Andrew Hutchins

Research Scientist Department of Biology   Research Group

My research program sits at the interface of experimental and computational science.

We use computational models to understand experimental observations, with a particular focus on the use of next generation sequencing technologies and their utility to bring systematic understanding to aspects of cell biology, epigenetics and human disease.

Personal Profile

My research program sits at the interface of experimental and computational science.

We use computational models to understand experimental observations, with a particular focus on the use of next generation sequencing technologies and their utility to bring systematic understanding to aspects of cell biology, epigenetics and human disease.

Research

All cells containing the same DNA, yet cells rarely change to alternate cell types, and in the adult cells retain only a limited ability to differentiate. The only time cell types can readily change, is during two processes: embryonic development when totipotent cells can give rise to all of the cell types of the adult, or in the diseased state. Our research work involves attempting to understand the epigenetic controls behind this process, and so understand normal and diseased states. We focus on the role of transposable elements (TEs), which make up nearly 50% of the total DNA in humans, and their role in epigenetic control, at multiple levels. Our work has led to insight into the epigenetic control of TEs, analysis of cell type, and our ongoing work is exploring the contribution of TEs to cell type heterogeneity, and cell fate control.


Teaching

2016/2017 : General Biology (Undergraduate Curriculum)

2017 : Bioinformatics and Genomics (Postgraduate Curriculum)

2017 : Scientific Writing and Communication (Postgraduate Curriculum)


Publications Read More

1.He J, Fu X, Zhang M, He F, Li W, Abdul M, Zhou J, Sun L, Chang C, Li Y, Liu H, Wu K, Babarinde IA, Zhuang Q, Loh YH, Chen J, Esteban MA, Hutchins AP. (2019). Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nature Communications. 10(1);34.

2.Guo L, Lin L, Wang X, Gao M, Cao S, Mai Y, Wu F, Kuang J, Liu H, Yang J, Chu S, Song H, Li D, Liu Y, Wu K, Liu J, Wang J, Pang G, Hutchins AP, Liu J, Pei D, Chen J. (2019) Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq. Mol Cell, 73(4)815-829.

3.Li J, Huang K, Hu G, Babarinde IA, Li Y, Dong X, Chen Y, Shang L, Guo W, Wang J, Chen Z, Hutchins AP, Yang Y, Yao H. (2019) An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote cell apoptosis. Nature Communications. Accepted.

4.Zhuang Q*, Li W*, Benda C*, Huang Z, Ahmed T, Liu P, Guo X, Ibañez D, Luo Z, Zhang M, Abdul M, Yang Z, Yang J, Huang Y, Zhang H, Huang D, Zhou J, Zhong X, Zhu X, Fu X, Fan W, Liu Y, Xu Y, Ward C, Khan M, Kanwal S, Mirza B, Tortorella M, Tse HF, Chen J, Qin B, Bao X, Gao S, Hutchins AP#, Esteban MA#. (2018) NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming. Nature Cell Biology. 20(4):400-412. *Co-first, #Co-corresponding

5.Yao M. Zhou X. Zhou J. Gong S. Hu G. Li J. Huang K. Lai P. Shi G. Hutchins AP. Sun H. Wang H. Yao H. (2018) PCGF5 is required for neural differentiation of embryonic stem cells. Nature Communications. 9(1);1463

6.Bao X*, Guo X*, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan M, Zhu X, Luo Z, Shao C, Lim D, Liu X, Li N, Wang W, He M, Liu Y, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang Y, Wang Y, Qin B, Anko M, Hutchins AP, Sun H, Wang H, Fu X, Zhang B#. Esteban MA#. (2018) Capturing the Interactome of Newly Transcribed RNA. Nature Methods. 15(3)213-220. *Co-first, #Co-corresponding

7.Li D*, Liu J*, Yang X*, Zhou C, Guo J, Wu C, Qin L, He J, Yu S, Liu H, Wang X, Wu F, Kuang J, Hutchins AP#, Chen J#, Pei D# (2017) Chromatin accessibility dynamics during iPSC reprogramming. Cell Stem Cell. 21(6):819-833. *Co-first, #Co-corresponding

