About

Eric Bennett received his PhD from Stanford University and completed postdoctoral work at Harvard Medical School. His research focuses on understanding the fundamental principles of how proteins are destroyed within cells, particularly through the ubiquitin-proteasome system (UPS), which functions as the cellular waste management and quality control system. His lab investigates mechanisms of UPS activity, including the regulation of deubiquitylating enzymes (Dubs), the regulation of Cullin-RING ligases (CRLs), and the global activity of UPS in protein quality control. The research employs integrated approaches combining biochemistry, cell biology, and systems-level techniques to elucidate how the UPS recognizes and degrades proteins, and how dysfunction in this pathway relates to human diseases such as ALS, Parkinson's disease, and cancer. His work aims to develop therapeutics that modulate protein degradation pathways and improve understanding of cellular protein homeostasis.

Research topics

• Biology
• Cancer research
• Cell biology
• Immunology
• Biochemistry
• Genetics
• Chemistry

Selected publications

• CRISPR-mediated conditional mutagenesis of <i>Smad1/5/8</i> reveals BMP/GDF signaling restricts postnatal bone overgrowth

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-23

  articleOpen access

  Abstract The BMP/GDF branch of TGF-β signaling regulates diverse aspects of skeletal biology, from skeletal development to maintenance and repair. However, the complexity, redundancy, and pleiotropy of BMP/GDF signaling have hamstrung a genetic dissection of its activities in different cell types over time. Here, we tested the feasibility of a three-transgene system using CRISPR/Cas9 to conditionally mutate six target sites, two each in the receptor-mediated Smad1 , Smad5 , and Smad8 transcriptional effectors of BMP/GDF signaling. Briefly, we used Prx1- cre to activate a conditional Cas9 transgene by recombination in early limb bud mesenchyme; this endonuclease then complexes with gRNAs expressed from a polycistronic tRNA-gRNA array for targeted mutagenesis. Slower than expected accumulation of gRNA-directed mutations in each Smad produced an unexpected postnatal skeletal phenotype. Beginning around one month after birth, all animals developed hyperostosis on the surface of all long limb bones, which progressively worsened with age. This woven bone expansion occurred through proliferation of RUNX2+ osteoprogenitor cells in the cambium layer of the periosteum, producing an abundance of periosteal osteoblasts. Endosteal osteoblasts did not increase in number but increased their mineralizing activity. As a result, the marrow cavities narrowed, and the patella and carpal elements, which have no periosteum, increased internal bone mass without altering shape and size. Thus, while BMP/GDF signaling is known to promote early postnatal bone growth, these data support an additional homeostatic role during late postnatal osteogenesis by regulating both periosteal and endosteal osteoblasts. Although this genetically simple approach requires further optimization to improve efficiency, combining three transgenes produced more than 160 conditionally mutagenized animals with a fully penetrant and reproducible phenotype. This is an advance over traditional cre/lox systems that scale in complexity with the number of target loci, and it highlights the potential to model a wide range of genetically complex traits and disorders.

  PublisherOA PDFDOI

• Proteostasis sustains T cell differentiation potential and tumor-infiltrating lymphocyte function

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-10 · 1 citations

  articleOpen access

  Summary Tumor-infiltrating lymphocytes (TIL) often fail to restrain tumor growth due to progressive differentiation to an ‘exhausted’ state. In healthy tissues, tissue-resident memory T cells (T RM ) maintain protection for years, and patient tumors that contain TIL with T RM features are associated with better prognosis. Proteomic and transcriptomic profiling of T cell populations identified proteostasis as a significant factor distinguishing T RM and progenitor-exhausted TIL from terminally-exhausted TIL, including loss of E3 ubiquitin ligases NEURL3, RNF149, and WSB1, with accumulation of unfolded proteins in spite of functional proteasome activity. Enforced expression of these ligases by TIL preserved stem-like TCF1 + populations and improved anti-tumor function, whereas their knockout impaired TIL and altered T cell differentiation in acute infection. Sustained ligase expression rescued accumulation of unfolded proteins in TIL and improved immunotherapy outcome in preclinical models, highlighting the critical role of proteostasis in TIL function and identifying new avenues for advancing cancer immunotherapy.

