와 같이
그러한 eQTL의 부위들은 같은 염색체에 위치한 그 유전자의 그 copy의 발현에만 영향을 미치고, 상동염색체의 (homologous chromosome) copy의 발현에는 영향을 미치지 않는다
Trans-effectNeighbouring gene (trans)1차적으로 조절 유전자 (regulatory)의 어떤 변이 또는 산물의 양이 2차적으로 최종 타겟 유전자의 발현량에 영향을 주는 경우
Distant eQTL 대다수는 local eQTL 인 경향을 보인다. Distant eQTL 이란 영향을 미치는 유전자와 물리적 거리가 먼 곳에 위치하거나 다른 염색체상에 존재하는 eQTL을 뜻하며, 원거리의 기준은 종별로 차이를 보인다. 모델 종에서는 종종 발견 되지만 사람 집단에서는 발견하기가 매우 어렵다.
인간 유전자 발현의 유전률의 대부분(60-75%)가 이러한 원거리 기여(distant contribution)로 설명되고 있다. 그러므로 원거리 eQTLs은 개체모델처럼 인간에게도 분명히 존재한다. 실제로 인간연구의 샘플크기가 커지면, 더 많은 원거리 eQTLs들이 발견될 것이다
  • 대부분의 확인된 eQTLs은 단백질 수준에서도 동일한 영향을 가지고 있었다. 인간세포주를 이용한 연구에서는 eQTLs과 pQTLs (protein quantitative trait loci) 가 상당히 겹쳐있었지만, 또한 mRNA에 명백한 영향이 없는 많은 수의 단백질 특이적 pQTLs을 발견했다. 단백질 수준에서는 mRNA에 비해 eQTLs의 효과가 약해지는 것처럼 보인다.
  • ■ Database of eQTL
    • ◆ eQTLGen and PsychENCODE18,19
  • ■ Examples of Eqtl

Js: we need Disease-specific, brain-specific eQTL ((Sieberts, 2020 #1684): we observed differences in eQTL patterns between cerebral and cerebellar brain regions.

Table 1 | Examples of disease risk loci correlated with eQTL genes

Disease/trait studyImplicated eQTL genes
AsthmaORMDL3
Blood lipid levelsSORT1, PPP1R3B, TTC39B
Body mass indexNEGR1, ZC3H4, TMEM160, MTCH2, NDUFS3, GTF3A, ADCY3, APOB48R, SH2B1, TUFM, GPRC5B, IQCK, SLC39A8, SULT1A1, SULT1A2
Breast cancerRRP1B
Coeliac diseaseMMEL1, NSF, PARK7, PLEK, TAGAP, RRP1, UBE2L3, ZMIZ1
Crohn's diseasePTGER4, CARD9, ERAP2, TNFSF11
Fat distributionGRB14, TBX15, PIGC, ZNRF3, STAB1, AA553656
HeightMultiple genes implicated
Kidney-ageingMMP20
MigraineMTDH
Multiple diseasesCDKN2A, CDKN2B, CDKN2B-AS1
Osteoporosis-relatedWLS, MEF2C, FOXC2, IBSP, TBC1D8, OSBPL1A, RAP1A, TNFRSF11B
Parkinson's diseaseMAPT, LRRC37A, HLA-DRA, HLA-DQA2, HLA-DRB5
PsoriasisSDC4, SYS1, DBNDD2, PIGT, RPS26*
QRS duration and cardiac ventricular conductionTKT, CDKN1A, C6orf204
Type 2 diabetesFADS1, FADS2, KLF14, CCNE2, IRS1, JAZF1, CAMK1D

Key points about eQTLs critical for target discovery efforts

Genetic Driven Drug Discovery: Genetic Variants — Association → Disease Phenotype

Linking Genetics to Gene Expression: Genetic Variants — Association → Tissue Specific Gene Expression

☐ Expression quantitative trait loci (eQTLs) are genetic variants that affect gene expression

Classification of eQTLs

Allele Specific Expression (ASE)

