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RAS proteins are key players in multiple cellular processes. To study the role of RAS proteins individually or in combination, we have developed MEFs that can be rendered RASless, i.e., devoid of all endogenous RAS isoforms. These cells have significantly contributed to our understanding of the requirements for RAS functions in cell proliferation as well as their implications in diverse cellular processes. Here, we describe methods using RASless MEFs to study RAS-dependent cellular activities with special emphasis on proliferation. We provide the details to identify inducers of RAS-independent proliferation in colony assays. We recommend following these stringent guidelines to avoid false-positive results. Moreover, this protocol can be adapted to generate RASless MEFs ectopically expressing RAS variants to interrogate their function in the absence of endogenous RAS isoforms or to perform experiments in the absence of RAS. Finally, we also describe protocols to generate and use RASless MEFs for cell cycle analyses using the FUCCI cell cycle indicator.

RAS proteins are key players in multiple cellular processes. To study the role of RAS proteins individually or in combination, we have developed MEFs that can be rendered RASless, i.e., devoid of all endogenous RAS isoforms. These cells have significantly contributed to our understanding of the requirements for RAS functions in cell proliferation as well as their implications in diverse cellular processes. Here, we describe methods using RASless MEFs to study RAS-dependent cellular activities with special emphasis on proliferation. We provide the details to identify inducers of RAS-independent proliferation in colony assays. We recommend following these stringent guidelines to avoid false-positive results. Moreover, this protocol can be adapted to generate RASless MEFs ectopically expressing RAS variants to interrogate their function in the absence of endogenous RAS isoforms or to perform experiments in the absence of RAS. Finally, we also describe protocols to generate and use RASless MEFs for cell cycle analyses using the FUCCI cell cycle indicator.

In mammals, the KRAS locus encodes two protein isoforms, KRAS4A and KRAS4B, which differ only in their C terminus via alternative splicing of distinct fourth exons. Previous studies have shown that whereas KRAS expression is essential for mouse development, the KRAS4A isoform is expendable. Here, we have generated a mouse strain that carries a terminator codon in exon 4B that leads to the expression of an unstable KRAS4B154 truncated polypeptide, hence resulting in a bona fide Kras4B-null allele. In contrast, this terminator codon leaves expression of the KRAS4A isoform unaffected. Mice selectively lacking KRAS4B expression developed to term but died perinatally because of hypertrabeculation of the ventricular wall, a defect reminiscent of that observed in embryos lacking the Kras locus. Mouse embryonic fibroblasts (MEFs) obtained from Kras4B-/- embryos proliferated less than did wild-type MEFs, because of limited expression of KRAS4A, a defect that can be compensated for by ectopic expression of this isoform. Introduction of the same terminator codon into a Kras FSFG12V allele allowed expression of an endogenous KRAS4AG12V oncogenic isoform in the absence of KRAS4B. Exposure of Kras +/FSF4AG12V4B- mice to Adeno-FLPo particles induced lung tumors with complete penetrance, albeit with increased latencies as compared with control Kras +/FSFG12V animals. Moreover, a significant percentage of these mice developed proximal metastasis, a feature seldom observed in mice expressing both mutant isoforms. These results illustrate that expression of the KRAS4AG12V mutant isoform is sufficient to induce lung tumors, thus suggesting that selective targeting of the KRAS4BG12V oncoprotein may not have significant therapeutic consequences. We thank Marta San Roman, Raquel Villar, and Nuria Cabrera for excellent technical assistance; Mayte Lamparero and Isabel Blanco (Animal Facility) for mouse work; the Histopathology Unit for processing of mouse tissues; Lola Martinez (Flow Cytometry Unit) for her help with flow cytometry analyses; Diego Megias and Manuel Perez (Confocal Microscopy Unit) for assistance with confocal microscopy; and the Mouse Genome Editing Unit for support with the generation of the mouse strains described here. We also thank Ignacio Perez de Castro (Instituto de Salud Carlos III, Madrid, Spain) for sharing the EGFP-KRAS4B plasmid and Orlando Dominguez (Genomics Unit) and Pedro P. Lopez-Casas (Clinical Research Program) for their advice on exome sequencing. This work was supported by grants from the European Research Council (ERC-2015-AdG/695566, THERACAN), the Spanish Ministry of Science, Innovation and Universities (RTC-2017-6576-1), and the Autonomous Community of Madrid (B2017/BMD-3884 iLUNG-CM); a grant from the CRIS Cancer Foundation (to M.B.); and a grant from the Spanish Ministry of Science, Innovation and Universities (RTI2018-094664-B-I00, to M.B. and M.M.). M.B. is a recipient of an Endowed Chair from the AXA Research Fund. M.S. was supported by predoctoral contract "Severo Ochoa" (BES-2016-079096) from the SpanishMinistry of Science, Innovation and Universities. G.P. was a recipient of a "Young Ph.D." grant from the Government of the Community of Madrid. F.F.-G. was supported by a formacion de profesorado universitario (FPU) fellowship from the Spanish Ministry of Science, Innovation and Universities. Sí

