Yang Liu's Lab

About the lab

The laboratory of Dr. Yang Liu integrates a multidisciplinary approaches of engineering, chemistry, physics, computer science, medicine and biology and develop advanced optical imaging technologies and biosensors to improve cancer detection and treatment. We develop a suite of nanoscale imaging techniques and sensors. We push the limit of imaging technologies the technical capability by making them faster, cheaper and more robust. We apply these tools to detect subtle molecular changes in cells at risk for cancer development and cancer biomarkers at single molecule sensitivity. We also use these imaging tools to advance our understanding of cancer biology and learn how normal cells are transformed into malignancy and why their natural courses differ in different patients.

Featured research (9)

Imaging chromatin organization at the molecular-scale resolution remains an important endeavor in basic and translational research. Stochastic optical reconstruction microscopy (STORM) is a powerful superresolution imaging technique to visualize nanoscale molecular organization down to the resolution of ~20 to 30 nm. Despite the substantial progress in imaging chromatin organization in cells and model systems, its routine application on assessing pathological tissue remains limited. It is, in part, hampered by the lack of simple labels that consistently generates high-quality STORM images on the highly processed clinical tissue. We developed a fast, simple, and robust small-molecule fluorescent probe—cyanine 5–conjugated Hoechst—for routine superresolution imaging of nanoscale nuclear architecture on clinical tissue. We demonstrated the biological and clinical significance of imaging superresolved chromatin structure in cancer development and its potential clinical utility for cancer risk stratification.
We present an erratum to our Letter [Opt. Lett.46, 3825 (2021)OPLEDP0146-959210.1364/OL.433740]. This erratum corrects an error in Eq. (2). All the simulations and experiments in the original Letter were performed using the correct equation, and therefore, this correction does not affect the results and conclusions of the original Letter.
After nearly 15 years since its initial debut, super-resolution localization microscopy that surpasses the diffraction-limited resolution barrier of optical microscopy has rapidly gotten out of the ivory tower and entered a new phase to address various challenging biomedical questions. Recent advances in this technology greatly increased the imaging throughput, improved the imaging quality, simplified the sample preparation, and reduced the system cost, making this technology suitable for routine biomedical research. We will provide our perspective on the recent technical advances and their implications in serving the community of biomedical research.
Genomic DNA is folded into a higher-order structure that regulates transcription and maintains genomic stability. Although progress has been made on understanding biochemical characteristics of epigenetic modifications in cancer, the in-situ higher-order folding of chromatin structure during malignant transformation remains largely unknown. Here, using optimized stochastic optical reconstruction microscopy (STORM) for pathological tissue (PathSTORM), we uncover a gradual decompaction and fragmentation of higher-order chromatin folding throughout all stages of carcinogenesis in multiple tumor types, and prior to tumor formation. Our integrated imaging, genomic, and transcriptomic analyses reveal functional consequences in enhanced transcription activities and impaired genomic stability. We also demonstrate the potential of imaging higher-order chromatin disruption to detect high-risk precursors that cannot be distinguished by conventional pathology. Taken together, our findings reveal gradual decompaction and fragmentation of higher-order chromatin structure as an enabling characteristic in early carcinogenesis to facilitate malignant transformation, which may improve cancer diagnosis, risk stratification, and prevention. Aberrant chromatin structure is often found in cancer. Here, the authors optimise super-resolution microscopy for pathological tissue and discovered a significant decompaction of chromatin folding in early carcinogenesis prior to tumour formation.
Patients with inflammatory bowel disease (IBD) colitis are at an increased risk of developing colorectal cancer and are currently recommended to undergo extensive annual or biennial colonoscopy, a costly and invasive procedure. Most surveillance colonoscopies are negative with no existing objective measures for assessing their risk of developing cancer. We have recently developed a less invasive, cost-effective and objective method to assess cancer risk by detecting the presence of colonic neoplasia via 3-dimensional (3D) nanoscale nuclear architecture mapping (nanoNAM) of normal-appearing rectal biopsies. To establish its translational relevance, we prospectively recruited 103 patients with IBD colitis undergoing surveillance colonoscopy and measured submicroscopic alterations in aberrant intrinsic nuclear architecture of epithelial cells from normal-appearing rectal biopsies with nanoNAM. The results were correlated with the histologic diagnoses from all random biopsies obtained during initial and follow-up colonoscopy within 3 years. Using nanoNAM-based structural characterization as input features into a soft margin-based ν-SVM risk classifier, we show that nanoNAM detects colonic neoplasia with AUC of 0.87 ± 0.04, sensitivity of 0.81 ± 0.09, and specificity of 0.82 ± 0.07 in the independent validation set. In addition, projecting nanoNAM features onto a 2-sphere reveals patients with low-risk and high-risk IBD colitis existing on separate hemispheres. Finally, we show that this ability to assess cancer risk translates to clinically-relevant estimation of individual-patient likelihood of being truly at risk. We demonstrate the potential of nanoNAM to identify patients with IBD at higher risk of developing cancer from normal-appearing rectum tissue, which may aid clinicians in patients with personalized IBD colitis surveillance.

Lab head

Yang Liu
  • Departments of Medicine and Bioengineering

Members (2)

Jianquan Xu
  • University of Pittsburgh
Hongqiang Ma
  • University of Pittsburgh

Alumni (5)

Shikhar Uttam
  • University of Pittsburgh
Hoa V Pham
  • University of Pittsburgh
Rao Fu
  • Northeast electric power university
Meihan Duan
  • University of Pittsburgh