Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation.

Inducing protein degradation via small molecules is a transformative therapeutic paradigm. Although structural requirements of target degradation are emerging, mechanisms determining the cellular response to small-molecule degraders remain poorly understood. To systematically delineate effectors required for targeted protein degradation, we applied genome-scale CRISPR/Cas9 screens for five drugs that hijack different substrate receptors (SRs) of cullin RING ligases (CRLs) to induce target proteolysis. We found that sensitivity to small-molecule degraders is dictated by shared and drug-specific modulator networks, including the COP9 signalosome and the SR exchange factor CAND1. Genetic or pharmacologic perturbation of these effectors impairs CRL plasticity and arrests a wide array of ligases in a constitutively active state. Resulting defects in CRL decommissioning prompt widespread CRL auto-degradation that confers resistance to multiple degraders. Collectively, our study informs on regulation and architecture of CRLs amenable for targeted protein degradation and outlines biomarkers and putative resistance mechanisms for upcoming clinical investigation.

Orpinolide disrupts a leukemic dependency on cholesterol transport by inhibiting OSBP.

Metabolic alterations in cancer precipitate in associated dependencies that can be therapeutically exploited. To meet this goal, natural product-inspired small molecules can provide a resource of invaluable chemotypes. Here, we identify orpinolide, a synthetic withanolide analog with pronounced antileukemic properties, via orthogonal chemical screening. Through multiomics profiling and genome-scale CRISPR-Cas9 screens, we identify that orpinolide disrupts Golgi homeostasis via a mechanism that requires active phosphatidylinositol 4-phosphate signaling at the endoplasmic reticulum-Golgi membrane interface. Thermal proteome profiling and genetic validation studies reveal the oxysterol-binding protein OSBP as the direct and phenotypically relevant target of orpinolide. Collectively, these data reaffirm sterol transport as a therapeutically actionable dependency in leukemia and motivate ensuing translational investigation via the probe-like compound orpinolide.

Design principles for cyclin K molecular glue degraders.

Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.

ERF deletion rescues RAS deficiency in mouse embryonic stem cells.

MEK inhibition in combination with a glycogen synthase kinase-3ß (GSK3ß) inhibitor, referred as the 2i condition, favors pluripotency in embryonic stem cells (ESCs). However, the mechanisms by which the 2i condition limits ESC differentiation and whether RAS proteins are involved in this phenomenon remain poorly understood. Here we show that RAS nullyzygosity reduces the growth of mouse ESCs (mESCs) and prohibits their differentiation. Upon RAS deficiency or MEK inhibition, ERF (E twenty-six 2 [Ets2]-repressive factor), a transcriptional repressor from the ETS domain family, translocates to the nucleus, where it binds to the enhancers of pluripotency factors and key RAS targets. Remarkably, deletion of Erf rescues the proliferative defects of RAS-devoid mESCs and restores their capacity to differentiate. Furthermore, we show that Erf loss enables the development of RAS nullyzygous teratomas. In summary, this work reveals an essential role for RAS proteins in pluripotency and identifies ERF as a key mediator of the response to RAS/MEK/ERK inhibition in mESCs.

Powering prescription: Mitochondria as "Living Drugs" - Definition, clinical applications, and industry advancements.

Mitochondria's role as engines and beacons of metabolism and determinants of cellular health is being redefined through their therapeutic application as "Living Drugs" (LDs). Artificial mitochondrial transfer/transplant (AMT/T), encompassing various techniques to modify, enrich, or restore mitochondria in cells and tissues, is revolutionizing acellular therapies and the future of medicine. This article proposes a necessary definition for LDs within the Advanced Therapeutic Medicinal Products (ATMPs) framework. While recognizing different types of LDs as ATMPs, such as mesenchymal stem cells (MSCs) and chimeric antigen receptor T (CAR T) cells, we focus on mitochondria due to their unique attributes that distinguish them from traditional cell therapies. These attributes include their inherent living nature, diverse sources, industry applicability, validation, customizability for therapeutic needs, and their capability to adapt and respond within recipient cells. We trace the journey from initial breakthroughs in AMT/T to the current state-of-the-art applications by emerging innovative companies, highlighting the need for manufacturing standards to navigate the transition of mitochondrial therapies from concept to clinical practice. By providing a comprehensive overview of the scientific, clinical, and commercial landscape of mitochondria as LDs, this article contributes to the essential dialogue among regulatory agencies, academia, and industry to shape their future in medicine.