  PublisherDOI

• Mapping the functional importance of site-specific ubiquitination across the human proteome

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-08 · 2 citations

  preprintOpen access

  Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme activation. Mass spectrometry-based proteomics has allowed proteome-scale quantification of hundreds of thousands of ubiquitination sites (ubi-sites), however the functional importance and regulatory roles of most ubi-sites remain undefined. Here, we assembled a human reference ubiquitinome of 108,341 ubi-sites by harmonizing public proteomics data. We identified a core subset of ubi-sites under evolutionary constraint through alignment of ubiquitin proteomics data from six non-human species, and determined ultra-conserved ubi-sites recurring at regulatory hotspots within protein domains. Perturbation proteomics revealed that these highly conserved ubi-sites are more likely to regulate signaling functions rather than proteasomal degradation. To further prioritize functional ubi-sites with roles in cellular signaling, we constructed a functional score for more than 100,000 ubi-sites by integrating evolutionary, proteomic, and structural features using machine learning. Our score identifies ubi-sites regulating diverse protein functions and rationalizes mechanisms of genetic disease. Finally, we employed chemical genomics to validate the functional relevance of high-scoring ubi-sites and leveraged genetic code expansion to demonstrate that ubiquitination of K320 in the RNA-regulator ELAVL1 disrupts RNA binding. Our work reveals systems-level principles of the ubiquitinome and provides a powerful resource for studying protein ubiquitination.

  PublisherOA PDFDOI

• The proteostasis network is a therapeutic target in acute myeloid leukemia

  Blood · 2025-10-20 · 4 citations

  articleOpen access

  ABSTRACT: Oncogenic growth places great strain and dependence on protein homeostasis (proteostasis). This has made proteostasis pathways attractive therapeutic targets in cancer, but efforts to drug these pathways have yielded disappointing clinical outcomes. One exception is proteasome inhibitors, which are approved for the frontline treatment of multiple myeloma. However, proteasome inhibitors are largely ineffective for the treatment of other cancers at tolerable doses, including acute myeloid leukemia (AML), although reasons for these differences are unknown. Here, we determined that proteasome inhibitors are ineffective in AML due to their inability to disrupt proteostasis. In response to proteasome inhibition, AML cells activated HSF1 and increased autophagic flux to preserve proteostasis. Genetic inactivation of HSF1 sensitized AML cells to proteasome inhibition, marked by accumulation of unfolded protein, activation of the protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK)-mediated integrated stress response, severe reductions in protein synthesis, proliferation and cell survival, and significant slowing of disease progression and extension of survival in vivo. Similarly, combined autophagy and proteasome inhibition suppressed proliferation, synergistically killed human AML cells, and significantly reduced AML burden and extended survival in vivo. Furthermore, autophagy and proteasome inhibition preferentially suppressed protein synthesis and colony formation and induced apoptosis in cells from patients with primary AML, including AML stem/progenitor cells, compared with normal hematopoietic stem/progenitor cells. Combined autophagy and proteasome inhibition activated a terminal integrated stress response, which was surprisingly PKR. These studies unravel how proteostasis pathways are coopted to promote AML growth, progression and drug resistance and reveal that disabling the proteostasis network is a promising strategy to therapeutically target AML.

  PublisherOA PDFDOI

• Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor

  RNA · 2025-05-29 · 2 citations

  articleOpen access

  Translation elongation stalls trigger mRNA decay and degradation of the nascent polypeptide via translation-dependent quality control pathways. One such pathway, non-stop mRNA decay (NSD), targets aberrant mRNAs that lack stop codons, for example, due to premature polyadenylation. Here we identify Angel1, a CCR4 deadenylase homolog whose biochemical activity remains poorly defined, as a rate-limiting factor for NSD in human cells. Angel1 associates with mRNA coding regions and proteins involved in ribosome-associated quality control and mRNA decay, consistent with a factor that monitors translation elongation stalls. Depletion of Angel1 causes stabilization of reporter mRNAs that are targeted for NSD by the absence of stop codons, but not an mRNA targeted for nonsense-mediated decay. A conserved catalytic residue of Angel1 is critical for its function in NSD. Our findings identify Angel1 as a human NSD factor and suggest that Angel1 catalytic activity plays a critical role in the NSD pathway.

  PublisherOA PDFDOI

• Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress

  Nature Neuroscience · 2025-06-01 · 27 citations

  articleOpen access

  Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging hallmarks, and we verified key findings in aged human and mouse brain tissue. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins-like the dementia- and ALS-associated protein TDP-43-mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components are typically recruited to stress granules, but aged neurons suffer from chronic cellular stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity and the failure to respond to new stress events. Together, our data demonstrate that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.

