John Ming Lu

All Publications

• Meta-Analysis of Single-Cell Transcriptomics Data of Cardiac Fibroblasts Reveals Temporal Heterogeneity of Cardiac Fibroblast Response after MI Lu, J., Januszyk, M., Griffin, M., Guo, J. L., Wan, D. C., Longaker, M. T. LIPPINCOTT WILLIAMS & WILKINS. 2023: S68

  View details for Web of Science ID 001094086300124

• Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding. Proceedings of the National Academy of Sciences of the United States of America Stacey, J. C., Tan, A., Lu, J. M., James, L. C., Dick, R. A., Briggs, J. A. 2023; 120 (16): e2220557120

  Abstract

  The mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical capsids from a lattice of hexamers and pentamers, and engages in and then relinquishes multiple interactions with cellular proteins in an orchestrated fashion. Cellular host factors including Nup153, CPSF6, and Sec24C engage the same pocket within CA hexamers. How CA assembles pentamers and hexamers of different curvatures, how CA oligomerization states or curvature might modulate host-protein interactions, and how binding of multiple cofactors to a single site is coordinated, all remain to be elucidated. Here, using single-particle cryoEM, we have determined the structure of the mature HIV-1 CA pentamer and hexamer from conical CA-IP6 polyhedra to ~3 Å resolution. We also determined structures of hexamers in the context of multiple lattice curvatures and number of pentamer contacts. Comparison of these structures, bound or not to host protein peptides, revealed two structural switches within HIV-1 CA that modulate peptide binding according to CA lattice curvature and whether CA is hexameric or pentameric. These observations suggest that the conical HIV-1 capsid has different host-protein binding properties at different positions on its surface, which may facilitate cell entry and represent an evolutionary advantage of conical morphology.

  View details for DOI 10.1073/pnas.2220557120

  View details for PubMedID 37040417

• Structures and distributions of SARS-CoV-2 spike proteins on intact virions NATURE Ke, Z., Oton, J., Qu, K., Cortese, M., Zila, V., McKeane, L., Nakane, T., Zivanov, J., Neufeldt, C. J., Cerikan, B., Lu, J. M., Peukes, J., Xiong, X., Krausslich, H., Scheres, S. W., Bartenschlager, R., Briggs, J. G. 2020

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude1. Heavily glycosylated S trimers bind to the angiotensin-converting enzyme 2 receptor and mediate entry of virions into target cells2-6. S exhibits extensive conformational flexibility: it modulates exposure of its receptor-binding site and subsequently undergoes complete structural rearrangement to drive fusion of viral and cellular membranes2,7,8. The structures and conformations of soluble, overexpressed, purified S proteins have been studied in detail using cryo-electron microscopy2,7,9-12, but the structure and distribution of S on the virion surface remain unknown. Here we applied cryo-electron microscopy and tomography to image intact SARS-CoV-2 virions and determine the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface. These results reveal the conformations of S on the virion, and provide a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.

  View details for DOI 10.1038/s41586-020-2665-2

  View details for Web of Science ID 000585787300001

  View details for PubMedID 32805734

• Understanding the Foreign Body Response via Single-Cell Meta-Analysis. Biology Liang, N. E., Parker, J. B., Lu, J. M., Januszyk, M., Wan, D. C., Griffin, M., Longaker, M. T. 2024; 13 (7)

  Abstract

  Foreign body response (FBR) is a universal reaction to implanted biomaterial that can affect the function and longevity of the implant. A few studies have attempted to identify targets for treating FBR through the use of single-cell RNA sequencing (scRNA-seq), though the generalizability of these findings from an individual study may be limited. In our study, we perform a meta-analysis of scRNA-seq data from all available FBR mouse studies and integrate these data to identify gene signatures specific to FBR across different models and anatomic locations. We identify subclusters of fibroblasts and macrophages that emerge in response to foreign bodies and characterize their signaling pathways, gene ontology terms, and downstream mediators. The fibroblast subpopulations enriched in the setting of FBR demonstrated significant signaling interactions in the transforming growth factor-beta (TGF-beta) signaling pathway, with known pro-fibrotic mediators identified as top expressed genes in these FBR-derived fibroblasts. In contrast, FBR-enriched macrophage subclusters highly expressed pro-fibrotic and pro-inflammatory mediators downstream of tumor necrosis factor (TNF) signaling. Cell-cell interactions were additionally interrogated using CellChat, with identification of key signaling interactions enriched between fibroblasts and macrophages in FBR. By combining multiple FBR datasets, our meta-analysis study identifies common cell-specific gene signatures enriched in foreign body reactions, providing potential therapeutic targets for patients requiring medical implants across a myriad of devices and indications.

  View details for DOI 10.3390/biology13070540

  View details for PubMedID 39056733

• Quantitative Analysis of the Collagen Matrix Ultrastructure in Mouse Hearts after Myocardial Infarction Lu, J., Griffin, M., Guo, J. L., Mascharak, S., Guardino, N. J., Longaker, M. T. LIPPINCOTT WILLIAMS & WILKINS. 2023: S13-S14

  View details for Web of Science ID 000989943300035

• Multi-Modal Analysis of Cell Populations and Architectural States Mediating the Progression and Resolution of Pulmonary Fibrosis Guo, J. L., Griffin, M., Guardino, N. J., Abbas, D., Lu, J., Spielman, A., Lintel, H., Cotterell, A. C., Wan, D. C., Longaker, M. T. LIPPINCOTT WILLIAMS & WILKINS. 2022: S82

  View details for Web of Science ID 000867877000204

• Research-driven schistosomiasis mass drug administration campaign in four Tanzanian villages along Lake Victoria Lu, J., Reinhart, P., Kiknadze, N., Kawira, E., Magatti, N., Toole, D., Ariely, S. 2016

  View details for DOI 10.1016/j.aogh.2016.04.392