A Genome-wide CRISPR Screen Identifies CDC25A as a Determinant of Sensitivity to ATR Inhibitors.

One recurring theme in drug development is to exploit synthetic lethal properties as means to preferentially damage the DNA of cancer cells. We and others have previously developed inhibitors of the ATR kinase, shown to be particularly genotoxic for cells expressing certain oncogenes. In contrast, the mechanisms of resistance to ATR inhibitors remain unexplored. We report here on a genome-wide CRISPR-Cas9 screen that identified CDC25A as a major determinant of sensitivity to ATR inhibition. CDC25A-deficient cells resist high doses of ATR inhibitors, which we show is due to their failure to prematurely enter mitosis in response to the drugs. Forcing mitotic entry with WEE1 inhibitors restores the toxicity of ATR inhibitors in CDC25A-deficient cells. With ATR inhibitors now entering the clinic, our work provides a better understanding of the mechanisms by which these compounds kill cells and reveals genetic interactions that could be used for their rational use.

Discovery and Mechanistic Elucidation of NQO1-Bioactivatable Small Molecules That Overcome Resistance to Degraders.

Degraders hold the promise to efficiently inactivate previously intractable disease-relevant targets. Unlike traditional inhibitors, degraders act substoichiometrically and rely on the hijacked proteolysis machinery, which can also act as an entry point for resistance. To fully harness the potential of targeted protein degradation, it is crucial to comprehend resistance mechanisms and formulate effective strategies to overcome them. We conducted a chemical screening to identify synthetic lethal vulnerabilities of cancer cells that exhibit widespread resistance to degraders. Comparative profiling followed by tailored optimization delivered the small molecule RBS-10, which shows preferential cytotoxicity against cells pan-resistant to degraders. Multiomics deconvolution of the mechanism of action revealed that RBS-10 acts as a prodrug bioactivated by the oxidoreductase enzyme NQO1, which is highly overexpressed in our resistance models. Collectively, our work informs on NQO1 as an actionable vulnerability to overcome resistance to degraders and as a biomarker to selectively exploit bioactivatable prodrugs in cancer.

Biophysical and Computational Approaches to Study Ternary Complexes: A 'Cooperative Relationship' to Rationalize Targeted Protein Degradation.

Degraders have illustrated that compound-induced proximity to E3 ubiquitin ligases can prompt the ubiquitination and degradation of disease-relevant proteins. Hence, this pharmacology is becoming a promising alternative and complement to available therapeutic interventions (e. g., inhibitors). Degraders rely on protein binding instead of inhibition and, hence, they hold the promise to broaden the druggable proteome. Biophysical and structural biology approaches have been the cornerstone of understanding and rationalizing degrader-induced ternary complex formation. Computational models have now started to harness the experimental data from these approaches with the aim to identify and rationally help design new degraders. This review outlines the current experimental and computational strategies used to study ternary complex formation and degradation and highlights the importance of effective crosstalk between these approaches in the advancement of the targeted protein degradation (TPD) field. As our understanding of the molecular features that govern drug-induced interactions grows, faster optimizations and superior therapeutic innovations for TPD and other proximity-inducing modalities are sure to follow.

The importance of developing open communication and a professional, long-term relationship between patients with chronic myeloid leukemia and their oncologist.

A good patient-doctor relationship and positive communication strongly influence patient quality of life and clinical outcomes. Demonstrating the importance of communication in the patient-doctor relationship are three patient authors who have 48 years of combined real-world experience with chronic myeloid leukemia (CML) in the USA. Using their own personal experiences, these patient authors and a healthcare professional provide suggestions related to improving patient-doctor relationships and communication at each stage of the journey from diagnosis to learning to live with CML. The authors believe these recommendations are applicable to patients with CML and with other diseases, their caregivers and healthcare professionals.

Podcast 3. Lessons learned: managing financial costs and where you can go for more information.

The patient authors with over 48 years of combined real-world experience with chronic myeloid leukemia, and a healthcare professional, use their own personal experiences to describe the factors that may affect the patien-doctor relationship, patient care and outcomes. The authors believe that this podcast series and associated manuscript will aid both patients and healthcare professionals to improve their patient-doctor relationships and communication through diagnosis, treatment decision-making and learning to live with CML (or another disease). In this episode, they discuss managing financial costs and where to find resources and support groups.

