About

Dominique Alfandari is a Professor in the Department of Veterinary and Animal Sciences at the University of Massachusetts Amherst. His research focuses on how the face of vertebrate embryos is built, primarily studying Cranial Neural Crest Cells (CNC), which are induced at the border of the neural plate and migrate ventrally to produce facial bones, cartilage, muscles, and ganglia. His laboratory is currently funded by a grant from the NIH to produce and characterize monoclonal antibodies to Xenopus, Axolotl, and Mouse proteins, in collaboration with colleagues such as Dr. Catherine McCusker. Dr. Alfandari's work includes investigating the roles of ADAM proteins in early embryogenesis, particularly how non-proteolytic ADAMs contribute to developmental processes. His team has identified ADAM11 as a novel regulator of Wnt and BMP4 signaling pathways in neural crest cells and cancer. His research also explores how Adam13 influences gene expression by regulating histone modifications, chromatin availability, and transcription factor binding, affecting gene expression and splicing in cranial neural crest cells. His contributions have advanced understanding of the molecular mechanisms underlying craniofacial development and neural crest cell regulation.

Research topics

• Biology
• Cell biology
• Genetics
• Anatomy
• Immunology
• Cancer research

Selected publications

• Bacterial ubiquitin ligase engineered for small molecule and protein target identification

  The EMBO Journal · 2026-01-03

  articleOpen access

  The Legionella SidE effectors ubiquitinate host proteins independently of the canonical E1-E2 cascade. Here we engineer the SidE ligases to develop a modular proximity ligation approach for the identification of targets of small molecules and proteins, which we call SidBait. We validate the method with known small molecule-protein interactions and use it to identify CaMKII as an off-target interactor of the breast cancer drug ribociclib. Structural analysis and activity assays confirm that ribociclib binds the CaMKII active site and inhibits its activity. We further customize SidBait to identify protein-protein interactions and discover the F-actin capping protein (CapZ) as a target of the Legionella effector RavB during infection. Structural and biochemical studies indicate that RavB allosterically binds CapZ and decaps actin, thus functionally mimicking eukaryotic CapZ interacting proteins. Collectively, our results establish SidBait as a reliable tool for identifying targets of small molecules and proteins.

  PublisherOA PDFDOI

• Planar polarization of endogenous ADIP during <i>Xenopus</i> neurulation

  Biology Open · 2026-01-28

  articleOpen access

  Coordinated cell polarity and force-responsive protein localization are essential for tissue morphogenesis, yet how embryonic cells sense forces and respond to mechanical cues remains a challenging question. Afadin- and α-actinin-binding protein (ADIP) has been implicated in microtubule minus-end anchoring, centrosome maturation and ciliogenesis. ADIP is also proposed to associate with the actomyosin cortex and regulate collective cell migration. ADIP behaves as a mechanosensitive planar cell polarity (PCP) protein when overexpressed in Xenopus embryos, but the distribution and regulation of endogenous ADIP has been unknown. Here we show that ADIP is present in early ectoderm as randomly distributed puncta that rapidly reorganize and polarize during epithelial wound repair. Endogenous ADIP also becomes enriched and planar polarized in the anterior neural plate towards the midline, consistent with its regulation by mechanical forces that operate during neural tube closure. ADIP polarization is attenuated by depletion of the core PCP component Diversin/Ankrd6, in agreement with the proposed interaction between the two proteins during PCP establishment. Finally, pharmacological disruption of microtubules, F-actin, and nonmuscle myosin II eliminates ADIP polarization in the neuroectoderm, indicating roles for microtubules and actomyosin networks in PCP. Together, these findings suggest that endogenous ADIP senses mechanical cues via the cytoskeletal machinery and functions in a context-dependent manner to control collective cell behaviors during vertebrate morphogenesis.

  PublisherOA PDFDOI

• Immune response in breastmilk of Black women to SARS-CoV-2 infection and vaccination against COVID-19

