Functional Genomics and Systems Genetics in Cancer

Project Leader
Gonghong Wei, Ph.D., Professor, Academy Research Fellow

Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu

Background and Significance

The transcription factors (TFs) in a given genome can be classified into distinct families by structurally conserved DNA-binding domains (DBDs), often with similar DNA recognition properties. However, the members of the family always display distinct functions and activities in various biological processes such as cancer and normal development. The likelihood and nature are different in the network hubs of gene transcriptional regulation, which is often composed of intertwined regulatory relationships between TF protein complexes, epigenome regulaotrs, and chromatinized gene regulatory elements, including promoters, insulators and enhancers (Wei et al. 2004; Wei et al. 2005). Therefore, it is of crucial importance to identify genome-wide chromatin locations of a given TF or chromatin regulator with biological significance. Furthermore, we hypothesize that some cancer risk-associated single nucleotide polymorphisms (SNPs) discovered by genome-wide association studies (GWASs) may alter chromatin binding of TFs or transcriptional regulatory complexes to the key enhancers, thereby initiating aberrant gene expression programs underlying cancer susceptibility. Thus, the perturbation of gene regulatory networks may eventually cause cancer initiation and progression.

To address the questions, we carried out genome-wide analysis of binding sites (cistrome) for several key TFs, including TMPRSS2-ERG, HOXB13, FOXA1 and androgen receptor (AR) (Figure 1), which are often overexpressed and constitutively activated in many clinical prostate cancer specimens. In combination with global ChIP-seq study of enhancer epigenetic marks, we have thus identified thousands of prostate cancer cell-type-specific enhancers. To define the role of key prostate cancer TFs, we are using integrative and complementary genome-wide approaches including ChIP-seq, RNA-seq, and 3C-derived methods together with novel and classic molecular and biochemical assays, and also up-to-date computational and statistical methods. Recently, we found that prostate cancer-associated key TFs, including HOXB13, FOXA1 and ERG extensively cooperate with AR signaling to regulate target genes, implicating in prostate cancer cell growth and tumor progression. In addition, we observed that our integrated genomic data are working well in functional interpretation and mechanistic understanding of GWAS-discovered prostate cancer risk SNPs, such as the prostate cancer risk-associated variant rs339331, through enhancing HOXB13 chromatin binding, driving up-regulation of a transcriptional regulatory gene RFX6, which confers a risk of prostate cancer (Huang et al., 2014).


Figure 1. Genome-wide mapping of TF binding sites and enhancers in prostate cancer cells. Human chromosomes are shown around the outer ring. Other tracks contain ChIP-seq data of the TFs and enhancer marks as indicated.

Recent Progress

To map prostate cancer gene regulatory networks driven by key TFs, we for the first time profiled the cistome of HOXB13, a known critical regulator for prostate development and tumor progression. We observed that prostate cancer GWAS SNPs are significantly enriched in the HOXB13 cistrome (Huang et al. 2014; Chen et al. 2015). Intriguingly, the common genetic variant rs339331 at the prostate cancer susceptibility 6q22 locus lies within a functional HOXB13 binding site, and is precisely located at a HOXB13 ChIP-seq peak summit. rs339331 was reproducibly found to be associated with prostate cancer risk in men of African American, European ancestry, Japanese and Chinese population. The data suggest that rs339331 is a potential genetic marker for the evaluation of prostate cancer risk across different ethnic groups. Here we provided several lines of evidence to show that HOXB13 and AR favor binding to the risk T allele at rs339331 in vivo, and RFX6 is a plausible causative gene in an eQTL with rs339331. Together with our recent finding that rs339331 is a motif disruptor for AR/HOXB13 heterodimer, we thus proposed an extended model in which enhanced chromatin binding of HOXB13 and AR signaling to the T risk allele at rs339331 results in increased RFX6 expression, conferring predisposition to prostate cancer. CRISPR/Cas9-mediated knockout of rs339331 region also proves the association of rs339331 genotype and RFX6 expression (unpublished). Moreover, we are working on the identification of genes and pathways regulated by RFX6 protein, and investigating the biological roles of RFX6 in other types of cancers.  

We have also been working towards systems annotation of all prostate cancer risk-associated loci using integrative data sets of functional genomics, bioinformatics, statistics and high-throughput eQTL analysis with prostate cancer tissue samples (Whitington et al. 2016). We thus presented the first, deep and high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates regulatory genomic data from over 300 prostate cancer ChIP-seq experiments with genotype and gene expression data from over 600 prostate cancer tissue samples. The analysis reveals new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary AR/FOXA1, AR/HOXB13 and FOXA1/HOXB13 complexes and competitive binding mechanisms. We finally made our integrated analysis to be accessed through an interactive visualization tool (http://tomwhi.github.io/prcagwas/). This knowledge resource reveals how genome sequence variation affects disease predisposition via gene regulatory mechanisms, and identifies relevant genes for downstream biomarker and drug development.

