One-shot design elevates functional expression levels of a voltage-gated potassium channel.

Membrane proteins play critical physiological roles as receptors, channels, pumps, and transporters. Despite their importance, however, low expression levels often hamper the experimental characterization of membrane proteins. We present an automated and web-accessible design algorithm called mPROSS (https://mPROSS.weizmann.ac.il), which uses phylogenetic analysis and an atomistic potential, including an empirical lipophilicity scale, to improve native-state energy. As a stringent test, we apply mPROSS to the Kv1.2-Kv2.1 paddle chimera voltage-gated potassium channel. Four designs, encoding 9-26 mutations relative to the parental channel, were functional and maintained potassium-selective permeation and voltage dependence in Xenopus oocytes with up to 14-fold increase in whole-cell current densities. Additionally, single-channel recordings reveal no significant change in the channel-opening probability nor in unitary conductance, indicating that functional expression levels increase without impacting the activity profile of individual channels. Our results suggest that the expression levels of other dynamic channels and receptors may be enhanced through one-shot design calculations.

Pancreatic Walled-Off Necrosis: Cross-Sectional Imaging Depiction of Debris Predicts the Success of Endoscopic Drainage Using Lumen Apposing Metal Stents.

BACKGROUND: The use of endoscopic ultrasound-guided (EUS) transmural stent placement for pancreatic walled-off-necrosis (WON) drainage is widespread. This study retrospectively analyzes imaging parameters predicting the outcomes of WON endoscopic drainage using lumen apposing metal stents (LAMS). METHODS: The study analyzed data of 115 patients who underwent EUS-guided debridement using LAMS from 2011 to 2015. Pre-intervention CT or MRI were used to analyze WON total volume, percentage of debris, multilocularity, and density. Success measures included technical success, the number of endoscopic sessions, requirement of percutaneous drainage, long-term success, and recurrence. RESULTS: The primary cause of pancreatitis was gallstones (50.4%), followed by alcohol (27.8%), hypertriglyceridemia (11.3%), idiopathic (8.7%), and autoimmune (1.7%). The mean WON size was 674 mL. All patients underwent endoscopic necrosectomies, averaging 3.1 sessions. Stent placement was successful in 96.5% of cases. Procedural complications were observed in 13 patients (11.3%) and six patients (5.2%) needed additional percutaneous drainage. No patients reported recurrent WON post-treatment. Univariate analysis indicated a significant correlation between debris percentage and the need for additional drainage and long-term success (p <0.001). The number of endoscopic sessions correlated significantly with debris percentage (p < 0.001). CONCLUSIONS: Preprocedural imaging, particularly debris percentage within WON, significantly predicts the number of endoscopic sessions, the need for further percutaneous drainage, and overall long-term success.

Characterizing Trends in Chronic Superficial Venous Disease Treatment among Medicare Beneficiaries from 2010 to 2018.

This study describes trends in surgical versus endovascular interventions for treatment of chronic superficial venous disease (SVD) in the Medicare population. Medicare Part B data from 2010 to 2018 were obtained. Claims for SVD treatment were identified using Healthcare Common Procedure Coding System codes. Total percentage change in utilization rates and market share was determined for each provider group. Utilization of SVD treatments increased by 58%, mostly owing to growing utilization of endovascular treatments. There was a 66% decrease in surgical treatments. The utilization of ablation and sclerotherapy plateaued in 2016 and decreased in 2017-2018 with the advent of mechanochemical ablation, endovenous microfoam, and cyanoacrylate adhesive, respectively. Analysis showed that endovascular utilization increased across most specialties, with the largest growth seen in cardiology by 427%. Radiologists showed utilization growth of 125%, encompassing 11% of the market share. Endovascular treatment for SVD remains predominant, with increased utilization and concomitant decrease in surgical methods.

Hepatic Steatosis After Partial Pancreatectomy in a Cohort of Patients with Intraductal Papillary Mucinous Neoplasm.

Background/Aims: Nonalcoholic fatty liver disease (NAFLD) has been observed in patients after partial pancreatectomy. Previous studies have been performed on oncologic patients who underwent partial pancreatectomy and received adjuvant chemotherapy. By studying a cohort of patients with intraductal papillary mucinous neoplasms (IPMNs) who did not receive chemotherapy, the authors investigate the isolated effect of partial pancreatectomy on the development of fatty liver. Methods: A retrospective search for patients with pancreatic IPMNs who underwent partial pancreatectomy at an academic center from 2006 to 2014 identified 63 patients, including 42 who had pancreaticoduodenectomy (PD) and 21 who had distal pancreatectomy (DP). Fourteen patients with preoperative hepatic steatosis, diabetes, obesity, on steroid therapy, history of malignancy, or incomplete data were excluded. No patient received chemotherapy. Liver fat signal fraction (LFSF) was computed by the Dixon method using pre- and postoperative in- and out-of-phase MRI. Results: Of the 49 patients included in the study, 29 (59%) underwent PD and 20 (41%) underwent DP. A total of 17 patients (34%) developed fatty liver after surgery. The entire cohort developed significant weight loss, 72.1 versus 69.4 kg (P < 0.01). Postoperatively, there was significant increase in LFSF, 1.3% versus 9.6% following PD (P < 0.01), and 2.1% versus 9.4% following DP (P = 0.01). Conclusion: Partial pancreatectomy increases the risk of NAFLD independent of chemotherapy-induced hepatotoxicity. The underlying mechanism remains unclear and possibly related to pancreatic exocrine insufficiency and malnutrition.

