Download Curriculum Vitae

The focus of my current research is to understand mechanisms of cellular signaling at the level of the primary cilia, and its relevance to human health and disease. As a starting assistant professor at the Department of Cell Biology at UT Southwestern, my current and future research aims at utilizing a variety of biochemical, cell biological, and reverse genetic approaches to investigate signaling pathways mediated by cilia, and to dissect their role during normal development and disease. During my graduate years in Dr. Piali Sengupta’s lab at Brandeis University, I utilized C. elegans to study the mechanisms that determine the distinctive ciliary morphology of their sensory neurons, and discovered that the membrane architecture of the olfactory sensory cilia is patterned by coincidental signaling inputs. In my postdoctoral years in Dr. Peter Jackson’s lab in Genentech, I used high-confidence proteomic approaches to study ciliary signaling pathways. In particular, our identification of the tubby family protein Tulp3 as an effector of the ciliary intraflagellar complex A (IFT-A), and in regulating ciliary G protein-coupled receptor (GPCR) trafficking provides intriguing insights into molecular mechanisms regulating ciliary function in diverse processes, such as in sonic hedgehog (Shh) signaling during neural tube development and in neuronal control of obesity. Most importantly, we have identified a novel Tulp3/IFT-A–regulated ciliary GPCR, Gpr161 that acts as a negative regulator of Shh signaling in the neural tube via cAMP signaling.

            Currently, we are determining mechanisms underlying trafficking of signaling molecules in and out of cilia and the phenotypes resulting from changes in ciliary trafficking. In addition, we are heavily invested in understanding the role of primary cilia at an organismal level. To this end, we are determining the role of primary cilia signaling in limb and skeletal development, polycystic kidney disease, neural tube defects, and tumorigenesis. Our results demonstrate that basal suppression of the downstream hedgehog pathway by Gpr161, even in the absence of morphogen is critical in regulating limb/skeletal development and cerebellar tumorigenesis. Overall, our expertise in Shh signaling and its regulation by cilia, our demonstrated strengths in utilizing a multi-pronged approach including proteomics, cell biology, and reverse genetics to discover novel Shh pathway regulators, including the discovery of the Tulp3-Gpr161 axis, and further engineering of conditional knock out and knock in alleles targeting these factors, uniquely position us to determine the role of basal suppression of Shh signaling in these diverse processes. Finally, the collaborative nature of research and the strong focus on translational biomedical research at UT Southwestern is instrumental for studying these diverse developmental paradigms aiming at understanding the role of primary cilia in development and disease.


(1998), Medicine
Medical School
Banaras Hindu University (2002), Medicine
Graduate School
Brandeis University (2008), Biology

Research Interest

  • Ciliary signaling pathways
  • Functional proteomics in ciliary diseases  
  • Primary cilia in normal development and cancer


Featured Publications LegendFeatured Publications

Cellular signalling by primary cilia in development, organ function and disease.
Anvarian Z, Mykytyn K, Mukhopadhyay S, Pedersen LB, Christensen ST Nat Rev Nephrol 2019 Feb
Dominant negative GPR161 rare variants are risk factors of human spina bifida.
Kim SE, Lei Y, Hwang SH, Wlodarczyk BJ, Mukhopadhyay S, Shaw GM, Elizabeth Ross M, Finnell RH Hum. Mol. Genet. 2018 Sep
Using Primary Neurosphere Cultures to Study Primary Cilia.
Shimada IS, Badgandi H, Somatilaka BN, Mukhopadhyay S J Vis Exp 2017 Apr 122
G-protein-coupled receptor signaling and neural tube closure defects.
Shimada IS, Mukhopadhyay S Birth Defects Res. Part A Clin. Mol. Teratol. 2016 Oct
TCTEX1D2, a potential link to skeletal ciliopathies.
Mukhopadhyay S Cell Cycle 2015 Jan 0
Studying G protein-coupled receptors: immunoblotting, immunoprecipitation, phosphorylation, surface labeling, and cross-linking protocols.
Pal K, Badgandi H, Mukhopadhyay S Methods Cell Biol. 2015 127 303-22
G-protein-coupled receptors and localized signaling in the primary cilium during ventral neural tube patterning.
Hwang SH, Mukhopadhyay S Birth Defects Res. Part A Clin. Mol. Teratol. 2014 Jun
Primary cilium and sonic hedgehog signaling during neural tube patterning Role of GPCRs and Second Messengers.
Pal K, Mukhopadhyay S Dev Neurobiol 2014 May
Cilia, tubby mice, and obesity.
Mukhopadhyay S, Jackson PK Cilia 2013 Jan 2 1 1
An ARL3-UNC119-RP2 GTPase cycle targets myristoylated NPHP3 to the primary cilium.
Wright KJ, Baye LM, Olivier-Mason A, Mukhopadhyay S, Sang L, Kwong M, Wang W, Pretorius PR, Sheffield VC, Sengupta P, Slusarski DC, Jackson PK Genes Dev. 2011 Nov 25 22 2347-60

Honors & Awards

  • Alex Lemonade Stand Foundation A-grant awardee
  • W.W. Caruth, Jr. Scholar in Biomedical Research
    Endowed scholar, UT Southwestern (2013)
  • CPRIT Scholar in Cancer Research

Professional Associations/Affiliations

  • Member, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center. (2013)
  • American Society for Cell Biology. (2005)