Bio


Yiyun Chen, Ph.D. is a Postdoctoral Fellow at Professor Crystal Mackall’s group at Stanford Cancer Institute.

Dr. Chen studied biochemistry and structural biology in her undergraduate and master trainings at The Hong Kong University of Science and Technology, where she eventually obtained her Ph.D. degree in computational biology under the supervision of Professor Jiguang Wang. During her Ph.D. training, she has developed her skill sets in analyzing and integrating various types of patient-derived sequencing data, published three first-author and four co-author papers, and received two awards for top postgraduate students. Through interdisciplinary collaborations with cancer biologist and clinicians in US and Asia, her work has uncovered tumor-specific immune cell subtypes and novel noncoding RNAs and generated new insights into precision medicine in glioma, lymphoma and gastric cancer.

Applying her expertise in computational cancer biology and immunology, her current research is focused on identifying molecular mechanisms that contribute to the clinical outcomes of patients undergoing CAR-T immunotherapy. At Mackall Lab, she will contribute to tailoring computational pipelines for profiling the spatiotemporal dynamics of the tumor and immune microenvironment and translate new discoveries into cancer therapeutics.

Professional Education


  • Doctor of Philosophy, Hong Kong University Of Science & Technology (2021)
  • Master of Philosophy, Hong Kong University Of Science & Technology (2017)
  • Bachelor of Science, Hong Kong University Of Science & Technology (2014)
  • PhD, The Hong Kong University of Science and Technology, Computational Biology (2021)
  • MPhil, The Hong Kong University of Science and Technology, Structural and Molecular Biology (2017)
  • BSc, The Hong Kong University of Science and Technology, Biochemistry (2014)

Stanford Advisors


Lab Affiliations


All Publications


  • Classifying gastric cancer using FLORA reveals clinically relevant molecular subtypes and highlights LINC01614 as a biomarker for patient prognosis ONCOGENE Chen, Y., Cheng, W., Shi, H., Huang, S., Chen, H., Liu, D., Xu, W., Yu, J., Wang, J. 2021; 40 (16): 2898-2909

    Abstract

    Molecular-based classifications of gastric cancer (GC) were recently proposed, but few of them robustly predict clinical outcomes. While mutation and expression signature of protein-coding genes were used in previous molecular subtyping methods, the noncoding genome in GC remains largely unexplored. Here, we developed the fast long-noncoding RNA analysis (FLORA) method to study RNA sequencing data of GC cases, and prioritized tumor-specific long-noncoding RNAs (lncRNAs) by integrating clinical and multi-omic data. We uncovered 1235 tumor-specific lncRNAs, based on which three subtypes were identified. The lncRNA-based subtype 3 (L3) represented a subgroup of intestinal GC with worse survival, characterized by prevalent TP53 mutations, chromatin instability, hypomethylation, and over-expression of oncogenic lncRNAs. In contrast, the lncRNA-based subtype 1 (L1) has the best survival outcome, while LINC01614 expression further segregated a subgroup of L1 cases with worse survival and increased chance of developing distal metastasis. We demonstrated that LINC01614 over-expression is an independent prognostic factor in L1 and network-based functional prediction implicated its relevance to cell migration. Over-expression and CRISPR-Cas9-guided knockout experiments further validated the functions of LINC01614 in promoting GC cell growth and migration. Altogether, we proposed a lncRNA-based molecular subtype of GC that robustly predicts patient survival and validated LINC01614 as an oncogenic lncRNA that promotes GC proliferation and migration.

    View details for DOI 10.1038/s41388-021-01743-3

    View details for Web of Science ID 000630675000005

    View details for PubMedID 33742127

    View details for PubMedCentralID PMC8062268

  • Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells NATURE GENETICS Laffleur, B., Lim, J., Zhang, W., Chen, Y., Pefanis, E., Bizarro, J., Batista, C. R., Wu, L., Economides, A. N., Wang, J., Basu, U. 2021; 53 (2): 230-+

    Abstract

    Noncoding RNAs are exquisitely titrated by the cellular RNA surveillance machinery for regulating diverse biological processes. The RNA exosome, the predominant 3' RNA exoribonuclease in mammalian cells, is composed of nine core and two catalytic subunits. Here, we developed a mouse model with a conditional allele to study the RNA exosome catalytic subunit DIS3. In DIS3-deficient B cells, integrity of the immunoglobulin heavy chain (Igh) locus in its topologically associating domain is affected, with accumulation of DNA-associated RNAs flanking CTCF-binding elements, decreased CTCF binding to CTCF-binding elements and disorganized cohesin localization. DIS3-deficient B cells also accumulate activation-induced cytidine deaminase-mediated asymmetric nicks, altering somatic hypermutation patterns and increasing microhomology-mediated end-joining DNA repair. Altered mutation patterns and Igh architectural defects in DIS3-deficient B cells lead to decreased class-switch recombination but increased chromosomal translocations. Our observations of DIS3-mediated architectural regulation at the Igh locus are reflected genome wide, thus providing evidence that noncoding RNA processing is an important mechanism for controlling genome organization.

