Description of Research Expertise

Research Interests
Tube development and epithelial matrix biology in C. elegans

Key words: C. elegans, signaling, genetics, cell biology, epithelia, matrix.


Description of Research
Most of the organs in our body are composed of tubes that transport vital nutrients and waste and serve as important gatekeepers between us and the outside environment. Many diseases are essentially “plumbing problems” in which these tubes clog, leak or collapse.

Our lab’s research utilizes the nematode C. elegans as a model system for studying the mechanisms that build, shape and stabilize epithelial tubes. We are especially interested in the cell biology and developmental roles of the apical extracellular matrix (aECM) that fills the lumen of these tubes.

Model organism research: why we love the worm!
The nematode Caenorhabditis elegans is a multicellular animal perfect for studying “single cell biology” because it has a very simple and well described anatomy that can be visualized by live imaging and that allows phenotypic analysis at single-cell resolution. C. elegans shares many genes and pathways with more complex organisms, and it is highly amenable to powerful forward and reverse genetic approaches to find genes involved in a process of interest. Many novel and conserved aspects of biology have been discovered in this system.

Multicellular Tubes
Most tubes in the body are made up of multiple different cells whose apical surfaces face a common lumen. The shapes and sizes of the individual cells will determine the overall diameter and shape of the tube.

We use the C. elegans vulva to study multi-cellular tube development and shaping. The vulva contains 22 cells arranged to form 7 stacked rings. Cells within each ring have different identities and shapes. Both EGF-Ras-ERK and Notch signaling play important roles in patterning vulva cell fates.

Unicellular Tubes
The tiniest tubes, such as many mammalian capillaries, are unicellular, with the lumen actually inside the cell. More than half of all capillaries in the brain and in the renal glomeruli are unicellular tubes. Capillary defects are associated with cardiovascular diseases, stroke and age-associated dementia, and are a devastating side effect of diabetes, but little is known about how narrow capillaries are formed or protected.

We use the “excretory” or renal-like system of C. elegans as a model system for studying unicellular tubes. This organ system contains 3 unicellular tubes that form in different ways and take on very different shapes.

Some of the questions we're addressing are:

How does auto-fusion promote seamless tube growth and shaping?
Receptor Tyrosine Kinase (RTK) signaling patterns cell fates in most tubular organs. We showed that EGF-Ras-ERK signaling controls many aspects of unicellular tube morphology through a key target, the transmembrane fusogen AFF-1. AFF-1 fuses plasma membranes to convert an autocellular "seamed" tube into a "seamless" tube that lacks adherens junctions or tight junctions along its length. AFF-1 then mediates additional intracellular membrane-merging events that grow and shape the tube – specifically, we’ve proposed that AFF-1 promotes endocytic scission to allow transcytosis of membrane from the basal to apical surfaces (Soulavie et al 2018). We are studying this role of AFF-1 and other vesicle trafficking pathways that allow seamless tubes to adopt very complex, elongated shapes.

How does the luminal extracellular matrix shape and protect tubes?
Most tubes secrete various proteoglycans, glycoproteins and lipoproteins into their developing lumens. Examples in mammals include the vascular glycocalyx, lung surfactant, and the mucus-rich linings of the gut and upper airway. There is a growing appreciation of the importance of this luminal matrix or “aECM” in development and disease. However, relatively little is known about how aECMs assemble within lumens or the mechanisms by which they shape developing tubes. Furthermore, aECMs are very difficult to visualize and study in most systems because they are transparent by light microscopy and destroyed by most standard fixation approaches used for immunofluorescence.

We’ve identified components of an early C. elegans aECM that shapes developing epithelia, including the vulva and excretory duct and pore tubes (Gill, Cohen et al 2016; Cohen et al 2020). Many of these components belong to conserved protein families also found in mammalian ECMs. We can visualize these components in live worms using fluorescent tags inserted into the endogenous loci. We can also visualize the luminal matrix in preserved samples processed for electron microscopy using high pressure freezing. Our foundational studies have shown that the vulva luminal matrix is extremely complex and dynamic, and that the 7 different cell types produce and assemble different parts of this matrix. We are now poised to address many questions related to how the various components traffic to their correct locations and assemble to form these beautiful patterns.

