Choice of fusion proteins, expression host, and analytics solves difficult-to-produce protein challenges in discovery research

High quality biological reagents are a prerequisite for pharmacological research. Herein a protein production screening approach, including quality assessment methods, for protein-based discovery research is presented. Trends from 2895 expression constructs representing 253 proteins screened in mammalian and bacterial hosts-91% of which are successfully expressed and purified-are discussed. Mammalian expression combined with the use of solubility-promoting fusion proteins is deemed suitable for most targets. Furthermore, cases utilizing stable cell line generation and choice of fusion protein for higher yield and quality of difficult-to-produce proteins (Leucine-rich repeat-containing G-protein coupled receptor 4 (LGR4) and Neurturin) are presented and discussed. In the case of Neurturin, choice of fusion protein impacted the target binding 80-fold. These results highlight the need for exploration of construct designs and careful Quality Control (QC) of difficult-to-produce protein reagents.

Designed Endocytosis-Triggering Proteins mediate Targeted Degradation

Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by interaction with endogenous ligands. Therapeutic approaches such as LYTAC1,2 and KineTAC3, have taken advantage of this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. While powerful, these approaches can be limited by possible competition with the endogenous ligand(s), the requirement in some cases for chemical modification that limits genetic encodability and can complicate manufacturing, and more generally, there may not be natural ligands which stimulate endocytosis through a given receptor. Here we describe general protein design approaches for designing endocytosis triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for the IGF-2R, ASGPR, Sortillin, and Transferrin receptors, and show that fusing these tags to proteins which bind to soluble or transmembrane protein leads to lysosomal trafficking and target degradation; as these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. The modularity and genetic encodability of EndoTags enables AND gate control for higher specificity targeted degradation, and the localized secretion of degraders from engineered cells. The tunability and modularity of our genetically encodable EndoTags should contribute to deciphering the relationship between receptor engagement and cellular trafficking, and they have considerable therapeutic potential as targeted degradation inducers, signaling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody drug and RNA conjugates.

Ascertainment of aortic valve disease using administrative claims

Background

Administrative claims may be useful for characterizing patients with aortic stenosis (AS) and aortic regurgitation (AR) and estimating disease prevalence. However, the accuracy of diagnostic codes for aortic valve disease has not been well studied.

Purpose

To evaluate the validity of International Classification of Diseases, 10th Revision (ICD-10) codes for identification of AS and AR.

Methods

Using a large, transthoracic echocardiographic (TTE) report dataset linked to Medicare Fee-for-service (FFS) claims, 2017–2018, the performance of candidate claims to ascertain AS/AR status using standard TTE definitions was evaluated. Recursive partitioning with 10-fold cross validation was used to build the optimal prediction tree for AS/AR status using all ICD-10 codes as candidate predictors. The optimal performing claims algorithm was tested against patient outcomes in a separate 100% sample of Medicare FFS inpatient and outpatient claims, 2017–2019.

Results

Of those included in the derivation dataset (N=5497, mean age 74.4±11.0 years, 49.7% female), any AS or AR was present in 24% and 38.8%, respectively. The code I35.0 was optimal for identification of any AS with a sensitivity and specificity for any AS of 53.1% and 94.8%, respectively (Table 1). Amongst those with an I35.0 code, 40.3% had severe AS. Claims were unable to distinguish disease severity (i.e. severe vs. non-severe) or subtypes (e.g. bicuspid or rheumatic AS), and were insensitive and nonspecific for AR of any severity. Among all Medicare beneficiaries who received an TTE (N=3,783,249), those with an I35.0 code, compared to those without, had a higher risk of all-cause mortality (HR 1.65, 95% CI 1.63–1.67), heart failure hospitalization (HR 2.17, 95% CI 2.11–2.24), and aortic valve replacement (HR 32.35, 95% CI 31.46–33.27) (Table 2).