    View details for DOI 10.1038/s41588-020-00772-0

    View details for Web of Science ID 000613615200001

    View details for PubMedID 33526923

    View details for PubMedCentralID PMC8011275

  • Noncoding RNA transcription alters chromosomal topology to promote isotype-specific class switch recombination SCIENCE IMMUNOLOGY Rothschild, G., Zhang, W., Lim, J., Giri, P., Laffleur, B., Chen, Y., Fang, M., Chen, Y., Nair, L., Liu, Z., Deng, H., Hammarstrom, L., Wang, J., Basu, U. 2020; 5 (44)

    Abstract

    B cells undergo two types of genomic alterations to increase antibody diversity: introduction of point mutations into immunoglobulin heavy- and light-chain (IgH and IgL) variable regions by somatic hypermutation (SHM) and alteration of antibody effector functions by changing the expressed IgH constant region exons through IgH class switch recombination (CSR). SHM and CSR require the B cell-specific activation-induced cytidine deaminase (AID) protein, the transcription of germline noncoding RNAs, and the activity of the 3' regulatory region (3'RR) super-enhancer. Although many transcription regulatory elements (e.g., promoters and enhancers) reside inside the IgH and IgL sequences, the question remains whether clusters of regulatory elements outside IgH control CSR. Using RNA exosome-deficient mouse B cells where long noncoding RNAs (lncRNAs) are easily detected, we identified a cluster of three RNA-expressing elements that includes lncCSRIgA (that expresses lncRNA-CSRIgA). B cells isolated from a mouse model lacking lncRNA-CSRIgA transcription fail to undergo normal levels of CSR to IgA both in B cells of the Peyer's patches and grown in ex vivo culture conditions. lncRNA-CSRIgA is expressed from an enhancer site (lncCSRIgA ) to facilitate the recruitment of regulatory proteins to a nearby CTCF site (CTCFlncCSR) that alters the chromosomal interactions inside the TADlncCSRIgA and long-range interactions with the 3'RR super-enhancer. Humans with IgA deficiency show polymorphisms in the lncCSRIgA locus compared with the normal population. Thus, we provide evidence for an evolutionarily conserved topologically associated domain (TADlncCSRIgA) that coordinates IgA CSR in Peyer's patch B cells through an lncRNA (lncRNA-CSRIgA) transcription-dependent mechanism.

    View details for DOI 10.1126/sciimmunol.aay5864

    View details for Web of Science ID 000519520300005

    View details for PubMedID 32034089

    View details for PubMedCentralID PMC7608691

  • Deciphering Brain Complexity Using Single-cell Sequencing GENOMICS PROTEOMICS & BIOINFORMATICS Mu, Q., Chen, Y., Wang, J. 2019; 17 (4): 344-366

    Abstract

    The human brain contains billions of highly differentiated and interconnected cells that form intricate neural networks and collectively control the physical activities and high-level cognitive functions, such as memory, decision-making, and social behavior. Big data is required to decipher the complexity of cell types, as well as connectivity and functions of the brain. The newly developed single-cell sequencing technology, which provides a comprehensive landscape of brain cell type diversity by profiling the transcriptome, genome, and/or epigenome of individual cells, has contributed substantially to revealing the complexity and dynamics of the brain and providing new insights into brain development and brain-related disorders. In this review, we first introduce the progresses in both experimental and computational methods of single-cell sequencing technology. Applications of single-cell sequencing-based technologies in brain research, including cell type classification, brain development, and brain disease mechanisms, are then elucidated by representative studies. Lastly, we provided our perspectives into the challenges and future developments in the field of single-cell sequencing. In summary, this mini review aims to provide an overview of how big data generated from single-cell sequencing have empowered the advancements in neuroscience and shed light on the complex problems in understanding brain functions and diseases.