In addition, my lab keeps close collaborations with Manninen lab at University of Oulu, revealed a crosstalk between integrin (α6 and αV) signaling and oncogene K-Ras driving tumorigenesis and progression to metastasis (Zhang et al. 2017). We have also collaborated with the researchers from Guangxi Medical University and Turku University by performing case-only association analysis of aggressive prostate cancer in a cohort of 1303 cases, and identified a novel locus rs3217869/CCND2 implicating in prostate cancer aggressiveness and tumor progression (Chen et al. 2017). Meanwhile, together with a team from Peking Union Medical College, we performed a large-scale functional screening of cancer risk-associated regulatory variants using a genome-wide enhancer reporter assays followed by deep, integrated validation using approaches including CRISPR-Cas9-mediated genome editing (Liu et al. 2017). More recently, we have been working greatly with several international institutions, including Shanghai Changhai Hospital, BGI-Shenzhen and Mayo Clinic College of Medicine for whole-genome and transcriptome sequencing of tumor-benign paired tissues from 65 Chinese prostate cancer patients (Ren et al. 2017). This work represents the first study of Asian prostate cancer genome and comparisons of the genetic landscape with white men, indicating both similarities and differences. The data may explain why Asian men have relatively low risk of prostate cancer compared to that in white men, and promote prostate cancer precision medicine. We are going to set up further collaborative projects to explore the mechanisms and maximize clinical translation of a large set of genomic alterations that are likely to contribute to prostate cancer pathogenesis and disease progression.

Future Goals

The mechanisms by which the aberrant gene expression, epigenomic and genomic alterations contribute to cancer development are generally not understood. GWASs have identified thousands of SNPs associated with predisposition to various types of cancers, and whole genome sequencing has revealed a substantial amount of driver mutations and alterations. However, the causal actions and biological effects of these genetic variations and genomic alterations remain poorly understood; thereby the clinical translation is a daunting challenge. We will continue to address the biology and clinical implications of these cancer risk genetic variants and genomic drivers that confer cancer susceptibility, initiation and progression. The study is in general utilizing systems analysis of gene and cellular regulatory networks via classical molecular and biochemical methods, as well as state-of-the-art functional genomics and systems genetics approaches – the combined strength of genomics, genetics and bioinformatics.

Selected Publications

  1. Gao P, Xia JH, Sipeky C, Dong XM, Zhang Q, Yang Y, Zhang P, Cruz SP, Zhang K, Zhu J, Lee HM, Suleman S, Giannareas N, Liu S; PRACTICAL Consortium, Tammela TLJ, Auvinen A, Wang X, Huang Q, Wang L, Manninen A, Vaarala MH, Wang L, Schleutker J, Wei GH. Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus. Cell. 174:576-589, 2018

    Highlighted in: Bulger M. Changing the Guard at a Prostate Cancer SNP. Cell. 174:501-502, 2018

  2. Zhang P#, Xia J#, Zhu J, Gao P, Tian YJ, Du M, Guo CY, Suleman S, Zhang Q, Kohli M, Tillmans L, Thibodeau SN, French AJ, Cerhan JR, Wang LD*, Wei GH* & Wang L*. High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing. Nature Communications. 9, 2022, 2018
     
  3. Zhang B*, Chen MY, Sheng YJ, Zuo XB, Gao P, Zhou FS, Liang B, Zhu J, Zhang Q, Suleman S, Xu YH, Xu MG, Xu JK, Liu CC, Zhao Y, Huang ZL, Yang Z, Cheng HD, Li N, Hong YY, Li W, Zhang MJ, Yu KD, Li G, Sun MH, Chen ZD, Wei GH* & Shao ZM*. A large-scale, exome-wide association study of Han Chinese women identifies three novel loci predisposing to breast cancer. Cancer Research. 2018 Mar 23. pii: canres.1721.2017. doi: 10.1158/0008-5472.CAN-17-1721. [Epub ahead of print]
     
  4. Ren S*, Wei GH*, Liu D*, Wang L*, Hou Y*, Cheng Y, Zhu S, Zhang Q, Peng L, Zhou X, Zhang J, Su H, Li F, Zheng H, Zhao Z, Yin C, He Z, Gao X, Zhau HE, Chu CY, Wu JB, Collins C, Volik SV, Bell R, Huang J, Wu K, Xu D, Ye D, Yu Y, Zhu L, Qiao M, Lee HM, Yang Y, Wang F, Zhu Y, Shi X, Zhang W, Chen R, Wang Y, Xu W, Cheng Y, Xu C, Gao X, Zhou T, Yang B, Hou J, Liu L, Zhang Z, Zhu Y, Qin C, Shao P, Pang J, Chung LWK, Xu J, Xu X, Li Y, Zhang X, Wang J, Yang H, Wang J, Huang H & Sun Y. Whole-genome and transcriptome sequencing of prostate cancer identify new genetic alterations driving disease progression. European Urology. 73:322-339, 2018 (Cover story)

