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Recent Highlights

Not all foam cells are bad!—AtheroSpectrum story on Circulation, Jan 18th 2022

News at UCONN Today

UConn Researchers Improve Prediction of Heart Attacks

    NiCir–To predict therapeutic response in immunotherapy Patients (JEM, Jan 2022)

    Announcements

      • Congratulations to Alyssa, Lili, and Chuan for your abstracts accepted for presentation at the Scientific Sessions 2020 by the American Heart Association in Nov, 2020. Chuan was selected for an oral presentation on this new research revealed by AtheroSpectrum. Lili and Alyssa were selected for their poster presentation on dynamic B cell function in obesity (Alyssa) and T subset in atherosclerosis (Lili).
      • We are glad to be part of an important study of fatty liver using single-cell seq with Dr. Jiandie Lin's team at U Michigan. Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis. Mol Cell. 2019 Aug 8;75(3):644-660.e5
      • Chuan's presentation at ATVB 2019 received top score and was invited by AHA Scientific Sessions 2019 for re-presentation in Nov, 2019 at Phili.
      • Congratulations on the acceptance of our new publication, "Single-cell transcriptomics based-MacSpectrum reveals novel macrophage activation signatures in diseases," by JCI Insight!
      • Congratulations to Chuan Li and Lili Qu to present at ATVB 2019, Boston MA Chuan also won the competitive Travel Award for Young Scientists (ATVB 2019). Bravo!

      MacSpectrum and MacBrowser

      Macrophage Annotation Programs–MacSpectrum, MacBrowser, AtheroSpectrum

      MacSpectrum (R package)

      MacSpectrum is a macrophage annotation system that allows comprehensive analysis of heterogeneous subpopulations and their multifaceted activation states under various in vitro and in vivo conditions, including the identification of condition-specific signature genes. Each subpopulation identified by MacSpectrum can be further analyzed for cell function and intracellular signaling networks in conjunction with other programs, such as Ingenuity Pathway Analysis by Qiagen, NIH DAVID, and others.

      Citation: Chuan Li, Antoine Menoret, Cullen Farragher, Zhengqing Ouyang, Christopher Bonin, Paul Holvoet, Anthony T. Vella, Beiyan Zhou.  Single cell transcriptomics-based MacSpectrum reveals novel macrophage activation signatures in diseases. JCI insight.  April 16 2019PMID: 30990466

       

      MacBrowser 

      You can check the MPI/AMDI plots and gene expressions of murine bone marrow derived macrophages that were not stimulated (“M0”), or stimulated LPS+IFNγ (“M1”) or IL4+IL13 (“M2”). You can see their MPI/AMDI distributions and expression patterns of any genes. Please refer to our JCI insight publication (PMID: 30990466) for more details of the dataset.

       

       

      AtheroSpectrum (Comming soon)

      AtheroSpectrum Reveals Novel Macrophage Foam Cell Gene Signatures Associated With Atherosclerotic Cardiovascular Disease Risk

      Chuan Li*,  Lili Qu*, Alyssa J. Matz*, Patrick A. MurphyYongmei LiuAni W. ManichaikulDerek AguiarStephen S. RichDavid M. HerringtonDavid VuW. Craig ohnsonJerome I. RotterWendy S. PostAnthony T. VellaAnnabelle Rodriguez-Oquendo, and  Beiyan Zhou#   Originally published 16 Dec 2021https://doi.org/10.1161/CIRCULATIONAHA.121.054285  Circulation. 2022;145:206–218

      To request an R package--please contact us.

      Due to server issues, We have changed the venue for those who want to use MacSpectrum for their research--request the R package

      email:   bzhou@uchc.edu

      You can check out your gene of interest using MacBrowser using the BMDM single cell seq data from our lab. MacSpectrum is a macrophage annotation system that allows comprehensive analysis of heterogeneous subpopulations and their multifaceted activation states under various in vitro and in vivo conditions, including the identification of condition-specific signature genes. Each subpopulation identified by MacSpectrum can be further analyzed for cell function and intracellular signaling networks in conjunction with other programs, such as Ingenuity Pathway Analysis by Qiagen, NIH DAVID, and others.  Further information can be accessed on MacSpectrum with step-by-step instructions. For other functions, and specific questions, please contact us.

      Access MacSpectrum Using the QR Code