  Frontiers in Nutrition · 2026-01-12

  articleOpen access

  Introduction: In the United States, Black lactating women are underrepresented in health-related studies. This underrepresentation is a concern when interpreting results from studies of the immune response to SARS-CoV-2 in breastmilk because we know that individuals vary greatly in their response to both infection and vaccination. Additionally, few studies of the immune response in human milk include analysis of mammary epithelium permeability, despite the knowledge that elevated permeability can alter constituents in milk. To address these gaps, we enrolled local Black breastfeeding mothers during a 3-day breastfeeding conference in New Orleans to assess the immune response in milk to infection or vaccination with SARS-CoV-2. Materials and methods: = 16) received kits with instructions to collect bilateral milk samples, dried blood spots (DBS), and saliva. Concentrations of anti-SARS-CoV-2 antibodies against both the Wuhan and Omicron variants were determined in milk, DBS, and saliva using the ELISA test. The concentration of a panel of cytokines was determined in milk, and the permeability of the mammary gland was assessed. Results: Among the 16 lactating women who provided samples, 8 had a positive COVID-19 test within the previous 19 months, and 12 had received an mRNA-based COVID-19 vaccine within the previous 16 months. Milk and maternal blood spots from all participants were positive for all anti-SARS-CoV-2 antibody classes tested, while only a subset of saliva samples were positive for all anti-SARS-CoV-2 antibody classes. A significant correlation was found between mammary epithelium permeability and concentrations of IL-1β, IL-6, and IL-8 cytokines. Conclusion: Results from this small pilot study supported the need to include a diverse population in breastmilk studies, as the immune response in milk varied greatly among individuals. Future studies assessing the response to infections and vaccinations in lactating women should include analysis of milk from both breasts, as well as assessment of mammary epithelium permeability.

  PublisherOA PDFDOI

• Planar polarization of endogenous ADIP during <i>Xenopus</i> neurulation

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-15

  article

  Abstract Coordinated cell polarity and force-responsive protein localization are essential for tissue morphogenesis, yet how embryonic cells sense forces and respond to mechanical cues remains a challenging question. Afadin- and alpha-actinin-binding protein (ADIP) has been implicated in microtubule minus-end anchoring, centrosome maturation and ciliogenesis. ADIP is also proposed to associate with the actomyosin cortex and regulate collective cell migration. ADIP behaves as a mechanosensitive planar cell polarity (PCP) protein when overexpressed in Xenopus embryos, but the distribution and regulation of endogenous ADIP has been unknown. Here we show that ADIP is present in early ectoderm as randomly distributed puncta that rapidly reorganize and polarize during epithelial wound repair. Endogenous ADIP also becomes enriched and planar polarized in the anterior neural plate towards the midline, consistent with its regulation by mechanical forces that operate during neural tube closure. ADIP polarization is attenuated by depletion of the core PCP component Diversin/Ankrd6, in agreement with the proposed interaction between the two proteins during PCP establishment. Finally, pharmacological disruption of microtubules, F-actin, and nonmuscle myosin II eliminates ADIP polarization in the neuroectoderm, indicating roles for microtubules and actomyosin networks in PCP. Together, these findings suggest that endogenous ADIP senses mechanical cues via the cytoskeletal machinery and functions in the context-dependent manner to control collective cell behaviors during vertebrate morphogenesis.

  PublisherDOI

• Spinal cord regeneration in <i>Xenopus</i>

  Research Explorer (The University of Manchester) · 2026-01-27

  article

  After an injury, adult mammals do not regenerate or repair their central nervous system in general, and their spinal cord in particular, leading to life-long disabilities. However, many aquatic species such as zebrafish, salamanders and frogs as well as some land reptiles (turtles and lizard) have the remarkable ability to regenerate their spinal cords. In the case of anurans such as Xenopus, this is a transient ability that disappears after metamorphosis, making it an interesting model with accessible regenerative and non-regenerative stages within the same species. Here, we will summarise our current understanding of the mechanisms that underly spinal cord regeneration in Xenopus tadpoles and describe methods to study changes in cellular state after different paradigms of spinal cord injury.

  Publisher

• Delamination of chick cephalic neural crest cells requires an MMP14-dependent downregulation of Cadherin-6B

  Differentiation · 2025-01-15 · 1 citations

  articleOpen access

  Matrix Metalloproteinases (MMPs) are known for their role in matrix remodeling via their catalytic activities in the extracellular space. Interestingly, these enzymes can also play less expected roles in cell survival, polarity and motility via other substrates (e.g. receptors, chemokines), through an intracellular localization (e.g. the nucleus) or via non-catalytic functions. Most of these unconventional functions are yet to be functionally validated in a physiological context. Here, we used the delamination of the cephalic Neural Crest (NC) cells of the chicken embryo, a well described experimental model of epithelial-mesenchymal transition (EMT), to study the in vivo function of MMP14 (a.k.a MT1-MMP). MMP14 is a transmembrane MMP known for its importance in cell invasion and often associated with poor prognosis in cancer. We found that MMP14 is expressed and required for cephalic NC delamination. More specifically, MMP14 is necessary for the downregulation of Cadherin-6B and a co-inhibition of Cadherin-6B and MMP14 expressions is sufficient to restore NC delamination. Cadherin-6B is normally repressed by Snail2. Surprisingly, in MMP14 knockdown this lack of Cadherin-6B repression occurs in the context of a normal expression and nuclear import of Snail2. We further show that MMP14 is not detected in the nucleus and that Snail2 and MMP14 do not physically interact. These data reveals that a yet to be identified MMP14-dependent signaling event is required for the Snail2-dependent repression of Cadherin-6B. In conclusion, this work provides an in vivo example of atypical regulation of Cadherins by an MMP which emphasizes the importance and diversity of non-canonical functions of MMPs.