Background Protein homeostasis, primarily regulated by the ubiquitin-proteasome system is crucial for proper function of cells. In tissues of post-mitotic cells, the impaired ubiquitin-proteasome system is found in a wide range of neuromuscular disorders. Activity-based probes (ABPs) measure proteasomal proteolytic subunits and can be used to report protein homeostasis. Despite the crucial role of the proteasome in neuromuscular pathologies, ABPs were not employed in muscle cells and tissues, and measurement of proteasomal activity was carried out in vitro using low-throughput procedures. Methods We screened six ABPs for specific application in muscle cell culture using high throughput call-based imaging procedures. We then determined an in situ proteasomal activity in myofibers of muscle cryosections. Results We demonstrate that LWA300, a pan-reactive proteasomal probe, is most suitable to report proteasomal activity in muscle cells using cell-based bio-imaging. We found that proteasomal activity is two-fold and three-fold enhanced in fused muscle cell culture compared with non-fused cells. Moreover, we found that proteasomal activity can discriminate between muscles. Across muscles, a relative higher proteasomal activity was found in hybrid myofibers whereas fast-twitch myofibers displayed lower activity. Conclusions Our study demonstrates that proteasomal activity differ between muscles and between myofiber types. We suggest that ABPs can be used to report disease progression and treatment efficacy.

Background Protein homeostasis, primarily regulated by the ubiquitin–proteasome system is crucial for proper function of cells. In tissues of post‐mitotic cells, the impaired ubiquitin–proteasome system is found in a wide range of neuromuscular disorders. Activity‐based probes (ABPs) measure proteasomal proteolytic subunits and can be used to report protein homeostasis. Despite the crucial role of the proteasome in neuromuscular pathologies, ABPs were not employed in muscle cells and tissues, and measurement of proteasomal activity was carried out in vitro using low‐throughput procedures. Methods We screened six ABPs for specific application in muscle cell culture using high throughput call‐based imaging procedures. We then determined an in situ proteasomal activity in myofibers of muscle cryosections. Results We demonstrate that LWA300, a pan‐reactive proteasomal probe, is most suitable to report proteasomal activity in muscle cells using cell‐based bio‐imaging. We found that proteasomal activity is two‐fold and three‐fold enhanced in fused muscle cell culture compared with non‐fused cells. Moreover, we found that proteasomal activity can discriminate between muscles. Across muscles, a relative higher proteasomal activity was found in hybrid myofibers whereas fast‐twitch myofibers displayed lower activity. Conclusions Our study demonstrates that proteasomal activity differ between muscles and between myofiber types. We suggest that ABPs can be used to report disease progression and treatment efficacy.

Activity-based protein profiling (ABPP) is a method to highlight enzymatic activities in a biological sample, which uses chemical probes that react covalently with the catalytic nucleophile of the enzyme. To circumvent disadvantages associated with the presence of reporter tags on chemical probes, the probe is equipped with a ligation handle to which the reporter can be reacted at the desired time and place in the ABPP workflow. This chapter demonstrates the power of a triple bioorthogonal ligation strategy which addresses the three activities of the proteasome: the β5-subunit selective norbornene-tagged probe is reacted with fluorescent tetrazine, the β1-selective azide-functionalized probe was addressed with a biotinylated phosphine, followed by an alkyne-substituted pan-reactive probe to label the remaining β2 activity to which an azide-coupled fluorophore was ligated. The result of the triple ligation was similar to each reaction performed separately demonstrating the value of the triple ligation strategy for a single experiment.

Activity-based protein profiling (ABPP) is a method to highlight enzymatic activities in a biological sample, which uses chemical probes that react covalently with the catalytic nucleophile of the enzyme. To circumvent disadvantages associated with the presence of reporter tags on chemical probes, the probe is equipped with a ligation handle to which the reporter can be reacted at the desired time and place in the ABPP workflow. This chapter demonstrates the power of a triple bioorthogonal ligation strategy which addresses the three activities of the proteasome: the β5-subunit selective norbornene-tagged probe is reacted with fluorescent tetrazine, the β1-selective azide-functionalized probe was addressed with a biotinylated phosphine, followed by an alkyne-substituted pan-reactive probe to label the remaining β2 activity to which an azide-coupled fluorophore was ligated. The result of the triple ligation was similar to each reaction performed separately demonstrating the value of the triple ligation strategy for a single experiment.

