Projects

Temporal coordination of stimulus response kinetics by RNA-Binding Proteins

Current projects:

Musashi and ZFP36L2

What is the mechanism by which these RBPs regulate target mRNA translation and/or decay?
How do Musashi/ZFP36L2-RNA interaction dynamics change in response to AngII stimulation?
How do this stimulus induced Musashi/ZFP36L2-RNA remodeling alter target mRNA regulation?

TRUB1

What are the RNA targets pseudouridylated by TRUB1 that are important for aldosterone production?
How does TRUB1 regulate target RNA outcomes?

Human adrenal steroidogenesis is an ideal model to study how dynamic RBP-RNA regulatory interactions temporally coordinate stimulus-induced gene expression. We recently discovered that RBPs and regulated RNA decay control AngII-stimulated expression kinetics to facilitate normal aldosterone production (see figure below).

Relevant publications:

Walters K, Sajek MP, Issaian A, Baldwin A, Harrison E, Murphy E, Daniels M, Haines J, Hansen K, D’Alessandro A, Mukherjee N. Small-molecule Ro-08-2750 interacts with many RNA-binding proteins and elicits MUSASHI2-independent phenotypes. RNA 2023.

Fu R*, Wellman K*, Baldwin A, Rege J, Walthers K, Riemondy K, Rainey WR, Mukherjee N. RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells. RNA 2021.

Wellman K*, Fu R*, Baldwin A, Rege J, Murphy E, Rainey WR, Mukherjee N. Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli. Cells 2021.

RBP-driven regulation of steroidogenesis and physiology

Although cell culture models are invaluable for dissecting molecular mechanisms and the kinetics of gene expression, they lack feedback and feedforward circuits inherent to endocrine systems and crucial for understanding physiology. Therefore, we are utilizing mouse models to explore how RBPs control hormone production in steroidogenic tissue such as the ovary and adrenal gland. This is a collaboration with Raj Kumar's lab, who have long-standing interest and expertise in mouse models of steroidogenesis.

Current projects:

Adrenal steroidogenesis

What is the role of Musashi proteins for regulating adrenal steroidogenesis in vivo?

Ovarian steroidogenesis

What are the TFs and RBPs downstream of FSH controlling these estrous stage-dependent regulatory networks?

Relevant publications:

Walters K, Baldwin A, Liu Z, Larsen M, Mukherjee N#, Kumar TR#. Discovery of FSH-regulated and estrous stage-specific transcriptional networks in mouse ovaries. PNAS 2025.

Human adrenal differentiation and pathophysiology

Defects resulting in either under- or over-production of these steroid hormones are pathological. For example, over-production of aldosterone is responsible for ~%10 of hypertensive individuals. Recently scientists discovered aldosterone producing macronodules (APMs) that are associated with primary aldosteronism and hypertension. We are using human adrenal tissue to understand the gene expression signature of APMs and the heteroigeneity between APCCs using spatial transcriptomics. This powerful approach also allows us to better understand the differentiation of adrenocortical stem cells in normal, aging, and pathological adrenal glands. This work is in collaboration with the labs of Lauren Fishbein and Katja Kisseljak-Vassiliades.

Relevant publications:

Fu R, Kaufman ML, Walters K, Koc K, Baldwin A, Clay MR, Basham KJ, Kiseljak-Vassiliades K#, Fishbein L#, Mukherjee N#. In situ spatial reconstruction of distinct normal and pathological cell populations within the human adrenal gland. Journal of the Endocrine Society 2023.

Targeting and dissecting mechanisms of translational regulation in cancer

We have numerous collaborative projects focused on understanding and targeting translational regulation in a variety of cancer types. Our primary interest is to determine the mechanism by which mRNA translation is dysregulated to gain a better understanding of how to specifically target these regulatory changes. Given the importance of Ribosome Profling (Ribo-seq) for these projects, and for research more generally, my lab is currently designing a translatomics analysis platform to enable experimentalists to analyze and explore Ribo-seq data.

Current projects:

Defining and targeting stress-induced translational control as a means to inhibit metastasis

How does specialized translation in response to stresses (such as hypoxia, nutrient deprivation etc) influence metastasis, with a focus on the eIF3 translational complex? Can we target this with small molecules? This is a collaboration with the Ford and Zhao labs.

Targeting the ribosome in multiple myeloma as well as head and neck cancers

How do multiple myeloma cells repogram translation to become resistant to the translation inhibitor omacetaxine? This is a collaboration with the Sherbenou lab.
Are there head and neck cancer specific translational changes in response to elongation inhibitors? What is the basis for this specificity? This is a collaboration with the Su lab.

Relevant publications:

Walker ZJ, Vaeth KF, Baldwin A, Ohlstrom DJ, Reiman LT, Denns KA, Matlin K, Idler BM, Stevens BM, Mukherjee N#, Sherbenou DW#. Ribosome Profiling Reveals Translational Reprogramming via mTOR Activation in Omacetaxine Resistant Multiple Myeloma. Mol Cancer Res. 2025.

Purdy SC, Matlin K, Alderman C, Baldwin A, Shrivastava N, Dutta S, Webb KJ, Wolin A, Boulton DP, Kapali J, Landua

JD, Lewis MT, Caino MC, Costello JC, Old W, Wang X, Zhao R#, Ford HL#, Neelanjan Mukherjee#. eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by novel small molecules.

Surveilling ribosomes to identify neoepitopes in Type 1 Diabetes

Ribosome profiling provides a comprehensive view of translational regulation and reveals novel or unannotated open reading frames (nuORFs). These ORFs harbor peptides that are processed and presented to the cell surface where they can be surveilled by the immune system. Recent work has shown that a Defective Ribosomal products (DRiP) derived from such nuORFs can drive beta cell autoimmunity. We developed a cell-type specific proteogenomic approach to discover these nuORFs using transcriptomics, ribosomal profiling, and proteomic/immunopeptidomic analysis of human pancreatic beta cells using stem cell derived beta cells and/or cadaveric islets to identify neoepitopes driving beta cell autoimmunity. This is a collaboration with the Russ lab.

Current projects:

Identifying and prioritizing MHC-presented peptides for t cell activation screening.

How do stresses (such as cytokine stimulation of viral infection) change the identify nuORFs and MHC-presented peptides?
What are the features important for presentation and T-cell reactivity in the presented peptides?

Relevant publications:

Walters K*, Guiterrez RC*, Sakhar S, Baldwin A,. Nakayasu ES, Mukherjee N#, Russ HA#. Proteogenomic discovery of novel and regulatory open reading frames in human beta cells. In revision.

Evolutionary dynamics of RNA regulatory elements

The poly(A) signal, along with auxiliary elements, directs the cleavage of pre-mRNA, determining the 3′ end of the mature transcript. While the AAUAAA hexamer is common in many species, Giardia lamblia uses a distinct AGURAA hexamer and lacks known auxiliary elements. Our study shows that the AAUAAA hexamer is likely ancestral, with the Giardia version being derived. Additionally, the use and strength of auxiliary elements vary, indicating that the motifs controlling pre-mRNA cleavage are dynamic over evolutionary timescales. This work is in collaboration with the Rissland lab.

Relevant publications:

Sajek MP, Bilodeau DY, Beer MA, Horton E, Miyamoto Y, Velle KB, Eckmann L, Fritz-Laylin L, Rissland OS#, Mukherjee N#. Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists. Genome Res 2024.