8.Zhou Z, Yang Y, He J, Liu J, Wu F, Yu S, Liu Y, Lin R, Liu H, Cui Y, Wang X, Cao S, Guo L, Lin L, Wang T, Peng X, Hutchins AP, Pei D#, Chen J#. (2017) Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function. Cell Reports. 21(8):2160-2170. #Co-corresponding

9.Fu X, He F, Li Y, Shahveranov A, Hutchins AP# (2017) Genomic and molecular control of cell type and cell type conversions. Cell Regeneration. 6:1. #Corresponding

10.Hutchins AP#, Yang Z, Li Y, He F, Fu X, Wang X, Li D, Liu K, He J, Wang Y, Chen J, Esteban MA, Pei D#. (2017) Models of global gene expression define major domains of cell type and tissue identity. Nucleic Acids Research. 45(5):2354. #Co-corresponding

11.Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizugichi K, Ahmad S. (2017) Predicting conformational ensembles and genome-wide transcription factor binding from DNA sequences. Scientific Reports. 7(1):4071

12.Li Q*, Hutchins AP*, Chen Y, Li S, Shan Y, Liao B, Zheng D, Shi X, Li Y, Chan W, Pan G, Wei S, Shu X#, Pei D#. (2017) A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes. Nature Communications. 8:15166. *Co-first, #Co-corresponding

13.Yang J*, Wang Y*, Zhou T, Wong L, Tian X, Hong X, Lai W, Au K, Wei R, Liu Y, Cheng L, Liang G, Huang Z, Fan W, Zhao P, Wang X, Ibanez DP, Luo Z, Li Y, Chen S, Wang D, Li L, Lai L, Qin B, Hutchins AP, Siu C, Huang Y, Esteban MA#, Tse H#. (2017) Generation of Human Liver Chimeric Mice with Hepatocytes from Familial Hypercholesterolemia Induced Pluripotent Stem Cells. Stem Cell Reports. 8(3):605-618. *Co-first, #Co-corresponding

14.Li H*, Lai P*, Jia J*, Song Y, Xia Q, Huang K, He N, Ping W, Chen J, Yang Z, Li J, Yao M, Gong X, Zhao J, Hou C, Esteban MA, Gao S, Pei D, Hutchins AP, Yao H. (2017) RNA Helicase DDX5 Inhibits Reprogramming to pluripotency by miRNA-based repression of RYBP and its PRC1-dependent and -independent Functions. Cell Stem Cell. 20(4):462 *Co-first authors

15.Huang K*, Gao J*, Du J*, Ma N, Zhu Y, Wu P, Zhang T, Wang W, Li Y, Chen Q, Hutchins AP, Yang Z, Zheng Y, Shan Y, Li X, Liao B, Liu J, Wang J, Liu D, Pan G (2016) Generation and analysis of GATA2w/eGFP human ESCs reveal ITGB3/CD61 as a reliable marker for defining hemogenic endothelial cells during hematopoiesis. Stem Cell Reports. 7(5):854-868. *Co-first authors

16.Pugacheva E, Teplyakov E, Wu Q, Li J, Chen C, Meng C, Liu J, Robinson S, Loukinov D, Hutchins AP, Boukaba A, Lobanenkov V, Strunnikov AV. (2016) The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. Epigenetics & Chromatin. 9(1):35

17.Xu Y, Zhang M, Li W, Zhu X, Bao X, Hutchins AP#, Esteban MA#. (2016) Transcriptional control of somatic cell reprogramming. Trends in Cell Biology. 26(4):272-88 #Co-corresponding

18.Zheng Y, Cai J, Hutchins AP, Jia L, Liu P, Chen S, Ge L, Pei D, Wei S (2016) Remission for loss of odontogenic potential in a new micromilieu in vitro. PLoS ONE. 11(4):e0152893

19.Wang L, Li X, Huang W, Zhou T, Wang H, Lin A, Hutchins AP, Su Z, Chen Q, Pei D, Pan G. (2016) TGFβ signaling regulates the choice between pluripotent and neural fates during reprogramming of human urine derived cells. Scientific Reports. 6: 22484

20.Ying Z, Chen K, Zheng L, Wu Y, Li L, Wang R, Long Q, Yang L, Guo J, Yao D, Li Y, Bao F, Xiang G, Liu J, Huang Q, Wu Z, Hutchins AP, Pei D, Liu X. (2016) Transient Activation of Mitoflashes Modulates Nanog at the Early Phase of Somatic Cell Reprogramming. Cell Metabolism. 23(1):220-6

21.Hutchins AP#, Pei D#. (2015) Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming and long non-coding RNAs. Scientific Bulletin. 60(20):1722-1733. (Featured cover article) #Co-corresponding

22.Hutchins AP#, Robson P#. (2015) Transcriptional Intricacies of Stem Cells. Cell Systems. 1(2); 100-101. #Co-corresponding authors.