    View details for DOI 10.1016/j.gpb.2018.07.007

    View details for Web of Science ID 000505053300003

    View details for PubMedID 31586689

    View details for PubMedCentralID PMC6943771

  • Mutational Landscape of Secondary Glioblastoma Guides MET-Targeted Trial in Brain Tumor CELL Hu, H., Mu, Q., Bao, Z., Chen, Y., Liu, Y., Chen, J., Wang, K., Wang, Z., Nam, Y., Jiang, B., Sa, J. K., Cho, H., Her, N., Zhang, C., Zhao, Z., Zhang, Y., Zeng, F., Wu, F., Kang, X., Liu, Y., Qian, Z., Wang, Z., Huang, R., Wang, Q., Zhang, W., Qiu, X., Li, W., Nam, D., Fan, X., Wang, J., Jiang, T. 2018; 175 (6): 1665-+

    Abstract

    Low-grade gliomas almost invariably progress into secondary glioblastoma (sGBM) with limited therapeutic option and poorly understood mechanism. By studying the mutational landscape of 188 sGBMs, we find significant enrichment of TP53 mutations, somatic hypermutation, MET-exon-14-skipping (METex14), PTPRZ1-MET (ZM) fusions, and MET amplification. Strikingly, METex14 frequently co-occurs with ZM fusion and is present in ∼14% of cases with significantly worse prognosis. Subsequent studies show that METex14 promotes glioma progression by prolonging MET activity. Furthermore, we describe a MET kinase inhibitor, PLB-1001, that demonstrates remarkable potency in selectively inhibiting MET-altered tumor cells in preclinical models. Importantly, this compound also shows blood-brain barrier permeability and is subsequently applied in a phase I clinical trial that enrolls MET-altered chemo-resistant glioma patients. Encouragingly, PLB-1001 achieves partial response in at least two advanced sGBM patients with rarely significant side effects, underscoring the clinical potential for precisely treating gliomas using this therapy.

    View details for DOI 10.1016/j.cell.2018.09.038

    View details for Web of Science ID 000451771700023

    View details for PubMedID 30343896

  • Somatic MAP3K3 mutation defines a subclass of cerebral cavernous malformation AMERICAN JOURNAL OF HUMAN GENETICS Weng, J., Yang, Y., Song, D., Huo, R., Li, H., Chen, Y., Nam, Y., Zhou, Q., Jiao, Y., Fu, W., Yan, Z., Wang, J., Xu, H., Di, L., Li, J., Wang, S., Zhao, J., Wang, J., Cao, Y. 2021; 108 (5): 942-950

    Abstract

    Cerebral cavernous malformations (CCMs) are vascular disorders that affect up to 0.5% of the total population. About 20% of CCMs are inherited because of familial mutations in CCM genes, including CCM1/KRIT1, CCM2/MGC4607, and CCM3/PDCD10, whereas the etiology of a majority of simplex CCM-affected individuals remains unclear. Here, we report somatic mutations of MAP3K3, PIK3CA, MAP2K7, and CCM genes in CCM lesions. In particular, somatic hotspot mutations of PIK3CA are found in 11 of 38 individuals with CCMs, and a MAP3K3 somatic mutation (c.1323C>G [p.Ile441Met]) is detected in 37.0% (34 of 92) of the simplex CCM-affected individuals. Strikingly, the MAP3K3 c.1323C>G mutation presents in 95.7% (22 of 23) of the popcorn-like lesions but only 2.5% (1 of 40) of the subacute-bleeding or multifocal lesions that are predominantly attributed to mutations in the CCM1/2/3 signaling complex. Leveraging mini-bulk sequencing, we demonstrate the enrichment of MAP3K3 c.1323C>G mutation in CCM endothelium. Mechanistically, beyond the activation of CCM1/2/3-inhibited ERK5 signaling, MEKK3 p.Ile441Met (MAP3K3 encodes MEKK3) also activates ERK1/2, JNK, and p38 pathways because of mutation-induced MEKK3 kinase activity enhancement. Collectively, we identified several somatic activating mutations in CCM endothelium, and the MAP3K3 c.1323C>G mutation defines a primary CCM subtype with distinct characteristics in signaling activation and magnetic resonance imaging appearance.