The beginning: diagnosis and selecting your doctor.

The patient authors with over 48 years of combined real-world experience with chronic myeloid leukemia, and a healthcare professional, use their own personal experiences to describe the factors that may affect the patient-doctor relationship, patient care and outcomes. The authors believe that this podcast series and associated manuscript will aid both patients and healthcare professionals to improve their patient-doctor relationships and communication through diagnosis, treatment decision-making and learning to live with CML (or another disease). In this episode, they discuss the importance of the patient-doctor relationship, the patient authors' own diagnosis experiences and considerations when selecting a health care team.

Podcast 2. The journey: staying on top of your cancer.

The patient authors with over 48 years of combined real-world experience with chronic myeloid leukemia, and a healthcare professional, use their own personal experiences to describe the factors that may affect the patient-doctor relationship, patient care and outcomes. The authors believe that this podcast series and associated manuscript will aid both patients and healthcare professionals to improve their patient-doctor relationships and communication through diagnosis, treatment decision-making and learning to live with CML (or another disease). In this episode, they discuss communication between a patient and their healthcare team and establishing a treatment protocol.

Analysis of recurrence and risk factors in laparoscopic sandwich technique for parastomal hernia repair.

INTRODUCTION: Parastomal hernias are frequent and highly recurrent. The sandwich technique is a combination of the keyhole and Sugarbaker techniques, using a double intraperitoneal mesh. The objective of this study was to assess the outcomes of the sandwich technique, specifically focusing on recurrence rates. MATERIALS AND METHODS: Observational retrospective study conducted in two tertiary referral centers in Catalonia, Spain. All consecutive patients who underwent parastomal hernia repair using the sandwich technique between 1st January 2016 and 31st December 2021 were included. RESULTS: A total of 38 patients underwent the laparoscopic sandwich technique for parastomal hernia repair. The overall recurrence rate was 7.9% (3/38), with a median follow-up of 39 months (IQR: 12.3-56.5). According to the EHS classification for parastomal hernia, there were 47.4% (18/38) type I defects, 10.5% (4/38) type II defects, 28.9% (11/38) type III defects, and 13.2% (5/38) type IV defects. The used mesh was predominantly TiMesh® (76.3%; 29/38), followed by DynaMesh® IPOM (23.7%; 9/38). Patients with recurrence exhibited higher rates of seroma, hematoma, surgical site infection, and one case of early recurrence attributed to mesh retraction. Consequently, postoperative complications emerged as the primary risk factor for hernia recurrence. CONCLUSION: The sandwich technique demonstrated recurrence rates consistent with those reported in the existing literature.

A unique arginine cluster in PolDIP2 enhances nucleotide binding and DNA synthesis by PrimPol.

Replication forks often stall at damaged DNA. To overcome these obstructions and complete the DNA duplication in a timely fashion, replication can be restarted downstream of the DNA lesion. In mammalian cells, this repriming of replication can be achieved through the activities of primase and polymerase PrimPol. PrimPol is stimulated in DNA synthesis through interaction with PolDIP2, however the exact mechanism of this PolDIP2-dependent stimulation is still unclear. Here, we show that PrimPol uses a flexible loop to interact with the C-terminal ApaG-like domain of PolDIP2, and that this contact is essential for PrimPol's enhanced processivity. PolDIP2 increases primer-template and dNTP binding affinities of PrimPol, which concomitantly enhances its nucleotide incorporation efficiency. This stimulation is dependent on a unique arginine cluster in PolDIP2. Since the polymerase activity of PrimPol alone is very limited, this mechanism, where the affinity for dNTPs gets increased by PolDIP2 binding, might be critical for the in vivo function of PrimPol in tolerating DNA lesions at physiological nucleotide concentrations.

Factors associated with injury among Maine logging workers.

