Extracellular matrix – immune cell interactions Study
We have a postdoctoral position to investigate immune regulatory signals from the extracellular matrix (ECM) that shape infection, inflammation and autoimmunity. Our pioneering work on the ECM of the cornea identified lumican as a major structural protein. Our recent studies indicate that lumican and other related ECM proteins are widely expressed throughout the body where they regulate functions of neutrophils, macrophages, B and T lymphocytes. Lumican-null mice do not resolve bacterial infections of the cornea, lungs, and the peritoneum well. We discovered that lumican enters immune cells and regulates vesicular trafficking of toll-like receptors to modulate their immune signals (Maiti et. al., PNAS, 2021, PMID: 34215697).
The candidate will investigate molecular mechanisms in ECM-immune cell interactions and regulatory gene expression using specific ECM gene targeted mice, ChIP seq and ATAC seq and organoid culture systems. The ideal candidate will have a strong background in immunology, cell biology and next generation sequencing technologies. We expect the candidate to have significant training in cell culture, flow cytometry, mouse immunological techniques and some training in computational biology. The applicant will be expected to work independently and in a collaborative setting.
Keratoconus genetics and cell biology Study
We have a postdoctoral fellowship position to investigate keratoconus, a degenerative disease of the cornea. We are performing whole exome sequencing studies of keratoconus subjects to identify the genetic causes of keratoconus. We have identified genetic variants that regulate oxidative stress, extracellular matrix, primary cilium and cytoskeleton. Planned projects will explore functions of candidate genes and variants using human cornea organoids derived from induced pluripotent stem cell, and genetically altered mouse models. This candidate should have significant training in genetics, computational biology, CRISPR/Cas9 technology, and training in standard cell culture and protein analyses. The ideal candidate should be highly motivated, able to work independently and in a collaborative setting.
Interested candidates should apply by email by sending their current CV and names of three references to Dr. Chakravarti at Shukti.Chakravarti@nyumc.org.
Below are some research topics that may be of interest to potential students.
- Genetic studies of keratoconus on familial and isolated cases using whole genome and exome sequencing approaches.
- Gene editing in induced pluripotent stem cells and development of cornea organoids for functional studies of novel keratoconus variants. These studies will establish functions of novel genes in the cornea and their relevance to corneal diseases.
- ECM-immune cell interactions and their implications in infections and autoimmunity. Lumican, decorin, biglycan and fibromodulin are proteoglycans of the ECM that regulate collagen fibril architecture and interact with immune cells. We have several projects that are ready to address how these proteoglycans interact with immune cells and their consequences on innate and adaptive immunity.