Conclusions

Amongst those receiving TTE, the ICD-10 code I35.0 in any position was optimal for identification of AS and identified a population at significant greater risk of all-cause mortality, heart failure hospitalization, and receipt of aortic valve replacement. Though 40.3% of those with I35.0 had severe AS, claims were unable to distinguish disease severity of subtype. Claims may be feasibly used to identify those with AS who may be at risk for adverse valve-related cardiovascular events and require future treatment.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): National, Heart, Lung, and Blood Institute

Variations in the Course of the Carotid Arteries in Patients with Retropharyngeal Parathyroid Adenomas

The carotid arteries, classically described as taking a relatively straight course through the neck, deviate medially in a minority of patients. At the extreme, the internal carotid arteries may "kiss" in the midline, coming extremely close to the pharyngeal wall. In this clinical report, we describe 5 patients with primary hyperparathyroidism, all with ectopic retropharyngeal parathyroid adenomas but all with varying carotid artery anatomy. We describe these variations using a previously developed clinical grading system that highlights 1) the relationship between carotid artery location and risk of injury during pharyngeal procedures and 2) the importance of universal, objective criteria to classify carotid anatomy. Radiologists should be familiar with variations in carotid anatomy and communicate them to the operative team.

A Simple Formula to Estimate Parathyroid Weight on 4D-CT, Predict Pathologic Weight, and Diagnose Parathyroid Adenoma in Patients with Primary Hyperparathyroidism

BACKGROUND AND PURPOSE

Parathyroid gland weight is a clinically relevant parameter used to diagnose parathyroid adenomas intraoperatively. We evaluated the accuracy of a formula to estimate parathyroid weight on preoperative 4D-CT.

MATERIALS AND METHODS

A single-institution retrospective study was performed in patients with primary hyperparathyroidism who underwent 4D-CT between January 2013 and December 2014 with subsequent parathyroidectomy and surgical cure. All patients had correct localization of a solitary parathyroid adenoma. The longest 3 dimensions of all identified parathyroid glands were measured on CT, and weight was estimated using the formula: weight_4D-CT (mg) = 1 mg/mm³ × Length (mm) × Width (mm) × Height (mm) × π/6. We correlated weight_4D-CT with pathology specimen weight (weight_pathology). Using receiver operating characteristic analysis, we estimated the performance of weight_4D-CT to discriminate a parathyroid adenoma from normal glands on 4D-CT and determined the optimal threshold based on the Youden index.

RESULTS

One hundred sixteen patients (85 women, 31 men) were evaluated. Weight_4D-CT was shown to be strongly correlated with weight_pathology as demonstrated by Spearman ρ = 0.73 (P < .01), concordance correlation coefficient = 0.92 (95% CI, 0.89-0.94), and Cronbach α = 0.96. The performance of weight_4D-CT for the diagnosis of parathyroid adenoma was excellent, with an area under the curve of 0.955 (95% CI, 0.925-0.985; P < .001). Based on the Youden index, the optimal threshold was >50 mg, with a sensitivity of 96.7% and a specificity of 95.7%.

CONCLUSIONS

Radiologists can accurately estimate parathyroid adenoma weight on 4D-CT. This metric is highly correlated with pathologic weight, and a threshold cutoff of >50 mg can be used to distinguish parathyroid adenoma from normal glands.

Comparison of morphological changes of muscle fibers in response to dynamic electrical muscle contraction and dynamic hydraulic stimulation in a rat hindlimb disuse model