In related studies, we've also identified several types of lipophilic cargo binding proteins that are required to shape and protect the narrow duct and pore tubes, and to prevent them from bursting or leaking. We've also identified suppressor mutations that "fix" these tube problems. Current studies are examining links between lipid transporters and luminal matrix organization.

What controls cuticle collagen matrix assembly?
C. elegans external epithelia eventually become coated by a cuticle or exoskeleton that is different than the earlier "pre-cuticle" matrix present during tissue morphogenesis. The cuticle is primarily made up of collagens, but these collagens are quite different than the highly studied vertebrate Type I collagen - instead they have interesting similarities to the relatively understudied vertebrate transmembrane collagens. We are beginning to study the maturation of these collagens during assembly of the first cuticle and the pre-cuticle to cuticle transition (Birnbaum et al 2023).

How are complex aECM structures shaped in the extracellular environment?
Animal surfaces are often decorated with intricately shaped structures such as denticles, ridges, or scales that are composed of extracellular matrix materials. We are using C. elegans cuticle ridges or "alae" to understand how extracellular materials get sculpted into appropriate shapes. Alae development begins when long actin filament bundles form beneath the apical plasma membrane; these are required to pattern the transient pre-cuticle matrix, which then patterns the cuticle matrix (Katz, Barker et al 2022). We are studying actin-binding proteins that we think mechanically link the actin cytoskeleton to the overlying matrix to cause local matrix delaminations that initiate ridge formation.


Lab personnel:
Prioty Sarwar (postdoctoral fellow)
Helen Schmidt (postdoctoral fellow)
Nick Serra (postdoctoral fellow)
Chelsea Darwin (research specialist)


Lab alums: Where are they now?

graduate students
Robyn Howard-Barfield (1999-2004), now Group Leader at Catalent Pharma
Craig Stone (2003-2008), now Principal Medical writer at Medtronic
Kelly Howell (2004-2010), now Scientist at SMA Foundation
Vincent Mancuso (2006-2011), now Coordinator of English Learning Center, Catholic Charities, Camden NJ
Ishmail Abdus-Saboor (2007-2012), now faculty at Columbia U.
Jennifer Cohen (2015-2020), now postdoc at Harvard U.

postdoctoral fellows
Ranjana Kishore (1998-2002), now Staff Scientist at Caltech
Gautam Kao (1999-2003), now Researcher at Gothenburg U. (Sweden)
Kyunghee Koh (2001-2003), now faculty at Jefferson U.
Chris Rocheleau (2000-2005), now faculty at McGill U.
David Raizen (2001-2007), now faculty at UPenn
Olena Vatamaniuk (2004-2005), now faculty at Cornell U.
Jean Parry (2010-2014), now faculty at Georgian U.
Pu (Emily) Pu (2012-2017), now Group Leader at Innovent Biologics (China)
Fabien Soulavie (2013-2018), now Researcher at IBDM, Marseille (France)

technical staff
Nathaniel Dudley: PhD, UNC
David Garbe: PhD, UPenn
Laura Sherritt Girard: biotech industry
Jeff Doto: MCIT, UPenn
Yelena Bernstein: PharmD, Temple U.
Priti Batta: MD, Albert Einstein
Kelly Kraus: VMD, UPenn
Anne-Marie McKnight: MPH/PhD, Johns Hopkins
Kevin Cullison: MD, St Louis U.
Ariel Junio: biotech industry
Kate Palozola: PhD, UPenn
Brian Gantick: web design
Jennifer Cohen: PhD, UPenn
Hasreet Gill: PhD, Harvard
Rachel Forman-Rubinsky: in PhD program, U. Pittsburgh
Alessandro Sparacio: computer software co.
Alexandra Belfi: in MD program, Vanderbilt
Susanna Birbaum: in Genetic counseling masters program, UPenn
Trevor Barker: in MD program, Albert Einstein