INTRODUCTION: Despite dramatic improvements in safety, logging remains one of the most dangerous industries in the United States. The purpose of this study was to explore longitudinal injury trends among Maine logging workers. METHODS: Loggers participated in seven quarterly surveys, over the course of 18 months. Categorical and free text data related to traumatic and acute injury, musculoskeletal disorders (MSD), and chronic pain were exported from REDCap into SAS 9.4, Excel, and NVivo, for quantitative and qualitative analysis, respectively. Time to injury was modeled using two different approaches: (1) time to the occurrence of first injury modeled by proportional hazard regression and (2) an intensity model for injury frequency. Two research team members also analyzed qualitative data using a content analysis approach. RESULTS: During the study, 204 injuries were reported. Of the 154 participants, 93 (60.4%) reported musculoskeletal pain on at least one survey. The majority of injuries were traumatic, including fractures, sprains, and strains. Lack of health insurance was found to be related to increased risk of first injury [HR = 1.41, 95% CI = 0.97-2.04, p = 0.069]. Variables found to be related to injury intensity at the univariate level were: (1) a lack of health insurance [HR = 1.51, 95% CI = 1.04-2.20, p = 0.030], (2) age [HR for 10-year age increase;= 1.12, 95% CI = 0.99-1.27, p = 0.082], and (3) years employed in logging industry [HR for 10-year increase = 1.12, 95% CI = 0.99-1.26, p = 0.052]. Seeking medical attention for injury was not a priority for this cohort, and narratives revealed a trend for self-assessment. A variety of barriers, including finances, prevented loggers from seeking medical attention. DISCUSSION: We found that loggers still experience serious, and sometimes disabling, injuries associated with their work. It was unsurprising that many injuries were due to slips, trips, and falls, along with contact with logging equipment and trees/logs. The narratives revealed various obstacles preventing loggers from achieving optimal health. Examples included geographic distance from healthcare, lack of time to access care, and entrenched values that prioritized independence and traditional masculinity. Financial considerations were also consistently cited as a primary barrier to adequate care. CONCLUSION: There is a continued need to emphasize occupational health and safety in the logging industry. Implementation of relevant safety programs is key, but it is likely that the benefits of these will not be fully realized until a cultural shift takes place within this industry.

Quality, Usability, and Effectiveness of mHealth Apps and the Role of Artificial Intelligence: Current Scenario and Challenges.

The use of artificial intelligence (AI) and big data in medicine has increased in recent years. Indeed, the use of AI in mobile health (mHealth) apps could considerably assist both individuals and health care professionals in the prevention and management of chronic diseases, in a person-centered manner. Nonetheless, there are several challenges that must be overcome to provide high-quality, usable, and effective mHealth apps. Here, we review the rationale and guidelines for the implementation of mHealth apps and the challenges regarding quality, usability, and user engagement and behavior change, with a special focus on the prevention and management of noncommunicable diseases. We suggest that a cocreation-based framework is the best method to address these challenges. Finally, we describe the current and future roles of AI in improving personalized medicine and provide recommendations for developing AI-based mHealth apps. We conclude that the implementation of AI and mHealth apps for routine clinical practice and remote health care will not be feasible until we overcome the main challenges regarding data privacy and security, quality assessment, and the reproducibility and uncertainty of AI results. Moreover, there is a lack of both standardized methods to measure the clinical outcomes of mHealth apps and techniques to encourage user engagement and behavior changes in the long term. We expect that in the near future, these obstacles will be overcome and that the ongoing European project, Watching the risk factors (WARIFA), will provide considerable advances in the implementation of AI-based mHealth apps for disease prevention and health promotion.

External validation of yonsei nomogram predicting chronic kidney disease development after partial nephrectomy: An international, multicenter study.

OBJECTIVE: To externally validate Yonsei nomogram. METHODS: From 2000 through 2018, 3526 consecutive patients underwent on-clamp PN for cT1 renal masses at 23 centers were included. All patients had two kidneys, preoperative eGFR ≥60 ml/min/1.73 m2, and a minimum follow-up of 12 months. New-onset CKD was defined as upgrading from CKD stage I or II into CKD stage ≥III. We obtained the CKD-free progression probabilities at 1, 3, 5, and 10 years for all patients by applying the nomogram found at https://eservices.ksmc.med.sa/ckd/. Thereafter, external validation of Yonsei nomogram for estimating new-onset CKD stage ≥III was assessed by calibration and discrimination analysis. RESULTS AND LIMITATION: Median values of patients' age, tumor size, eGFR and follow-up period were 47 years (IQR: 47-62), 3.3 cm (IQR: 2.5-4.2), 90.5 ml/min/1.73 m2 (IQR: 82.8-98), and 47 months (IQR: 27-65), respectively. A total of 683 patients (19.4%) developed new-onset CKD. The 5-year CKD-free progression rate was 77.9%. Yonsei nomogram demonstrated an AUC of 0.69, 0.72, 0.77, and 0.78 for the prediction of CKD stage ≥III at 1, 3, 5, and 10 years, respectively. The calibration plots at 1, 3, 5, and 10 years showed that the model was well calibrated with calibration slope values of 0.77, 0.83, 0.76, and 0.75, respectively. Retrospective database collection is a limitation of our study. CONCLUSIONS: The largest external validation of Yonsei nomogram showed good calibration properties. The nomogram can provide an accurate estimate of the individual risk of CKD-free progression on long-term follow-up.