Poly(A) Binding Protein Nuclear 1 (PABPN1) is a multifunctional regulator of mRNA processing, and its expression levels specifically decline in aging muscles. An expansion mutation in PABPN1 is the genetic cause of oculopharyngeal muscle dystrophy (OPMD), a late onset and rare myopathy. Moreover, reduced PABPN1 expression correlates with symptom manifestation in OPMD. PABPN1 regulates alternative polyadenylation site (PAS) utilization. However, the impact of PAS utilization on cell and tissue function is poorly understood. We hypothesized that altered PABPN1 expression levels is an underlying cause of muscle wasting. To test this, we stably down-regulated PABPN1 in mouse tibialis anterior (TA) muscles by localized injection of adeno-associated viruses expressing shRNA to PABPN1 (shPab). We found that a mild reduction in PABPN1 levels causes muscle pathology including myofiber atrophy, thickening of extracellular matrix and myofiber-type transition. Moreover, reduced PABPN1 levels caused a consistent decline in distal PAS utilization in the 3’-UTR of a subset of OPMD-dysregulated genes. This alternative PAS utilization led to up-regulation of Atrogin-1, a key muscle atrophy regulator, but down regulation of proteasomal genes. Additionally reduced PABPN1 levels caused a reduction in proteasomal activity, and transition in MyHC isotope expression pattern in myofibers. We suggest that PABPN1-mediated alternative PAS utilization plays a central role in aging-associated muscle wasting., Author Summary PABPN1 is a multifunctional regulator of mRNA processing and its levels are reduced in skeletal muscles from midlife onwards. Reduced PABPN1 levels in a mouse model causes muscle atrophy and muscle fiber switches. We show that PABPN1-regulated muscle atrophy is regulated, in part, by up regulation of Atrogin1 and reduced expression of proteasome genes via an alternative polyadenylation site utilization. This study reveals a functional role for alternative polyadenylation site utilization in muscle atrophy and suggests a role for RNA processing in muscle aging.

Adaptive resistance of myeloma to proteasome inhibition represents a clinical challenge, whose biology is poorly understood. Proteasome mutations were implicated as underlying mechanism, while an alternative hypothesis based on low activation status of the unfolded protein response was recently suggested (IRE1/XBP1-low model). We generated bortezomib- and carfilzomib-adapted, highly resistant multiple myeloma cell clones (AMO-BTZ, AMO-CFZ), which we analyzed in a combined quantitative and functional proteomic approach. We demonstrate that proteasome inhibitor-adapted myeloma cells tolerate subtotal proteasome inhibition, irrespective of a proteasome mutation, and uniformly show an 'IRE1/XBP1-low' signature. Adaptation of myeloma cells to proteasome inhibitors involved quantitative changes in >600 protein species with similar patterns in AMO-BTZ and AMO-CFZ cells: proteins involved in metabolic regulation, redox homeostasis, and protein folding and destruction were upregulated, while apoptosis and transcription/translation were downregulated. The quantitatively most upregulated protein in AMO-CFZ cells was the multidrug resistance protein (MDR1) protein ABCB1, and carfilzomib resistance could be overcome by MDR1 inhibition. We propose a model where proteasome inhibitor-adapted myeloma cells tolerate subtotal proteasome inhibition owing to metabolic adaptations that favor the generation of reducing equivalents, such as NADPH, which is supported by oxidative glycolysis. Proteasome inhibitor resistance may thus be targeted by manipulating the energy and redox metabolism.

Cleavage analyses of 20S proteasomes with natural or synthetic substrates allowed to infer the substrate specificities of the active sites and paved the way for the rational design of high-affinity proteasome inhibitors. However, details of cleavage preferences remained enigmatic due to the lack of appropriate structural data. In a unique approach, we here systematically examined substrate specificities of yeast and human proteasomes using irreversibly acting α',β'epoxyketone (ep) inhibitors. Biochemical and structural analyses provide unique insights into the substrate preferences of the distinct active sites and highlight differences between proteasome types that may be considered in future inhibitor design efforts. (1) For steric reasons, epoxyketones with Val or Ile at the P1 position are weak inhibitors of all active sites. (2) Identification of the β2c selective compound Ac-LAE-ep represents a promising starting point for the development of compounds that discriminate between β2c and β2i. (3) The compound Ac-LAA-ep was found to favor subunit β5c over β5i by three orders of magnitude. (4) Yeast β1 and human β1c subunits preferentially bind Asp and Leu in their S1 pockets, while Glu and large hydrophobic residues are not accepted. (5) Exceptional structural features in the β1/2 substrate binding channel give rise to the β1 selectivity of compounds featuring Pro at the P3 site. Altogether, 23 different epoxyketone inhibitors, five proteasome mutants, and 43 crystal structures served to delineate a detailed picture of the substrate and ligand specificities of proteasomes and will further guide drug development efforts toward subunit-specific proteasome inhibitors for applications as diverse as cancer and autoimmune disorders.