23.Liu J, Han Q, Peng T, Peng M, Wei B, Li D, Wang X, Yu S, Yang J, Cao S, Huang K, Hutchins AP, Liu H, Kuang J, Zhou Z, Chen J, Wu H, Lin G, Chen Y, Chen Y, Li X, Wu H, Liao B, He W, Song H, Yao H, Pan G, Chen J, Pei D. (2015) The oncogene c-Jun impedes somatic reprogramming. Nature Cell Biology. 17(7):856-67.

24.Hatzihristidis T, Desai N, Hutchins AP, Meng T, Tremblay ML, Miranda-Saavedra D. (2015) A Drosophila-centric view of protein tyrosine phosphatases. FEBS Letters. 589(9):951-966.

25.Hutchins AP#, Takahashi Y, Miranda-Saavedra D#. (2015) Genomic analysis of LPS-stimulated myeloid cells indicates a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses. Scientific Reports. 5:9100. #Co-corresponding

26.Bao X, Wu H, Zhu X, Guo X, Hutchins AP, Luo Z, Song H, Chen Y, Lai K, Yin M, Xu L, Zhou L, Chen J, Wang D, Qin B, Frampton J, Pei D, Wang H, Zhang B, Esteban MA. (2015) The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Research. 25(1):80-92.

27.Pike KA*, Hutchins AP*, Vinette V, Theberge J, Sabbagh L, Tremblay M, Miranda-Saavedra D. (2014) Protein tyrosine phosphatase-1B is a regulator of the IL-10 induced transcriptional program in macrophages. Science Signaling. 6;7(324)ra43. *Co-first authors

28.Hutchins AP#, Dyla M, Jauch R, Miranda-Saavedra D. (2014) glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data. Cell Regeneration. 3(1):1. #Corresponding author

29.Liu L, Xu Y, He M, Zhang M, Cui F, Lu L, Yao M, Tian W, Benda C, Zhuang Q, Huang Z, Li W, Li X, Zhao P, Fan W, Luo Z, Li Y, Wu Y, Hutchins AP, Wang D, Tse HF, Schambach A, Frampton J, Qin B, Bao X, Yao H, Zhang B, Sun H, Pei D, Wang H, Wang J, Esteban MA. (2014) Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming. Cell Stem Cell. 15(5):574-88

30.Zheng H, Hutchins AP, Pan G, Li Y, Pei D, Pei G. (2014) Where cell fate conversions meet Chinese philosophy. Cell Research. 24(10):1162-3

31.Diez D, Hutchins AP, Miranda-Saavedra D. (2014) Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. Nucleic Acids Research. 42(1); e6

32.Bussières-Marmen S, Hutchins AP, Schirbel A, Rebert N, Tiganis T, Fiocchi C, Miranda-Saavedra D, Tremblay ML. (2014) Characterization of PTPN2 and its use as a biomarker. Methods. 65(2);239-46

33.Hatzihristidis T, Liu S, Pryszcz L, Hutchins AP, Gabaldon T, Tremblay ML, Miranda-Saavedra D. (2014) PTP-central: A Comprehensive Resource of Protein Tyrosine Phosphatases in Eukaryotic Genomes. Methods. 65(2);156-64

34.Hutchins AP#, Choo SW, Mistri TK, Rahmani M, Woon CT, Ng CKL, Jauch R, Robson P#. (2013) Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells. Stem Cells. 31(2):269-281. #Co-corresponding

35.Aksoy I*, Jauch R*, Chen J, Dyla M, Divakar U, Bogu GK, Ng CKL, Herath W, Hutchins AP, Robson P, Kolatkar PR, Stanton LW. (2013) Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO Journal. 32(7);938-953. *As co-first authors