This study attempted to compare the muscle fiber morphological responses to dynamic electrical muscle stimulation (DEMS) and dynamic hydraulic stimulation (DHS) in rats under hindlimb suspension (HLS). DEMS at 1 Hz, 50 Hz and 100 Hz for 10 min/day, 5 days/week were introduced to the animals' right quadriceps. Static and 2 Hz DHS were introduced to the right tibiae of other animal groups on a "10 min on - 5 min off - 10 min on" loading regime for 5 days/week. In the end of the 4-week experiments, histological changes in the corresponding soleus, gastrocnemius and quadriceps of the stimulated sites were examined. Compared to age-matched, HLS led to muscle atrophy and strongly reduced muscle wet weights and averaged cross-sectional fiber areas. Among the tested DEMS frequencies, the averaged cross-sectional quadriceps fiber area in the 50 Hz group was 29 % larger than the 100 Hz group. In contrast, difference in the muscle fiber response to the static and 2 Hz DHS was not observed in either soleus or gastrocnemius. Muscle fiber morphological responses to the active DEMS was in a load frequency dependent manner under disuse condition. Relatively passive compressions, either via static or 2Hz DHS, were unable to induce any difference in the muscle fiber responses under functional disuse.

Critical role of activation induced cytidine deaminase in experimental autoimmune encephalomyelitis

Multiple Sclerosis (MS) is a neurodegenerative autoimmune disorder caused by chronic inflammation and demyelination within the central nervous system (CNS). Clinical studies in MS patients have demonstrated efficacy with B cell targeted therapies such as anti-CD20. However, the exact role that B cells play in the disease process is unclear. Activation Induced cytidine deaminase (AID) is an essential enzyme for the processes of antibody affinity maturation and isotype switching. To evaluate the impact of affinity maturation and isotype switching, we have interrogated the effect of AID-deficiency in an animal model of MS. Here, we show that the severity of experimental autoimmune encephalomyelitis (EAE) induced by the extracellular domain of human myelin oligodendrocyte glycoprotein (MOG1-125) is significantly reduced in Aicda deficient mice, which, unlike wild-type mice, lack serum IgG to myelin associated antigens. MOG specific T cell responses are comparable between wild-type and Aicda knockout mice suggesting an active role for antigen experienced B cells. Thus affinity maturation and/or class switching are critical processes in the pathogenesis of EAE.

HectD1 E3 ligase modifies adenomatous polyposis coli (APC) with polyubiquitin to promote the APC-axin interaction

The adenomatous polyposis coli (APC) protein functions as a negative regulator of the Wnt signaling pathway. In this capacity, APC forms a "destruction complex" with Axin, CK1α, and GSK3β to foster phosphorylation of the Wnt effector β-catenin earmarking it for Lys-48-linked polyubiquitylation and proteasomal degradation. APC is conjugated with Lys-63-linked ubiquitin chains when it is bound to Axin, but it is unclear whether this modification promotes the APC-Axin interaction or confers upon APC an alternative function in the destruction complex. Here we identify HectD1 as a candidate E3 ubiquitin ligase that modifies APC with Lys-63 polyubiquitin. Knockdown of HectD1 diminished APC ubiquitylation, disrupted the APC-Axin interaction, and augmented Wnt3a-induced β-catenin stabilization and signaling. These results indicate that HectD1 promotes the APC-Axin interaction to negatively regulate Wnt signaling.

Endoscopic mucosal resection for early cancers of the upper gastrointestinal tract

The purpose of this literature review is to examine recent advances in technique and technology of endoscopic mucosal resection of superficial early cancers of the upper gastrointestinal tract. Endoscopic mucosal resection (EMR) of superficial early cancers of the upper gastrointestinal tract is standard technique in Japan and is increasingly used in Western countries. Newer techniques of EMR allow removal of larger lesions en-bloc. These minimally invasive techniques, when applied correctly, allow safe and efficacious treatment in situations that would otherwise require major surgery. Through the establishment of long-term outcomes data, standardization of endoscopic and pathologic reporting, and newer EMR technology and techniques, the future treatment of early cancers in the upper gastrointestinal tract may be achieved primarily through the endoscope.

Single-nucleotide polymorphisms in the public domain: how useful are they?

