Getting in Shape: Targeting the Etiology of Protein Misfolding Diseases – Celebrating Jeffery Kelly's Pioneering Work

Abstract

We are excited to share this special issue dedicated to Jeffery Kelly, commemorating his 2023 Wolf Prize in Chemistry. This award recognizes his pioneering research accomplishments, which have dramatically changed our fundamental understanding of how proteins (mis)fold in vitro and in vivo while at the same time leveraging those discoveries to change the lives of patients across the globe. The award specifically refers to the latter: “for developing a clinical strategy to ameliorate pathological protein aggregation”. This is exemplified by the development of Tafamidis,¹ the first clinically approved molecule to treat a disease of protein misfolding.^{2, 3}

Jeff's discovery that protein misfolding of transthyretin (TTR) is an obligate step prior to protein aggregation⁴ established that preventing the accumulation of misfolded proteins can block disease pathology. Rigorous biochemical and biophysical characterization established that transthyretin tetramer dissociation into monomers is the rate-limiting step that initiates protein misfolding.⁵ This critical insight motivated the development of small molecules that could stabilize the native conformation of TTR,⁶ culminating in the development and clinical approval of Tafamidis.

Later, Jeff and his collaborators introduced the idea of protein homeostasis (or proteostasis).⁷ Protein folding and maturation into its native structure is not only governed by the intrinsic stability of each polypeptide chain, but in a cellular environment, the large ensemble of molecular chaperones, co-chaperones, other protein quality factors, and their interacting activities maintain the integrity of the proteome for cellular and organismal health. Importantly, dysregulation of the proteostasis network can lead to insufficient protein folding capacity and accumulation of misfolded proteins, which is associated with various disease states, ranging from neurodegeneration to diabetes and cancer.^{8, 9}

Several reviews and articles in this special issue address how a detailed understanding of protein misfolding and the proteostasis network can be leveraged in therapeutic development. These contributions highlight the impact that Jeff's work has had on the broader chemistry and biology research community.

Although transthyretin amyloidosis was once thought to be rare, we now know that millions of people are carriers of likely pathogenic variants.¹⁰ Following the success of Tafamidis, there are now many emerging approaches for therapeutic intervention in this disease class, as reviewed by Per Hammarström in this issue.¹¹ Another class of protein associated with systemic amyloidosis is immunoglobulin light chain, which lead to AL amyloidosis. Gareth Morgan reviews how both amyloidogenicity and the protein load contribute to the potential amyloidogenicity.¹² Importantly, the same kinetic stabilization strategy that worked for TTR has now been shown to be promising for protecting against AL. TTR and AL illustrate the challenge that diverse mutations present towards understanding protein folding and misfolding. To handle this challenge for the case of a loss-of-function system, Ting-Wei Mu and colleagues present a research article applying machine learning tools to predict the function of nearly saturating amino acid substitutions in GABA_A receptors, whose misfolding and consequent degradation is associated with familial epilepsy.¹³ As validation, they find a good correlation between predicted and reported clinical pathology for known diseases. Similar to GABA_A, there are diverse mutations in CFTR associated with misfolding and/or loss of function, causing cystic fibrosis disease. As one of the most investigated genetic disease targets in the past few decades, CFTR has well-characterized and effective stabilizing ligands that have dramatically enhanced patient lifespans.^{14, 15} Despite this success, Lars Plate and colleagues outline in their review how approved therapies do not benefit patients with all CFTR variants and discuss how new approaches can fill this gap.¹⁶ They also address how approaches learned from CFTR can be leveraged against other membrane protein misfolding diseases.

Post-translational modifications (PTMs) are critical in regulating protein functions, giving rise to many diverse proteoforms. However, some detrimental modifications also occur, often aggravated by aging, when the damaged proteins can no longer be cleared by degradation machinery and start to misfold and aggregate. The microtubule-associated protein tau is one important aggregation-prone protein associated with various neurodegenerative diseases. Jason Gestwicki and colleagues review how the tau aggregation processes are influenced by a large range of possible PTMs.¹⁷ As most aggregation-prone tau forms are cationic, interactions with other polyanionic biomolecules in the cytosol likely play an important regulatory role and can influence the nature of tau fibrils formed in different cell and tissue regions. Glycosylation is another prevalent PTM that regulates the functions of many secreted and cell-surface proteins. Matthew Shoulders and colleagues review the crosstalk between regulation of N- and O-linked glycosylation and secretory proteostasis by the Unfolded Protein Response (UPR).¹⁸ While the canonical function of the UPR is to enhance the folding capacity in the secretory pathway in response to folding stress, they highlight the IRE-XBP1 s arm of the UPR as having an underappreciated role as a central regulator of the glycome architecture. As UPR signaling is dysregulated in many disease states where alterations to the glycome have been observed, the interplay may have important functional consequences that remain to be explored.

The recognition that a decline in proteostasis is linked to a wide range of disease states has motivated researchers to better understand the regulation of the proteostasis network and develop avenues to therapeutically enhance proteostasis capacity.^{19, 20} The proteasome is one critical proteostasis component that degrades proteins that are no longer needed by the cell. Darci Trader and colleagues review how damages and declines in proteasome activity are linked to aging and disease states in not just humans but also other model organisms.²¹ They also highlight genetic and pharmacological approaches to restore proteasome activity. Disaggregases are proteostasis machinery that disassemble protein aggregates and potentially clear toxic protein conformations. Jim Shorter and colleagues review the recent discovery of the first metazoan mitochondrial disaggregase, Skd3.²² They discuss the structure, function, and diseases associated with genetic defects in Skd3. As discussed above, the UPR is one signaling pathway to upregulate the proteostasis capacity. Jonathan Lin and colleagues present research on PERK, one of the sensor proteins of the UPR and the integrated stress response that detects misfolded proteins in the endoplasmic reticulum lumen.²³ They assembled a dataset of PERK variants and characterized specific variants identified as risk factors for tauopathy disease, finding diminished PERK signaling. As an example of pharmacological intervention, Luke Wiseman and colleagues present a research article finding a small molecule regulator of protein disulfide isomerase (PDIA1) blocks inflammasome activation.²⁴ This study highlights that a pharmacological proteostasis regulator compound can be repurposed to influence other cellular activities.

Lastly, significant challenges remain to detect misfolded protein conformations, especially in an in vivo environment. Joseph Genereux and colleagues review new technologies for identifying misfolded proteins and their potential to reveal broader consequences about the proteome integrity in disease states.²⁵

Many of the articles published here have been contributed by former trainees and/or collaborators of Jeff, highlighting the lasting personal and scientific legacy that his research accomplishments and training efforts have made. We are incredibly grateful for his mentorship and support over the years and into the future. We hope that this special issue celebrating Jeff's highly deserved award serves as a tribute to the ideas that he pioneered and motivates others to make a lasting effort to improve human health.