36.Clarke M, Lohan AJ, et al., … Hutchins AP, … Miranda-Saavedra D, … Loftus B. (40 authors in total) (2013) Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of pattern recognition and tyrosine kinase signalling. Genome Biology. 14(2):R11

37.Hutchins AP, Diez D, Miranda-Saavedra D. (2013) The IL-10/STAT3-mediated anti-inflammatory response: recent developments and future challenges. Briefings in Functional Genomics. 12(6);489-98

38.Hutchins AP, Diez D, Miranda-Saavedra D. (2013) Genomic and computational approaches to dissect the mechanisms of STAT3’s universal and cell-type-specific functions. JAK-STAT. 2(4);e25097

39.Hutchins AP*, Liu S*, Diez D. Miranda-Saavedra D. (2013) The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. Molecular Biology and Evolution. 30(5);1172-1187. *As co-first authors

40.Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay M, Miranda-Saavedra D. (2013) Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. Nucleic Acids Research. 41(4):2155-2170

41.Hutchins AP, Poulain S, Fujii H, Miranda-Saavedra D. (2012) Discovery and characterization of new transcripts from RNA-seq data in mouse CD4+ T cells. Genomics. 100(5):303-313

42.Hutchins AP, Poulain S, Miranda-Saavedra D. (2012) Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages. Blood. 119(13):e110-e119

43.Jauch R*, Aksoy I*, Hutchins AP*, Ng CK, Tian XF, Chen J, Palasingam P, Robson P, Stanton LW, Kolatkar PR. (2011) Conversion of Sox17 into a Pluripotency Reprogramming Factor by Re-engineering its Association with Oct4 on DNA. Stem Cells. 29(6):940-951. *Co-first authors

44.Hutchins AP, Robson P. (2009) Unraveling the Human Embryonic Stem Cell Phosphoproteome. Cell Stem Cell. 5(2):126-128

45.Bush MS, Hutchins AP, Jones AME, Naldrett MJ, Jarmolowski A, Browning K, Lloyd CW, Doonan JH. (2009) Selective recruitment of proteins to 5' cap complexes during the growth cycle in Arabidopsis. Plant Journal. 59(3):400-412

46.Hutchins AP, Roberts GR, Lloyd CW, Doonan JH. (2004) In vivo interaction between CDKA and eIF4A: a possible mechanism linking translation and cell proliferation. FEBS Letters. 556(1-3):91-94

News More

  • Interview with Associate Professor Andrew Hutchins from the Biology Department

    2019-11-25
  • Professor Hutchins and his team publish new research on molecular arrangement of mouse cell types

    2019-11-25
  • Epigenetic remodeling of chromatin to promote pluripotent reprogramming— SUSTech-GIBH groups discover epigenetic roadblock Chris Edwards | 03/20/2018 177

    2019-11-25

Lab members Read More

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Team Group Website :  https://www.chrom-lab.org
 

Welcome to the Department of Biology! Since its establishment in 2012, the Department of Biology has attracted internationally renowned professors to join as leaders and dozens of young scientists to start their independent academic career here pursuit of excellence in research and teaching. The research interests of our faculty members include diverse topics such as systems biology, plant biology, neurobiology, structural biology and molecular cell biology. The primary goals of our faculty are to address the most significant fundamental biological questions and to develop new strategies to treat various complex diseases. Such efforts will benefit from the shared inter-disciplinary collaborative spirit deeply rooted in the minds of all the faculty members working in different departments at SUSTech.

Mentoring the next generation biologists with the highest standards is another primary task of the Department of Biology. Our professors choose internationally acclaimed textbooks to teach core courses biological sciences, biotechnology and bioinformatics. Undergraduates are encouraged to join the laboratory early to get firsthand working experience in basic and/or applied biological research, which helps them to consolidate the mastering of basic techniques, to broaden their knowledge horizons and to acquire the capabilities of problem identifying, hypothesis formulating and problem solving.

Life science, one of the fastest developing natural scientific disciplines, has been the driving force behind the growth of the world economy and provides the know for the development of new technologies serving to improve the human health and welfare at large. Wit generous financial support from the Shenzhen municipal government, we are confident that the Department of Biology in SUSTech will surely grow into a top tier globally-renowned research and teaching center!

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andrewh@sustech.edu.cn

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