There is a concerted effort by a number of public and private groups to identify a large set of human single-nucleotide polymorphisms (SNPs). As of March 2001, 2.84 million SNPs have been deposited in the public database, dbSNP, at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/SNP/). The 2.84 million SNPs can be grouped into 1.65 million non-redundant SNPs. As part of the International SNP Map Working Group, we recently published a high-density SNP map of the human genome consisting of 1.42 million SNPs (ref. 3). In addition, numerous SNPs are maintained in proprietary databases. Our survey of more than 1,200 SNPs indicates that more than 80% of TSC and Washington University candidate SNPs are polymorphic and that approximately 50% of the candidate SNPs from these two sources are common SNPs (with minor allele frequency of > or =20%) in any given population.

Purification and characterization of human lymphoblast N-acetylglucosamine-1-phosphotransferase

N-Acetylglucosamine-1-phosphotransferase (GlcNAcPTase) was solubilized with 2% Tergitol NP-10 from cultured human lymphoblast cells and purified 3840-fold with 14% recovery using lentil lectin-Sepharose 4B, DEAE-Sephacel and Sephacryl S-400 chromatographies. The partially purified enzyme requires the non-ionic detergent Tergitol NP-10 and a divalent cation, Mn2+ or Mg2+, for its activity and exhibits an optimal pH at 7.2-7.5 in Tris-maleate buffer. Kinetic studies demonstrated an apparent Km of 24 microM for the donor UDP-N-acetylglucosamine and of 117 mM for the artificial acceptor alpha-methylmannoside. The GlcNAcPTase is inhibited by UDP and UDP-glucose, and by negatively charged phospholipids including phosphatidylserine, phosphatidylglycerol and phosphatidic acid. The apparent mol. wt of the human lymphoblast GlcNAcPTase is approximately 1000 kDa, which is analogous to that reported for the partially purified enzyme from rat liver (Waheed et al., 1982).

Human intestinal brush border peptidases

Hydrolysis of small peptides, like disaccharide hydrolysis, is an important function of the intestinal brush border, but little is known of the individual human peptidases. The purposes of this study were to detect all human brush border enzymes hydrolyzing dipeptides and tripeptides, identify the most discriminating substrate for each enzyme in order to permit assays in crude mixtures, and begin biochemical characterization of each enzyme. Four brush border peptidases were identified. Enzymes I (aspartate aminopeptidase, E.C. 3.4.11.7) and III (amino-oligopeptidase, E.C. 3.4.11.2) are known brush border enzymes. Enzymes II (membrane Gly-Leu peptidase) and IV (zinc stable Asp-Lys peptidase) have not been identified in human brush border previously. They are distinct from dipeptidyl aminopeptidase IV, carboxypeptidase, and gamma-glutamyl transferase. The substrate most discriminating for each enzyme is alpha-Glu-beta-naphthylamide for I (100% of the brush border activity for this substrate is due to enzyme I), glycylleucine for II (80%), leucyl-beta-naphthylamide for III (91%), and aspartyl-lysine in 5 mM Zn2+ for IV (63%). The enzymes are immunologically distinct and antibodies to each one localize to the brush border on immunohistochemical staining. Purification of 142-, 79-, 158-, and 46-fold was achieved for enzymes I through IV, respectively. Biochemical characteristics include slightly alkaline pH optima, molecular weights of 91,000-190,000, and evidence of metal ion involvement in activity. These studies provide necessary information for determining the role of brush border peptidase deficiencies in human disease.

Structural analysis of the asparagine-linked oligosaccharides from three lysosomal enzymes of Dictyostelium discoideum. Evidence for an unusual acid-stable phosphodiester