    Highlighted in:
    Lamb AD et al., Orient Expression: Solving the Mystery of Asian Prostate Cancer? European Urology. 2018. 73(3):340-342.
    Stephen Freedland. Prostate cancer: Race and prostate cancer personalized medicine: the future. Nature Reviews Urology. 16 Jan 2018.
     
  5. Chen Y*, Zhang Q*, Wang Q*, Li J*, Sipeky C, Xia J, Gao P, Hu Y, Zhang H, Yang X, Chen H, Jiang Y, Yang Y, Yao Z, Chen Y, Gao Y, Tan A, Liao M, Schleutker J, Xu J, Sun Y, Wei GH#, Mo Z#. Genetic association analysis of the RTK/ERK pathway with aggressive prostate cancer highlights the potential role of CCND2 in disease progression. Scientific Reports. 2017 7:4538.
     
  6. Gao P, Wei GH. Genomic Insight into the Role of lncRNAs in Cancer Susceptibility. Int J Mol Sci 2017 Jun 9;18(6). Invited Review.
     
  7. Suleman S & Wei GH. Combined immunotherapy for advanced prostate cancer: Empowering the T cell army. Asian Journal of Urology 2017, 4(4):199-200.
     
  8. Liu S, Liu Y, Zhang Q, Wu J, Liang J, Yu S, Wei GH, White KP, Wang X. Systematic Identification of Regulatory Variants Associated with Cancer Risk. Genome Biology. 2017 18(1):194.
     
  9. Zhang K, Myllymäki SM, Gao P, Devarajan R, Kytölä V, Nykter M, Wei GH, Manninen A. Oncogenic K-Ras regulates and depends on α6 and αV-class integrins to modulate tumorigenesis and epithelial mesenchymal transition. Oncogene 2017 36:5681-5694.
     
  10. Li J, Rodriguez JP, Niu F, Pu M, Wang J, Hung LW, Shao Q, Zhu Y, Ding W, Liu Y, Da Y, Yao Z, Yang J, Zhao Y, Wei GH, Cheng G, Liu ZJ, Ouyang S. Structural basis for DNA recognition by STAT6. Proc Natl Acad Sci U S A. 113(46):13015-13020, 2016.
     
  11. Zhang K, Lee HM, Wei GH, Manninen A. Meta-analysis of gene expression and integrin-associated signaling pathways in papillary renal cell carcinoma subtypes. Oncotarget. 7(51):84178-84189, 2016.
     
  12. Whitington T, Gao P, Song W, Ross-Adams H, Lamb AD, Yang Y, Svezia I, Klevebring D, Mills IG, Karlsson R, Halim S, Dunning MJ, Egevad L, Warren AY, Neal DE, Grönberg H, Lindberg J, Wei GH, Wiklund F. Gene regulatory mechanisms underpinning prostate cancer susceptibility. Nature Genetics. 48:387-397, 2016

    Highlighted in: Prostate Cancer Risk Loci Are Associated with Gene Regulatory Mechanisms. Cancer Discovery 6:OF13, 2016
     
  13. Du M, Tillmans L, Gao J, Gao P, Yuan T, Dittmar RL, Song W, Yang Y, Sahr N, Wang T, Wei GH, Thibodeau SN, Wang L. Chromatin interactions and candidate genes at ten prostate cancer risk loci. Scientific Reports. 6:23202, 2016
     
  14. Taipale M, Jakkula E, Kämäräinen OP, Gao P, Skarp S, Barral S, Kiviranta I, Kröger H, Ott J, Wei GH, Ala-Kokko L, Männikkö M. Targeted re-sequencing of linkage region on 2q21 identifies a novel functional variant for hip and knee osteoarthritis. Osteoarthritis Cartilage. pii: S1063-4584(15)01390-4, 2015
     
  15. Heinonen H, Lepikhova T, Sahu B, Pehkonen H, Pihlajamaa P, Louhimo R, Gao P, Wei GH, Hautaniemi S, Jänne OA, Monni O. Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer. Int J Cancer. 137:2374-2383, 2015
     
  16. Chen H, Yu H, Wang J, Zhang Z, Gao Z, Chen Z, Lu Y, Liu W, Jiang D, Zheng SL, Wei GH, Issacs WB, Feng J, Xu J. Systematic enrichment analysis of potentially functional regions for 103 prostate cancer risk-associated loci. Prostate. 75:1264-1276, 2015
     
