Bokai Zhu

All Publications

• Robust single-cell matching and multimodal analysis using shared and distinct features. Nature methods Zhu, B., Chen, S., Bai, Y., Chen, H., Liao, G., Mukherjee, N., Vazquez, G., McIlwain, D. R., Tzankov, A., Lee, I. T., Matter, M. S., Goltsev, Y., Ma, Z., Nolan, G. P., Jiang, S. 2023

  Abstract

  The ability to align individual cellular information from multiple experimental sources is fundamental for a systems-level understanding of biological processes. However, currently available tools are mainly designed for single-cell transcriptomics matching and integration, and generally rely on a large number of shared features across datasets for cell matching. This approach underperforms when applied to single-cell proteomic datasets due to the limited number of parameters simultaneously accessed and lack of shared markers across these experiments. Here, we introduce a cell-matching algorithm, matching with partial overlap (MARIO) that accounts for both shared and distinct features, while consisting of vital filtering steps to avoid suboptimal matching. MARIO accurately matches and integrates data from different single-cell proteomic and multimodal methods, including spatial techniques and has cross-species capabilities. MARIO robustly matched tissue macrophages identified from COVID-19 lung autopsies via codetection by indexing imaging to macrophages recovered from COVID-19 bronchoalveolar lavage fluid by cellular indexing of transcriptomes and epitopes by sequencing, revealing unique immune responses within the lung microenvironment of patients with COVID.

  View details for DOI 10.1038/s41592-022-01709-7

  View details for PubMedID 36624212

• Spatial epitope barcoding reveals clonal tumor patch behaviors. Cancer cell Rovira-Clave, X., Drainas, A. P., Jiang, S., Bai, Y., Baron, M., Zhu, B., Dallas, A. E., Lee, M. C., Chu, T. P., Holzem, A., Ayyagari, R., Bhattacharya, D., McCaffrey, E. F., Greenwald, N. F., Markovic, M., Coles, G. L., Angelo, M., Bassik, M. C., Sage, J., Nolan, G. P. 2022

  Abstract

  Intratumoral heterogeneity is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are still largely unsuitable to accurately track phenotypes and clonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitopes for imaging using combinatorial tagging (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using EpicMIBI, we dissected the spatial component of cell lineages and phenotypes in xenograft models of small cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of clonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in these models. In a tumor model harboring a fraction of PTEN-deficient cancer cells, we observed a non-autonomous increase of clonal patch size in PTEN wild-type cancer cells. EpicMIBI facilitates in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity.

  View details for DOI 10.1016/j.ccell.2022.09.014

  View details for PubMedID 36240778

• Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments. Immunity Jiang, S., Chan, C. N., Rovira-Clave, X., Chen, H., Bai, Y., Zhu, B., McCaffrey, E., Greenwald, N. F., Liu, C., Barlow, G. L., Weirather, J. L., Oliveria, J. P., Nakayama, T., Lee, I. T., Matter, M. S., Carlisle, A. E., Philips, D., Vazquez, G., Mukherjee, N., Busman-Sahay, K., Nekorchuk, M., Terry, M., Younger, S., Bosse, M., Demeter, J., Rodig, S. J., Tzankov, A., Goltsev, Y., McIlwain, D. R., Angelo, M., Estes, J. D., Nolan, G. P. 2022

  Abstract

  Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.

  View details for DOI 10.1016/j.immuni.2022.03.020

  View details for PubMedID 35447093

• Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers. Cell reports. Medicine Nakayama, T., Lee, I. T., Jiang, S., Matter, M. S., Yan, C. H., Overdevest, J. B., Wu, C., Goltsev, Y., Shih, L., Liao, C., Zhu, B., Bai, Y., Lidsky, P., Xiao, Y., Zarabanda, D., Yang, A., Easwaran, M., Schurch, C. M., Chu, P., Chen, H., Stalder, A. K., McIlwain, D. R., Borchard, N. A., Gall, P. A., Dholakia, S. S., Le, W., Xu, L., Tai, C., Yeh, T., Erickson-Direnzo, E., Duran, J. M., Mertz, K. D., Hwang, P. H., Haslbauer, J. D., Jackson, P. K., Menter, T., Andino, R., Canoll, P. D., DeConde, A. S., Patel, Z. M., Tzankov, A., Nolan, G. P., Nayak, J. V. 2021: 100421