  • Two alleles are expressed differentially due to the presence of variant on one allele

  • Critical in understanding the change in direction of gene expression and helps in defining mechanisms of action of the target and therapeutic direction

  • Help bridge the gap between genetic variants and the candidate genes

  • Provide mechanistic insight into the disease process drivers as well as MOA of the candidate gene

  • Helps in targeted development with the understanding of the therapeutic direction

1 October 23, 2019 CONFIDENTIAL Takeda Pharmaceutical Company Limited

trans-eQTL Investigation

Rationale : Translating genetic discoveries into targets

  • Experimental mapping of the chromatin interactions is a cornerstone for identifying cell specific eQTLs

Combined effort : Experimental + Sequencing + Computational Analysis

Current and Forward Looking Goals

Human Genetic follow up (Target Discovery)Capability Build up + Resource Establishment
  • 1p36 locus and variant rs4654903 are protective in UC/IBD
    • however no causal SNP or target gene has been identified
  • Identify the causal SNP/target gene and MOA of the SNP/target gene driving the protective signal in epithelial cell types
  • Establish the approach/platform for generating high-quality genome wide chromatin interaction maps for cell lines or tissue types of interest
  • Establish the genome wide chromatin map for epithelial cell types relevant to IBD for driving genetics based target discovery

1 October 23, 2019 CONFIDENTIAL

eQTL Investigation of Human Spinal Cord Tissue

RationaleLack of resources for spinal cords!
  • Spinal cord involvement is a well-known and prominent feature of amyotrophic lateral sclerosis (ALS) and other motor neuron degeneration disorders
  • Spinal cord eQTLs can help in target identification and validation efforts for indications with major motor neuron involvement like ALS
  • No spinal cord eQTL and/or ASE dataset exists
  • No spinal cord cell type or transcriptome atlas available (for either normal samples or samples from ALS patients)
Establishing ASE eQTL resource for spinal cordsSpinal Cord single cell transcriptome atlas for ALS
Goal : Generate comprehensive spinal cord eQTL and ASE data to advance target discovery efforts and define therapeutic direction Goal : Identify molecular and pathophysiological markers of ALS
Investigate the differences in cell types, gene expression and pathways between normal and ALS patients

2 October 23, 2019 CONFIDENTIAL Takeda Pharmaceutical Company Limited

pLoF (predicted loss-of-function)

  • Definition
    • 3% of protein-coding genetic variants are predicted to result in loss of protein function through the introduction of a stop codon, frameshift, or the disruption of an essential splice site
  • ADVANtage
    • allow for the direct identification of a gene rather than a locus containing many candidate genes¹.
    • pLOF variants provide directionality of effect, unlike non-coding regulatory variants which may increase or decrease expression of a given gene.

Genetic engineering

결과ApplicationExamples
Removing DNAKnockouteither delete part of the DNA sequence or insert irrelevant DNA sequenceFrameshift (insertion or deletion)- Non-functional protein 만들수도, 아예 안 만들수도Loss-of-function mutation experiment

Uncertain Spans

locationtranscriptionuncertainty
연구 Flow table header좁혀 김The header reads 좁혀 김 (narrowed) but the second character is partly faded; OCR variants include 줍혀 김.
RegulomeDB bullet(조절딩하는)The verb-form parenthetical reads (조절딩하는); the third syllable is OCR-ambiguous between 딩 and 링/되.
Mechanism table, Cis-effect cellC Local regulatory variationThe leading C is part of the original Word inline figure label C Local regulatory variation; whether C is a figure-letter prefix (e.g. panel C) or part of a longer caption is unclear from this photo alone.
Genetic engineering tablebottom rows beyond Removing DNA / Knockout / FrameshiftThe Word table continues below the page edge (Adding / Introducing DNA, cignenic, If genetic material from the same species is added, another species, of one or more copies of a gene headers visible in the page status bar); the remaining rows are not visible in this photo and continue in 20240722_184643.

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