  17. Munne PM, Gu Y, Tumiati M, Gao P, Koopal S, Uusivirta S, Sawicki J, Wei GH, Kuznetsov SG. TP53 supports basal-like differentiation of mammary epithelial cells by preventing translocation of deltaNp63 into nucleoli. Scientific Reports. 4:4663, 2014
     
  18. Huang Q, Whitington T, Gao P, Lindberg JF, Yang Y, Sun J, Väisänen MR, Szulkin R, Annala M, Yan J, Egevad LA, Zhang K, Lin R, Jolma A, Nykter M, Manninen A, Wiklund F, Vaarala MH, Visakorpi T, Xu J, Taipale J, Wei GH. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding. Nature Genetics. 46:126-135, 2014

    Highlighted in:
    ** HOXB13, RFX6 and prostate cancer risk. Nature Genetics. 46:94-95, 2014
    ** Prostate cancer: HOXB13 and a SNP collaborate to increase risk. Nature Reviews Urology. 11:64, 2014
    ** A Prostate Cancer–Associated SNP Increases HOXB13 Binding. Cancer Discovery  4:268, 2014
    ** Recommended by Faculty of 1000: ★★ Very Good, good for teaching, new finding. In F1000Prime, 27 Jan 2014; DOI: 10.3410/f.718228195.793490008
    ** New evidence highlights the mechanism by which a single nucleotide polymorphism enhances prostate cancer progression. Oncology Central  Jan 17 2014
    ** New insight into Prostate Cancer susceptibility. CancerIndex Feb 1 2014
    ** Uusi geneettinen säätelymekanismi eturauhassyöpäriskin taustalla. Duodecim Feb 4 2014

    In the news:
    ** Mechanism affecting risk of prostate cancer found. Science Daily  Jan 10 2014
    ** Eturauhasyövälle altistava geenimuutos tunnistettu. KALEVA Jan 10 2014
    ** Eturauhassyöpään johtava geenimuutos löytyi Oulussa. HELSINGIN SANOMAT Jan 10 2014
    ** Eturauhassyövän riskitekijä löytyi. HELSINGIN SANOMAT  Jan 11 2014
     
  19. Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, and Taipale J. DNA Binding specificities of human transcription factors. Cell. 152:327-339, 2013
     
  20. Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J. Genome-Wide Analysis of ETS Family DNA-Binding in vitro and in vivo. EMBO J. 29:2147-2160, 2010
     
  21. Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Research. 20:861-873, 2010
     
  22. Tuupanen S, Turunen M, Lehtonen R, Hallikas O, Vanharanta S, Kivioja T, Björklund M, Wei G, Yan J, Niittymäki I, Mecklin JP, Järvinen H, Ristimäki A, Di-Bernardo M, East P, Carvajal-Carmona L, Houlston RS, Tomlinson I, Palin K, Ukkonen E, Karhu A, Taipale J, Aaltonen LA. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nature Genetics. 41:885-890, 2009
     
  23. Wei GH, Zhao GW, Song W, Hao DL, Lv X, Liu DP, Liang CC. Mechanisms of human gamma-globin transcriptional induction by apicidin involves p38 signaling to chromatin. Biochemical and Biophysical Research Communications.363:889-894, 2007
     
  24. Wei GH, Liu DP, Liang CC. Chromatin domain boundaries: insulators and beyond. Cell Research. 15:292-300, 2005
     
  25. Wei GH, Liu DP, Liang CC. Charting gene regulatory networks: strategies, challenges and perspectives. Biochemical Journal. 381:1-12, 2004

Research Group Members

Project Leader:
Gonghong Wei, Ph.D., Professor (Academy of Finland and University of Oulu)

Senior and Post-doctoral Investigators:
Ping Gao, Ph.D. (University of Oulu and Foundation)
Xiaoming Dong, Ph.D. (University of Oulu and Foundation)

Ph.D. Students:
Nikolaos Giannareas (University of Oulu)
Jihan Xia (University of Oulu)
Qin Zhang, M.Sc. (Academy of Finland)

Project Researchers:
Yuehong Yang, M.Sc. (Academy of Finland)

Main source of salary in brackets.

Foreign Scientists, 7

National and International Activities

Visiting Researchers in 2017 (over two weeks)

Elham Aryapour, B.Sc. (1 June 2017 - 30 June 2017), a master student from Master's Programme in Protein Science and Biotechnology, University of Oulu, Oulu, Finland

Ganga Deshar, B.Sc. (28 August - 25 September 2017), a master student from Master's Programme in Protein Science and Biotechnology, University of Oulu, Oulu, Finland

Last updated: 15.10.2018