  Abstract

  Understanding viral tropism is an essential step towards reducing SARS-CoV-2 transmission, decreasing mortality from COVID-19, and limiting opportunities for mutant strains to arise. Currently, little is known about the extent to which distinct tissue sites in the human head & neck region and proximal respiratory tract selectively permit SARS-CoV-2 infection and replication. In this translational study, we discover key variabilities in the expression of ACE2 and TMPRSS2, essential SARS-CoV-2 entry factors, among the mucosal tissues of the human proximal airways. We show that SARS-CoV-2 infection is present in all examined head & neck tissues, with a notable tropism for the nasal cavity and tracheal mucosa. Finally, we uncover an association between smoking and higher SARS-CoV-2 viral infection in the human proximal airway, which may explain the increased susceptibility of smokers to developing severe COVID-19. This is at least partially explained by differences in IFN-beta1 levels between smokers and non-smokers.

  View details for DOI 10.1016/j.xcrm.2021.100421

  View details for PubMedID 34604819

• Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging. Nature communications Rovira-Clave, X., Jiang, S., Bai, Y., Zhu, B., Barlow, G., Bhate, S., Coskun, A. F., Han, G., Ho, C. K., Hitzman, C., Chen, S., Bava, F., Nolan, G. P. 2021; 12 (1): 4628

  Abstract

  Simultaneous visualization of the relationship between multiple biomolecules and their ligands or small molecules at the nanometer scale in cells will enable greater understanding of how biological processes operate. We present here high-definition multiplex ion beam imaging (HD-MIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added structurally-unmodified small molecules. With this technology, the atomic constituents of the biomolecules themselves can be used in our system as the "tag" and we demonstrate measurements down to ~30nm lateral resolution. We correlated the subcellular localization of the chemotherapy drug cisplatin simultaneously with five subnuclear structures. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. Unexpectedly, cells surviving multi-drug treatment with cisplatin and the BET inhibitor JQ1 demonstrated near total cisplatin exclusion from the nucleus, suggesting that selective subcellular drug relocalization may modulate resistance to this important chemotherapeutic treatment. Multiplexed high-resolution imaging techniques, such as HD-MIBI, will enable studies of biomolecules and drug distributions in biologically relevant subcellular microenvironments by visualizing the processes themselves in concert, rather than inferring mechanism through surrogate analyses.

  View details for DOI 10.1038/s41467-021-24822-1

  View details for PubMedID 34330905

• SARS-CoV-2 infects human pancreatic beta cells and elicits beta cell impairment. Cell metabolism Wu, C., Lidsky, P. V., Xiao, Y., Lee, I. T., Cheng, R., Nakayama, T., Jiang, S., Demeter, J., Bevacqua, R. J., Chang, C. A., Whitener, R. L., Stalder, A. K., Zhu, B., Chen, H., Goltsev, Y., Tzankov, A., Nayak, J. V., Nolan, G. P., Matter, M. S., Andino, R., Jackson, P. K. 2021

  Abstract

  Emerging evidence points toward an intricate relationship between the pandemic of coronavirus disease 2019 (COVID-19) and diabetes. While preexisting diabetes is associated with severe COVID-19, it is unclear whether COVID-19 severity is a cause or consequence of diabetes. To mechanistically link COVID-19 to diabetes, we tested whether insulin-producing pancreatic beta cells can be infected by SARS-CoV-2 and cause beta cell depletion. We found that the SARS-CoV-2 receptor, ACE2, and related entry factors (TMPRSS2, NRP1, and TRFC) are expressed in beta cells, with selectively high expression of NRP1. We discovered that SARS-CoV-2 infects human pancreatic beta cells in patients who succumbed to COVID-19 and selectively infects human islet beta cells invitro. We demonstrated that SARS-CoV-2 infection attenuates pancreatic insulin levels and secretion and induces beta cell apoptosis, each rescued by NRP1 inhibition. Phosphoproteomic pathway analysis of infected islets indicates apoptotic beta cell signaling, similar to that observed in type 1 diabetes (T1D). In summary, our study shows SARS-CoV-2 can directly induce beta cell killing.