Chasing molecular glue degraders: screening approaches.

Protein-protein interactions (PPIs) govern all biological processes. Some small molecules modulate PPIs through induced protein proximity. In particular, molecular glue degraders are monovalent compounds that orchestrate interactions between a target protein and an E3 ubiquitin ligase, prompting the proteasomal degradation of the former. This and other pharmacological strategies of targeted protein degradation (e.g. proteolysis-targeting chimeras - PROTACs) overcome some limitations of traditional occupancy-based therapeutics. Here, we provide an overview of the "molecular glue" concept, with a special focus on natural and synthetic inducers of proximity to E3s. We then briefly highlight the serendipitous discoveries of some clinical and preclinical molecular glue degraders, and discuss the first examples of intentional discoveries. Specifically, we outline the different screening strategies reported in this rapidly evolving arena and our thoughts on future perspectives. By mastering the ability to influence PPIs, molecular glue degraders can induce the degradation of unligandable proteins, thus providing an exciting path forward to broaden the targetable proteome.

3'dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol.

PrimPol is a DNA primase/polymerase from the Archaeo-Eukaryotic Primase (AEP) superfamily that enables the progression of stalled replication forks by synthesizing DNA primers ahead of blocking lesions or abnormal structures in the ssDNA template. PrimPol's active site is formed by three AEP-conserved motifs: A, B and C. Motifs A and C of human PrimPol (HsPrimPol) harbor the catalytic residues (Asp114, Glu116, Asp280) acting as metal ligands, whereas motif B includes highly conserved residues (Lys165, Ser167 and His169), which are postulated to stabilize 3' incoming deoxynucleotides (dNTPs). Additionally, other putative nucleotide ligands are situated close to motif C: Lys297, almost invariant in the whole AEP superfamily, and Lys300, specifically conserved in eukaryotic PrimPols. Here, we demonstrate that His169 is absolutely essential for 3'dNTP binding and, hence, for both primase and polymerase activities of HsPrimPol, whereas Ser167 and Lys297 are crucial for the dimer synthesis initiation step during priming, but dispensable for subsequent dNTP incorporation on growing primers. Conversely, the elimination of Lys165 does not affect the overall primase function; however, it is required for damage avoidance via primer-template realignments. Finally, Lys300 is identified as an extra anchor residue to stabilize the 3' incoming dNTP. Collectively, these results demonstrate that individual ligands modulate the stabilization of 3' incoming dNTPs to optimize DNA primer synthesis efficiency during initiation and primer maturation.

Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity.

Acetylation is known to regulate the activity of cytosolic phosphoenolpyruvate carboxykinase (PCK1), a key enzyme in gluconeogenesis, by promoting the reverse reaction of the enzyme (converting phosphoenolpyruvate to oxaloacetate). It is also known that the histone acetyltransferase p300 can induce PCK1 acetylation in cells, but whether that is a direct or indirect function was not known. Here we initially set out to determine whether p300 can acetylate directly PCK1 in vitro. We report that p300 weakly acetylates PCK1, but surprisingly, using several techniques including protein crystallization, mass spectrometry, isothermal titration calorimetry, saturation-transfer difference nuclear magnetic resonance and molecular docking, we found that PCK1 is also able to acetylate itself using acetyl-CoA independently of p300. This reaction yielded an acetylated recombinant PCK1 with a 3-fold decrease in kcat without changes in Km for all substrates. Acetylation stoichiometry was determined for 14 residues, including residues lining the active site. Structural and kinetic analyses determined that site-directed acetylation of K244, located inside the active site, altered this site and rendered the enzyme inactive. In addition, we found that acetyl-CoA binding to the active site is specific and metal dependent. Our findings provide direct evidence for acetyl-CoA binding and chemical reaction with the active site of PCK1 and suggest a newly discovered regulatory mechanism of PCK1 during metabolic stress.