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Dr Yuxin Cui

Dr Yuxin Cui

Research Fellow

School of Medicine

Email
cuiy7@cardiff.ac.uk
Telephone
+44 (0)29 2068 7070
Campuses
Henry Wellcome Building for Biomedical Research, University Hospital of Wales, Heath Park, Cardiff, CF14 4XN
Users
Available for postgraduate supervision

Overview

My main research interests are cancer biomarker identification and drug discovery. I have built up bioinformatics analysis pipelines to integrate large-scale multi-omics data such as proteome, transcriptome, methylation, mutation, kinase profile, immune profile, single-cell sequencing, CRISPR dependency, inhibitors and clinicopathological parameters.  To overcome the hurdles of conventional approaches, I have been utilising the power of machine learning (ML) and artificial intelligence (AI) to evaluate the multivariate correlation, principal components, hierarchical clustering, risk score prediction and feature importance of potential biomarker candidates by computation programming using R, Python, SQL and SAS etc. To validate concepts of novel therapeutic intervention, in lab we regularly perform a variety of experimental assays including CRISPR design, viral vector construction, viral particle production, molecular cloning, primary immune cell isolation, 3D cell culture, cellular assays, HT drug response, multi-colour FACS, automated live-cell immunofluorescence, ELISA, ELISpot, multiplex cytokine assays, automated cell-tumour interaction profiling, proteomics, next-generation RNA-Seq, clinical cohort gene analysis, IHC of cancer tissue microarray, multiparametric high-content-screening cytotoxicity assay and in-vivo modelling.  

My recent projects provide insightful findings into the biomarker and therapeutical potential of Dead/H-box helicases in cancer. My bioinformatic analysis unveils that a cluster of DDX/DHX helicases has the most significant clinical significance in cancer. They are associated with some key causal signalling pathways such as MYC, TP53 and MUC16. They are involved in tumour microenvironment by the crosstalk with tumour-infiltrated immune cells such as CD8+ T and B cells. We further observe DHX36 is positively associated with patient survival and had a link with the clinicopathological conditions including immune profiles of breast cancer. The lentiviral-based stable knockdown (KD) of DHX36 promotes tumour growth in vivo. After the DHX36 KD, there is an increase in the invasion, the number of cells in the S-phase and a reduction of apoptosis with the response to cisplatin. DHX36 KD also desensitises the cytotoxic cellular response to paclitaxel and cisplatin. Transcriptomic profiling analysis by RNA sequencing indicated that DHX36 altered gene expression profile through the upstream activation of TNF, IFNγ, NFκb and TGFβ1. High throughput signalling analysis indicates that one cluster of stress-associated kinase proteins including p53, ROCK1 and JNK are suppressed, while the mitotic checkpoint protein-serine kinases CDK1 and CDK2 are activated, as a consequence of the DHX36 KD. My study on DHX36 in lung cancer also reveals DHX36 gene expression is positively associated with survival in lung adenocarcinoma.  The reduction of DHX36 expression sensitises the response of lung cancer cells to the chemotherapeutic drug etoposide through regulating RB1 and E2F1 pathways. 

I am conducting the small molecule drug screening by structure-guided protein pocket modelling and affinity prediction. Lentivirus-based Tet-on inducible cancer cell models will be developed to determine the therapeutic value of DHX36 as a master regulator of onco-related genes which are enriched with G4 structures. The disruption of telomere length by G4 structure resolving will be visualised using cutting-edge technology. Bioinformatic and statistical approaches including ML and AI will be further developed to better understand the key pathway checkpoints and accelerate new drug discovery.   

 

Biography

Education and qualifications

  • 2006: PhD, School of Pharmacy, University of Nottingham, UK

Career overview

  • 2013 - present: Research Fellow, Cardiff University

Honours and awards

Travel award (Morgan E Williams Grant), to attend the National Gastric Cancer Academic Conference (NGCAC) and the China-United Kingdom Cancer Conference 2014, Beijing, China 2014

Professional memberships

  • British Association of Cancer Research
  • European Association of Cancer Research
  • Institute of Biomedical Science (IBMS)

Speaking engagements

CUKC Conference Beijin, 2017. Invited speaker.

CUKC Conference Cardiff, 2015. Invited speaker.

National Gastric Cancer Academic Conference, Beijing, 2014. Invited speaker.

CUKC Conference, Beijing, 2014. Invited speaker.

Committees and reviewing

2015-present: China – UK cancer academic committee

2014-present; academic mentor

Publications

2021

2020

2019

2018

2017

2016

2015

Teaching

Postgraduate research supervision: PhD

Previous student - Valentina Flamini

Previous student - Robyn Bradbury

Provious student - Moon Meng

Undergraduate research supervision:

CUReS placements

Postgraduate teaching:

Cancer Biology and Therapeutics (MSc)

  1. Bioinformatics and statistical analysis for cancer biomarker identification and drug discovery.
  2. Integration and manipulation of large-scale multi-omics data.
  3. Disruption of the interaction between invasive tumour cells and other cells in a tumour microenvironment.
  4. Drug design and selection by high throughput non-invasive assays.
  5. Therapeutic potential of genomic editing in metastatic tumours.
  6. Therapeutic targeting of calcium-binding proteins in metastatic and chemo-resistant cancer cells.
  7. Preventing selective homing of tumour cells to an organ such as bone.
  8. Delivery and tracking of new microRNA therapeutics in cancer.
  9. Visualisation of DNA G4 structure and telomere dynamics.

Supervision

Xuefei Dong, PhD student, School of Medicine

Fangda Wu, PhD student, School of Engineer