  View details for DOI 10.1016/j.cmet.2021.05.013

  View details for PubMedID 34081912

• SARS-CoV-2 entry factors are expressed in nasal, ocular, and oral tissues: implications for COVID-19 prophylaxes/therapeutics Lee, I., Nakayama, T., Jiang, S., Goltsev, Y., Schurch, C., Zhu, B., McIlwain, D., Chu, P., Chen, H., Tzankov, A., Matter, M., Nayak, J., Nolan, G. MOSBY-ELSEVIER. 2021: AB2

  View details for Web of Science ID 000629158000005

• Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images. Frontiers in immunology Bai, Y., Zhu, B., Rovira-Clave, X., Chen, H., Markovic, M., Chan, C. N., Su, T., McIlwain, D. R., Estes, J. D., Keren, L., Nolan, G. P., Jiang, S. 2021; 12: 652631

  Abstract

  Multiplex imaging technologies are now routinely capable of measuring more than 40 antibody-labeled parameters in single cells. However, lateral spillage of signals in densely packed tissues presents an obstacle to the assignment of high-dimensional spatial features to individual cells for accurate cell-type annotation. We devised a method to correct for lateral spillage of cell surface markers between adjacent cells termed REinforcement Dynamic Spillover EliminAtion (REDSEA). The use of REDSEA decreased contaminating signals from neighboring cells. It improved the recovery of marker signals across both isotopic (i.e., Multiplexed Ion Beam Imaging) and immunofluorescent (i.e., Cyclic Immunofluorescence) multiplexed images resulting in a marked improvement in cell-type classification.

  View details for DOI 10.3389/fimmu.2021.652631

  View details for PubMedID 34295327

• Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell Ji, A. L., Rubin, A. J., Thrane, K. n., Jiang, S. n., Reynolds, D. L., Meyers, R. M., Guo, M. G., George, B. M., Mollbrink, A. n., Bergenstråhle, J. n., Larsson, L. n., Bai, Y. n., Zhu, B. n., Bhaduri, A. n., Meyers, J. M., Rovira-Clavé, X. n., Hollmig, S. T., Aasi, S. Z., Nolan, G. P., Lundeberg, J. n., Khavari, P. A. 2020

  Abstract

  To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.

  View details for DOI 10.1016/j.cell.2020.05.039

  View details for PubMedID 32579974

• Mass spectroscopy-based highly multiplexed super-resolution imaging method for fine details of tumor microenvironment monitoring and tumor-immune cell interactions Bai, Y., Zhu, B., Angelo, M., Zhao, Y., Jiang, S., Clave, X., Nolan, G. BMC. 2019

  View details for Web of Science ID 000496473200452

• Mapping the spatial architecture of acute myeloid leukemia in the bone marrow microenvironment by multiplexed ion beam imaging Rovira-Clave, X., Jiang, S., Bai, Y., Zhu, B., Bosse, M., Angelo, M., Banz, Y., Schurch, C., Nolan, G. BMC. 2019

  View details for Web of Science ID 000496473200424

• Multiplexed Imaging for the simultaneous detection of nucleic acids and proteins to dissect the tissue immune landscape and microenvironment of viral diseases Jiang, S., Clave, X., Chan, C., Zhu, B., Bai, Y., Bosse, M., McIlwain, D., Bendall, S., Angelo, M., Estes, J., Nolan, G. BMC. 2019

  View details for Web of Science ID 000496473200465

• Microbiome spatial patterns as markers of cancer immune therapy response Zhu, B., Bai, Y., Jiang, S., Rovira-Clave, X., Sonnenburg, J., Nolan, G. BMC. 2019

  View details for Web of Science ID 000496473200251

• Exposure to nanoplastics disturbs the gut microbiome in the soil oligochaete Enchytraeus crypticus ENVIRONMENTAL POLLUTION Zhu, B., Fang, Y., Zhu, D., Christie, P., Ke, X., Zhu, Y. 2018; 239: 408–15

  Abstract

  Microplastics are emerging pollutants that have recently aroused considerable concern but most toxicological studies have focused on marine biota, with little investigation of the influence of microplastics on terrestrial ecosystems. Here, we fed the soil oligochaete Enchytraeus crypticus with oatmeal containing 0, 0.025, 0.5, and 10% (dry weight basis) nano-polystyrene (0.05-0.1 μm particle size) to elucidate the impact of microplastics on the growth and gut microbiome of Enchytraeus crypticus. We observed a significant reduction of weight in the animals fed 10% polystyrene and an increase in the reproduction of those fed 0.025%. More importantly, using 16S rRNA amplification and high-throughput sequencing we found a significant shift in the microbiome of those fed 10% microplastics with significant decreases in the relative abundance of the families Rhizobiaceae, Xanthobacteraceae and Isosphaeraceae. These families contain key microbes that contribute to nitrogen cycling and organic matter decomposition.

  View details for DOI 10.1016/j.envpol.2018.04.017

  View details for Web of Science ID 000434744800042

  View details for PubMedID 29679938