    View details for DOI 10.1016/j.ajhg.2021.04.005

    View details for Web of Science ID 000658896700013

    View details for PubMedID 33891857

    View details for PubMedCentralID PMC8206158

  • Structural Basis for the High-Affinity Interaction between CASK and Mint1 STRUCTURE Wu, X., Cai, Q., Chen, Y., Zhu, S., Mi, J., Wang, J., Zhang, M. 2020; 28 (6): 664-+

    Abstract

    CASK forms an evolutionarily conserved tripartite complex with Mint1 and Veli critical for neuronal synaptic transmission and cell polarity. The CASK CaM kinase (CaMK) domain, in addition to interacting with Mint1, can also bind to many different target proteins, although the mechanism governing CASK-CaMK/target interaction selectivity is unclear. Here, we demonstrate that an extended sequence in the N-terminal unstructured region of Mint1 binds to CASK-CaMK with a dissociation constant of ∼7.5 nM. The high-resolution crystal structure of CASK-CaMK in complex with this Mint1 fragment reveals that the C-lobe of CASK-CaMK binds to a short sequence common to known CaMK targets and the N-lobe of CaMK engages an α helix that is unique to Mint1. Biochemical experiments together with structural analysis reveal that the CASK and Mint1 interaction is not regulated by Ca2+/CaM. The CASK/Mint1 complex structure provides mechanistic explanations for several CASK mutations identified in patients with brain disorders and cancers.

    View details for DOI 10.1016/j.str.2020.04.001

    View details for Web of Science ID 000538119800010

    View details for PubMedID 32348748

  • Ca (2+)-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single alpha Helix Lever Arm Extension STRUCTURE Li, J., Chen, Y., Deng, Y., Unarta, I., Lu, Q., Huang, X., Zhang, M. 2017; 25 (4): 579-+

    Abstract

    Several unconventional myosins contain a highly charged single α helix (SAH) immediately following the calmodulin (CaM) binding IQ motifs, functioning to extend lever arms of these myosins. How such SAH is connected to the IQ motifs and whether the conformation of the IQ motifs-SAH segments are regulated by Ca2+ fluctuations are not known. Here, we demonstrate by solving its crystal structure that the predicted SAH of myosin VIIa (Myo7a) forms a stable SAH. The structure of Myo7a IQ5-SAH segment in complex with apo-CaM reveals that the SAH sequence can extend the length of the Myo7a lever arm. Although Ca2+-CaM remains bound to IQ5-SAH, the Ca2+-induced CaM binding mode change softens the conformation of the IQ5-SAH junction, revealing a Ca2+-induced lever arm flexibility change for Myo7a. We further demonstrate that the last IQ motif of several other myosins also binds to both apo- and Ca2+-CaM, suggesting a common Ca2+-induced conformational regulation mechanism.

    View details for DOI 10.1016/j.str.2017.02.002

    View details for Web of Science ID 000401578200005

    View details for PubMedID 28262393

  • Inhibition of SOCE disrupts cytokinesis in zebrafish embryos via inhibition of cleavage furrow deepening INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY Chan, C. M., Chen, Y., Hung, T. S., Miller, A. L., Shipley, A. M., Webb, S. E. 2015; 59 (7-9): 289-301

    Abstract

    During the first few cell division cycles in zebrafish, distinct Ca(2+) transients are localized to the early embryonic cleavage furrows, where they accompany (and are required for) furrow positioning, propagation, deepening and apposition. It has previously been shown that the endoplasmic reticulum (ER) acts as the primary store for generating these Ca(2+) transients via release through inositol 1,4,5-trisphosphate receptors (IP 3Rs). We hypothesised that maintaining the elevated levels of intracellular Ca(2+) required for deepening and apposition of the cleavage furrows in these large eggs might result in the depletion of the available ER Ca(2+) store, thus the role of store-operated Ca(2+) entry (SOCE) was examined. Newly fertilized, dechorionated embryos were incubated with various SOCE inhibitors, starting just prior to the onset of the first cell division cycle. The effect of these inhibitors on mitosis, furrow positioning, propagation, deepening and apposition, and the generation of the cytokinetic Ca(2+) transients was determined. Treatment with 2-APB or SKF 96365 had no major effect on mitosis, furrow positioning or propagation, but inhibited furrow deepening resulting in regression of the cleavage furrow. Both of these inhibitors also blocked the furrowing Ca(2+) transient, with SKF 96365 having a more profound inhibitory effect than 2-APB. In zebrafish, SOCE does not appear to be required for mitosis or the early stages of cytokinesis during the early embryonic cell division cycles, but it does appear to be essential for maintaining the elevated levels of [Ca(2+)]i for the extended periods that are required during furrow deepening and daughter cell apposition.

    View details for DOI 10.1387/ijdb.150209sw

    View details for Web of Science ID 000367661400005

    View details for PubMedID 26679947