  PublisherOA PDFDOI

• RNF10 and RIOK3 facilitate 40S ribosomal subunit degradation upon 60S biogenesis disruption or amino acid starvation

  Cell Reports · 2025-02-28 · 19 citations

  articleOpen accessSenior author

  The initiation-specific ribosome-associated quality control pathway (iRQC) is activated when translation initiation complexes fail to transition to elongation-competent 80S ribosomes. Upon iRQC activation, RNF10 ubiquitylates the 40S proteins uS3 and uS5, which leads to 40S decay. How iRQC is activated in the absence of pharmacological translation inhibitors and what mechanisms govern iRQC capacity and activity remain unanswered questions. Here, we demonstrate that altering 60S:40S stoichiometry by disrupting 60S biogenesis triggers iRQC activation and 40S decay. Depleting the critical scanning helicase eIF4A1 impairs 40S ubiquitylation and degradation, indicating mRNA engagement is required for iRQC. We show that amino acid starvation conditions also stimulate iRQC-dependent 40S decay. We identify RIOK3 as a crucial iRQC factor that interacts with ubiquitylated 40S subunits to mediate degradation. Both RNF10 and RIOK3 protein levels increase upon iRQC pathway activation, establishing a feedforward mechanism that regulates iRQC capacity and subsequent 40S decay.

  PublisherOA PDFDOI

• ExoSloNano: multimodal nanogold labels for identification of macromolecules in live cells and cryo-electron tomograms

  Nature Methods · 2025-11-28 · 1 citations

  articleOpen access

  In situ cryo-electron microscopy (cryo-EM) enables the direct interrogation of structure-function relationships by resolving macromolecular structures in their native cellular environment. Recent progress in sample preparation, imaging and data processing has enabled the identification and determination of large biomolecular complexes. However, the majority of proteins are of a size that still eludes identification in cellular cryo-EM data, and most proteins exist in low copy numbers. Therefore, novel tools are needed for cryo-EM to identify macromolecules across multiple size scales (from microns to nanometers). Here we introduce nanogold probes for detecting specific proteins using correlative light and electron microscopy, cryo-electron tomography (cryo-ET) and resin-embedded electron microscopy. These nanogold probes can be introduced into live cells, in a manner that preserves intact molecular networks and cell viability. We use this ExoSloNano system to identify both cytoplasmic and nuclear proteins by room-temperature electron microscopy, and resolve associated structures by cryo-ET. By providing high-efficiency protein labeling in live cells and molecular specificity within cryo-ET tomograms, ExoSloNano expands the proteome available to electron microscopy.

  PublisherDOI

• 743 Proteostasis sustains T cell differentiation potential and tumor-infiltrating lymphocyte function

  Cell · 2025-11-01

  articleOpen access

  populations and improved function in tumors and chronic infection, whereas deficiency impaired TIL and altered T cell differentiation during acute infection. Sustained ligase expression rescued the accumulation of unfolded proteins in TIL and improved immunotherapy outcomes in preclinical models, underscoring the critical role of proteostasis in TIL function and highlighting a promising avenue for advancing cancer immunotherapy.

  PublisherDOI

• Cryo-tomography of 1.4 nm-HAN-488 labeled ribosomes inside cells (ExoSloNano)

  EMPIAR dataset · 2025-06-09

  datasetOpen access

  EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

  PublisherDOI

Recent grants

• Leveraging ubiquitin-dependent regulatory mechanisms to improve proteome quality in health and disease

  NIH · $2.1M · 2023–2028

• Defining the function and mechanism of regulatory ribosomal ubiquitylation

  NIH · $1.1M · 2021–2024

• NIH Grant DP2GM119132

  NIH · $2.3M · 2020

Frequent coauthors

• Marilyn Leonard

  32 shared

• Amit Fulzele

  Institute of Molecular Biology

  25 shared

• W Michelle

  Harvard University

  24 shared

• J. Wade Harper

  Harvard University

  24 shared

• Moritz Hunkeler

  Dana-Farber Cancer Institute

  24 shared

• Eric S. Fischer

  Dana-Farber Cancer Institute

  24 shared

• Cyrus Y Jin

  Dana-Farber Cancer Institute

  23 shared

• Katherine A. Donovan

  Dana-Farber Cancer Institute

  20 shared