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Department of Biochemistry and Molecular Biology

Houston, Texas

Images from biochemistry and molecular biology research
Verna and Marrs McLean Department of Biochemistry and Molecular Biology
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Zheng Zhou, Ph.D.

Zheng Zhou, Ph.D.

Department of Biochemistry and Molecular Biology


  • Ph.D., Baylor College of Medicine
  • Postdoctoral training: Massachusetts Institute of Technology
  • Postdoctoral fellowships awarded by: Cancer Research Fund of the Damon Runyon-Walter Winchill Foundation, The Medical Foundation Merck/MIT Collaboration Program

Research Interests

Clearance of Apoptotic and Necrotic Cells in the Nematode C. elegans

During an animal's development and adulthood many unwanted cells are eliminated by a process called "programmed cell death" or "apoptosis". Such cells undergo specific changes in appearance, die, and are quickly engulfed and digested by phagocytes, or engulfing cells. In addition, cells die due to injury, disease, or other pathological states, the “necrotic cells”, are also cleared efficiently within animal bodies. The clearance of dying cells is important because dying cells may contain material that, if released, could harm neighboring cells. Inefficient removal of dying cells or incorrect removal of cells that should normally live both result in human diseases. Therefore, understanding the mechanisms that control each step in the process of dying cell clearance has important meanings to biological and medical researches. However, despite the recent burst in the study of cell death mechanisms, the mechanisms behind the removal of dying cells remain largely unknown. My laboratory is interested in the molecular mechanisms that control the recognition, engulfment, and degradation of apoptotic cells. We use the nematode Caenorhabditis elegans as a model organism to identify genes and delineate the pathways controlling these events, with the belief that what we learn from C. elegans will be translated to humans.

Previously, I identified CED-1, a transmembrane C. elegans protein as a phagocytic receptor that is specifically expressed in engulfing cells, recognizes apoptotic cells, and initiates their engulfment. In my own laboratory, we have isolated a large number of C. elegans mutants defective in the removal of apoptotic cells. A combination of both forward and reverse genetic approaches have led us to identify proteins acting upstream or downstream of CED-1 in the signaling pathway, which provide conceptual advances in understanding how apoptotic cells are recognized, internalized, and degraded. Particularly, our research has focused on the following three critical steps that lead to the clearance of dying cells.

I. Recognition

  1. What is the molecular nature of the "eat me" signal(s) presented on the surface of apoptotic cells?
  2. What is the molecular mechanism that leads to the presentation of an “eat me” signal to the surface of apoptotic cells?
  3. How does the phagocytic receptor CED-1 recognize apoptotic cells? Is it through direct binding of the “eat me” signal or through interaction with a “bridging” molecule?
  4. Do phagocytes utilize similar or different mechanisms to recognize necrotic cells and apoptotic cells?

II. Engulfment

  1. How is CED-1 activated by its association with apoptotic cells?
  2. What are the signaling pathways that trigger and regulate the polarized extension of engulfing cell surfaces that embrace the apoptotic cells?
  3. How are the plasma membrane and the actin cytoskeleton underneath it rearranged during cell-surface extension?
  4. How is membrane trafficking involved in the engulfment of apoptotic cells?

III. Degradation

  1. What are the molecular events, in particular membrane trafficking events, that are involved in the phagosome maturation process, which leads to the degradation of apoptotic cells? Organelles in the endocytic pathway, such as early endosomes and lysosomes, are known to fuse with phagosomes and deliver digestive enzymes to phagosomal lumen. All together, how many kinds of intracellular organelles fuse to phagosomes and promote phagosome maturation?
  2. What are the signaling molecules that trigger the recruitment and fusion of intracellular organelles to phagosomes? What are the effectors of these signaling molecules? How do the effectors work on the molecular level?
  3. What are the signaling pathways that promote phagosome maturation? If there are multiple pathways, what is the functional relationship among these pathways?

To answer these questions, we have established effective experimental systems that include forward genetics screens for mutants defective in each one of the three steps of dying cell removal, genetic and molecular analyses of gene functions, and many cell biological tools, in particular the time-lapse fluorescence microscopy technique, which allows us to visualize many subcellular events that occur during the process of dying cell removal in developing C. elegans embryos in real time. The combination of genetic, cell biological, and molecular biological tools has enabled us to discover an “eat me” signal presented on the surface of both apoptotic and necrotic cells for attracting engulfing cells, and multiple proteins that are essential for the engulfment of dying cells. Furthermore, we successfully used these methods identify multiple signaling molecules and their effectors that drive phagosome maturation through a signaling pathway initiated by the activation of CED-1 on nascent phagosomes and mediated by the function of the large GTpase dynamin.

In summary, the recognition, engulfment, and degradation of apoptotic cells are three integral steps in the process of apoptotic-cell removal. C. elegans is a particular good system for studying the molecular mechanisms behind each step due to the existence of powerful tools for genetic and cell biological analyses. Continuing our research using C. elegans as a model organism will allow us to discover the molecular mechanisms that control each cellular event related to the removal of dying cells, and will further provide clues for us to expand our research into the phagocytic removal of other targets, such as invading pathogens.

Apoptotic cells engulfed by phagocytes
Figure 1. Apoptotic cells are engulfed by phagocytes and subsequently digested inside phagosomes in metazoans. (A) A diagram illustrating the process of apoptotic cell engulfment and degradation. (B) The sequential incorporated of early endosomes, late endosomes, and lysosomes to phagosomes drives phagosome maturation.

Time-lapsed recording of the engulfment and degradation of apoptotic cells in C. elegans embroys.
Figure 2. Time-lapsed recording of the engulfment and degradation of apoptotic cells in C. elegans embroys. Time lapse images of the co-expressed CED-1:GFP (a-g) and 2xFYVE:mRFP (h-u) around cell corpse C3 in a wild-type embryo. CED-1::CFP labels pseudopods. allowing the visualization of pseudopod extension and fusion along C3. 2xFYVE::mRFP, a Ptdlns(3)P reporter, labels a phagosome. 2xFYVE::GFP is used here to demonstrate the formation and the gradual shrinkage of a phagosome containing C3. a process that represents phagosome maturation and cargo degradation. 0 min: the time point that the engulfing cell extends pseudopods halfway around C3.

View articles published by Dr. Zhou.

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