  PublisherDOI

• ADAM Proteins Bridge Extracellular Signals and Epigenetic Control to Regulate Gene Expression in Cranial Neural Crest Cells

  SSRN Electronic Journal · 2025-01-01

  preprintOpen accessSenior author
  PublisherDOI

• Bacterial ubiquitin ligase engineered for small molecule and protein target identification

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-22 · 1 citations

  preprintOpen access

  Abstract The Legionella SidE effectors ubiquitinate host proteins independently of the canonical E1-E2 cascade. Here we engineer the SidE ligases to develop a modular proximity ligation approach for the identification of targets of small molecules and proteins, which we call SidBait. We validate the method with known small molecule-protein interactions and use it to identify CaMKII as an off-target interactor of the breast cancer drug ribociclib. Structural analysis and activity assays confirm that ribociclib binds the CaMKII active site and inhibits its activity. We further customize SidBait to identify protein-protein interactions, including substrates for enzymes, and discover the F-actin capping protein (CapZ) as a target of the Legionella effector RavB during infection. Structural and biochemical studies indicate that RavB allosterically binds CapZ and decaps actin, thus functionally mimicking eukaryotic CapZ interacting proteins. Collectively, our results establish SidBait as a reliable tool for identifying targets of small molecules and proteins.

  PublisherOA PDFDOI

• Mechanical cues polarize ADIP protein complexes to control vertebrate morphogenesis and wound healing

  Current Biology · 2025-06-24 · 5 citations

  articleOpen access
  PublisherOA PDFDOI

• A Dapl1+ subpopulation of naive CD8 T cells contains committed precursors of memory lineage.

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-08 · 2 citations

  preprint

  Memory CD8 T cells play a vital role in providing lasting immune protection, yet their origins remain incompletely understood. Contrary to classical models, emerging evidence suggests that heterogeneity within the naive T cell pool may influence fate decisions prior to antigen encounter. However, the markers of naive T cell heterogeneity have not yet been clearly defined. Here, we describe intraclonal heterogeneity within the naive T cell population marked by the protein Dapl1. Using novel monoclonal antibodies and a reporter-knockout mouse model, we found that Dapl1-positive naive CD8 T cells exhibit distinct phenotypes compared to their Dapl1-negative counterparts. Furthermore, this population includes a subset of pre-programmed precursors biased toward memory lineage fate. The differentiation of these precursors is independent of Dapl1 but relies on the transcription factor Bcl11b, resulting in the generation of Dapl1-positive central memory-like CD8 T cells in response to infection, and stem-like memory cells in response to cancer. Notably, naive Dapl1-positive T cells originate in the thymus among mature thymocytes and gradually appear in the periphery within several days after birth. Our findings suggest that committed memory precursors in the Dapl1-positive population may represent an alternative pathway for memory CD8 T cell generation, offering new avenues for therapeutic application.

  PublisherDOI

Recent grants

• Production and characterization of monoclonal antibodies to Xenopus Proteins

  NIH · $1.2M · 2017–2023

• Mechanism of Cranial Neural Crest Cell Migration

  NIH · $5.4M · 2006–2024

• Six1 Co-factors in Craniofacial Development

  NIH · $1.9M · 2018–2024

Frequent coauthors

• Hélène Cousin

  41 shared

• Thierry Darribère

  Sorbonne Université

  28 shared

• Philip J. Johnson

  26 shared

• Samuel J. Black

  Temple University Hospital

  25 shared

• James K. Belknap

  The Ohio State University

  25 shared

• Kathleen F. Arcaro

  University of Massachusetts Amherst

  21 shared

• Alban Gaultier

  University of Virginia

  21 shared

• Sallie S. Schneider

  Baystate Medical Center

  21 shared

Labs

• Alfandari DPI

Awards & honors

• Predoctoral fellowship MRT 1991-1994
• Postdoctoral fellowship FRM 1995-1996
• NIH RO1DE14365 (2001-2006)
• NIH RO1DE16289 (2006-2023)
• NSF 0544015 (2005-2008)