Lysosomal enzymes of the slime mold Dictyostelium discoideum contain mannose 6-phosphate and bind with high affinity to the phosphomannosyl receptor of human fibroblasts. In this study, we have partially characterized the Asn-linked oligosaccharide units present on these enzymes. [3H]Mannose-labeled alpha-D-mannosidase, beta-D-glucosidase, and beta-D-N-acetylglucosaminidase were purified from the spent growth medium of strain AX3 and glycopeptides were prepared by pronase digestion. Approximately 75% of the glycopeptides contained sulfate residues. These could be removed by solvolysis without degrading the underlying oligosaccharide. Following solvolysis (but not before), the oligosaccharides could be released by endo-beta-N-acetylglucosaminidase H, indicating the presence of high mannose-type units. Greater than 85% of the oligosaccharides contained one or two mannose 6-phosphate residues in the form of an unusual acid-stable phosphodiester. About 3% of the oligosaccharides contained phosphomonoesters and only 6% were neutral species. The major neutral oligosaccharide eluted in the position of Man9GlcNAc when analyzed by high performance liquid chromatography whereas the minor species appeared to be 1-2 residues larger. Acetolysis of the major phosphorylated fractions revealed that molecules with a single mannose 6-phosphate contained the phosphomannosyl residue on the branch linked alpha 1,6 to the beta-linked mannose whereas molecules with two phosphomannosyl residues had the residues on this branch as well as the branch linked alpha 1,3 to the beta-linked mannose. The mechanism of mannose phosphorylation in the slime mold must differ from that of mammalian cells since the phosphomannosyl residues are present as acid-resistant phosphodiesters rather than acid-labile phosphodiesters.

The mod A mutant of Dictyostelium discoideum is missing the alpha 1,3-glucosidase involved in asparagine-linked oligosaccharide processing

The recessive mutation, mod A, in the Dictyostelium discoideum strain M31 results in an alteration in the post-translational modification of lysosomal enzymes. We now report studies which indicate that mod A is deficient in glucosidase II, an enzyme which is involved in the processing of asparagine-linked oligosaccharides. [2-3H]Mannose-labeled glycopeptides were prepared from three purified mod A lysosomal enzymes and compared to the equivalent glycopeptides from parental enzymes. The mod A glycopeptides were deficient in high mannose oligosaccharides containing two phosphomannosyl residues and accumulated oligosaccharides with one phosphomannosyl residue. The phosphate was present in the form of an acid-stable phosphodiester in both instances. There was also an increase in the amount of nonphosphorylated high mannose oligosaccharides mod A and these were larger than the corresponding material from the parental enzymes. In addition, the nonphosphorylated oligosaccharides were only partially degraded by alpha-mannosidase, indicating the presence of a blocking moiety. In vitro enzyme assays demonstrated that the mod A cells cannot remove the inner 1 leads to 3-linked glucose from a glucosylated high mannose oligosaccharide. The cells are also deficient in membrane-bound neutral p-nitrophenyl-alpha-D-glucosidase activity. This activity has been attributed to glucosidase II in other systems. Removal of the outer 1 leads to 2-linked glucose from Glc3Man9Glc-NAc2 is normal, demonstrating the presence of glucosidase I activity. We conclude from these data that M31 cells are deficient in glucosidase II, the enzyme which removes the two inner glucose residues from the glucosylated oligosaccharides of newly glycosylated proteins. This defect can explain the mod A phenotype and is proposed to be the primary genetic defect in these cells.

The effects of sodium bisulfite, manganous chloride, and 2,4-dichlorophenol on peroxidase-catalyzed oxidation of indole-3-acetaldehyde

The effects of pH, sodium bisulfite, manganous chloride, and 2,4-dichlorophenol (DCP) on horseradish peroxidase (HRP) catalyzed oxidation of indole-3-acetaldehyde (IAAld) and indole-3-acetic acid (IAA) were studied. The enzymatic system is inactive toward oxidation of these indole derivatives at neutral to alkaline pH, whereas addition of NaHSO3 restores enzymatic activity at alkaline pH. In contrast, NaHSO3 (or Na2SO3) inhibits HRP-catalyzed oxidation of IAAld at acidic pH. Some kinetic data are presented to show how the bisulfite ions are involved in HRP-catalyzed oxidation of IAAld. Manganous chloride and DCP are excellent catalysts for HRP-catalyzed oxidation of IAA but have no effect on oxidation of IAAld.