Adaptive resistance of myeloma cells to proteasome inhibition is poorly understood. It is suggested to base on point mutations in PSMB5 and/or downmodulation of the activation state of the unfolded protein response (UPR) via reduced activity of its major regulatory axis IRE-1/XBP-1. We have generated subclones of the AMO-1 myeloma cell line resistant to bortezomib > 1000 nM (AMO-BTZ), or carfilzomib > 1000 nM (AMO-CFZ), that do or do not carry the PSMB5 A310G mutation in the β5 substrate pocket. We combine this model with a global quantitative proteomics approach, the analysis of the activation status of the IRE-1/XBP-1 pathway, and with an advanced set of proteasome activity-specific fluorescent affinity probes that allow direct, selective, simultaneous visualization of the activity of all six active β-subunits of the constitutive and the immunoproteasome. Our results demonstrate that the A310G mutation has a modest impact on β5c proteasome inhibition by bortezomib (increasing the IC50 from 25nM to 80 nM), and likewise by carfilzomib (IC50 increase from 10 nM to 50 nM). Strikingly, when AMO-CFZ or AMO-BTZ were exposed to the same functional level of proteasome inhibition (> 90% inhibition of β5c/5i, 20% inhibition of β1/1i, β2/2i) that resulted in 70-90% cytotoxicity in AMO-1 cells, no cytotoxicity was observed in AMO-BTZ and AMO-CFZ cells. Likewise, AMO-BTZ and AMO-CFZ cells were resistant to the next generation proteasome inhibitors ixazomib, oprozomib and dalanzomib, irrespective of the presence or absence of the PSMB5 mutation. Analysis of the UPR and its major regulators on protein and mRNA levels revealed that all clones of AMO-BTZ and AMO-CFZ showed significantly lower expression of IRE-1 and its product, spliced XBP-1, compared to AMO-1 cells, in contrast to all other major regulators of the UPR (ATF6, PERK, elF2a). Proteasome inhibitor treatment induced phosphorylation of IRE-1 and the induction of sXBP1 similarly in AMO-1, AMO-BTZ and AMO-CFZ cells, however, the induction of downstream proteins of the UPR (ATF4, PDI) was exclusively found in AMO-1 cells. Mass spectrometry-based quantitative global proteomic analysis was performed to compare AMO-1 cells with AMO-BTZ and AMO-CFZ with a cut off of at least a 50% change in abundance of differentially expressed proteins in at least 2 out of triplicate experiments. This yielded > 3500 identified individual proteins in proteasome inhibitor adapted cells, of which > 600 were differentially expressed and subsequently subjected to a protein-protein interaction (PPI) search and a Gene Ontology (GO) analysis, resulting in an average of 30 GO terms for the overexpressed proteins and 10 for downregulated species in AMO-BTZ and AMO-CFZ. Manual grouping of GO into functionally related clusters resulted in 5-6 groups that were largely concordant between AMO-BTZ and AMO-CFZ. The clusters found overexpressed in AMO-BTZ and AMO-CFZ were proteins involved in protein catabolism, redox control and protein folding. Uniform downregulation was observed for protein clusters involved in transcription/translation, differentiation, apoptosis and structural/cytoskeletal functions. The quantitatively largest group of proteins with significantly altered expression levels in AMO-BTZ/AMO-CFZ vs. AMO-1 control cells consisted of proteins involved in metabolic regulation. This big cluster comprised close to 50 % of all polypeptides with significant quantitative changes, suggesting a key role for metabolic homeostasis. The quantitatively most significantly upregulated protein in both AMO-CFZ and AMO-BTZ was NADPH dehydrogenase, the most important reducing enzyme in eukaryotic cells (4-6 x upregulated). The top individual upregulated protein in AMO-CFZ was the p-glycoprotein 1 (Pgp, 12 x upregulated), while the transcription factor IKZF3 was among the top downregulated proteins in AMO-BTZ cells (0.2 x). Our data indicate that proteasome gene mutations are not required for proteasome inhibitor resistance of myeloma cells, that proteasome inhibitor adapted myeloma cells can compensate subtotal proteasome inhibition irrespective of the type of inhibitor used, and that they have undergone complex adaptive changes in particular in proteins that regulate metabolic functions. Thus we suggest that the metabolic machinery rather than the proteasome should be explored for drug targets in myeloma cells with acquired proteasome inhibitor resistance. Disclosures No relevant conflicts of interest to declare.