Mega-scale experimental analysis of protein folding stability in biology and design.

Advances in DNA sequencing and machine learning are providing insights into protein sequences and structures on an enormous scale1. However, the energetics driving folding are invisible in these structures and remain largely unknown2. The hidden thermodynamics of folding can drive disease3,4, shape protein evolution5-7 and guide protein engineering8-10, and new approaches are needed to reveal these thermodynamics for every sequence and structure. Here we present cDNA display proteolysis, a method for measuring thermodynamic folding stability for up to 900,000 protein domains in a one-week experiment. From 1.8 million measurements in total, we curated a set of around 776,000 high-quality folding stabilities covering all single amino acid variants and selected double mutants of 331 natural and 148 de novo designed protein domains 40-72 amino acids in length. Using this extensive dataset, we quantified (1) environmental factors influencing amino acid fitness, (2) thermodynamic couplings (including unexpected interactions) between protein sites, and (3) the global divergence between evolutionary amino acid usage and protein folding stability. We also examined how our approach could identify stability determinants in designed proteins and evaluate design methods. The cDNA display proteolysis method is fast, accurate and uniquely scalable, and promises to reveal the quantitative rules for how amino acid sequences encode folding stability.

Designed active-site library reveals thousands of functional GFP variants.

Mutations in a protein active site can lead to dramatic and useful changes in protein activity. The active site, however, is sensitive to mutations due to a high density of molecular interactions, substantially reducing the likelihood of obtaining functional multipoint mutants. We introduce an atomistic and machine-learning-based approach, called high-throughput Functional Libraries (htFuncLib), that designs a sequence space in which mutations form low-energy combinations that mitigate the risk of incompatible interactions. We apply htFuncLib to the GFP chromophore-binding pocket, and, using fluorescence readout, recover >16,000 unique designs encoding as many as eight active-site mutations. Many designs exhibit substantial and useful diversity in functional thermostability (up to 96 °C), fluorescence lifetime, and quantum yield. By eliminating incompatible active-site mutations, htFuncLib generates a large diversity of functional sequences. We envision that htFuncLib will be used in one-shot optimization of activity in enzymes, binders, and other proteins.

Repurposing the KCa3.1 Blocker Senicapoc for Ischemic Stroke.

Senicapoc, a small molecule inhibitor of the calcium-activated potassium channel KCa3.1, was safe and well-tolerated in clinical trials for sickle cell anemia. We previously reported proof-of-concept data suggesting that both pharmacological inhibition and genetic deletion of KCa3.1 reduces infarction and improves neurologic recovery in rodents by attenuating neuroinflammation. Here we evaluated the potential of repurposing senicapoc for ischemic stroke. In cultured microglia, senicapoc inhibited KCa3.1 currents with an IC50 of 7 nM, reduced Ca2+ signaling induced by the purinergic agonist ATP, suppressed expression of pro-inflammatory cytokines and enzymes (iNOS and COX-2), and prevented induction of the inflammasome component NLRP3. When transient middle cerebral artery occlusion (tMCAO, 60 min) was induced in male C57BL/6 J mice, twice daily administration of senicapoc at 10 and 40 mg/kg starting 12 h after reperfusion dose-dependently reduced infarct area determined by T2-weighted magnetic resonance imaging (MRI) and improved neurological deficit on day 8. Ultra-high-performance liquid chromatography/mass spectrometry analysis of total and free brain concentrations demonstrated sufficient KCa3.1 target engagement. Senicapoc treatment significantly reduced microglia/macrophage and T cell infiltration and activation and attenuated neuronal death. A different treatment paradigm with senicapoc started at 3 h and MRI on day 3 and day 8 revealed that senicapoc reduces secondary infarct growth and suppresses expression of inflammation markers, including T cell cytokines in the brain. Lastly, we demonstrated that senicapoc does not impair the proteolytic activity of tissue plasminogen activator (tPA) in vitro. We suggest that senicapoc could be repurposed as an adjunctive immunocytoprotective agent for combination with reperfusion therapy for ischemic stroke.

Computational design and molecular dynamics simulations suggest the mode of substrate binding in ceramide synthases.

Until now, membrane-protein stabilization has relied on iterations of mutations and screening. We now validate a one-step algorithm, mPROSS, for stabilizing membrane proteins directly from an AlphaFold2 model structure. Applied to the lipid-generating enzyme, ceramide synthase, 37 designed mutations lead to a more stable form of human CerS2. Together with molecular dynamics simulations, we propose a pathway by which substrates might be delivered to the ceramide synthases.

Computational design of BclxL inhibitors that target transmembrane domain interactions.

Several methods have been developed to explore interactions among water-soluble proteins or regions of proteins. However, techniques to target transmembrane domains (TMDs) have not been examined thoroughly despite their importance. Here, we developed a computational approach to design sequences that specifically modulate protein-protein interactions in the membrane. To illustrate this method, we demonstrated that BclxL can interact with other members of the B cell lymphoma 2 (Bcl2) family through the TMD and that these interactions are required for BclxL control of cell death. Next, we designed sequences that specifically recognize and sequester the TMD of BclxL. Hence, we were able to prevent BclxL intramembrane interactions and cancel its antiapoptotic effect. These results advance our understanding of protein-protein interactions in membranes and provide a means to modulate them. Moreover, the success of our approach may trigger the development of a generation of inhibitors targeting interactions between TMDs.

Outcomes of Acceptance and Commitment Therapy for depression and predictors of treatment response in Veterans Health Administration patients.

BACKGROUND: Acceptance and Commitment Therapy for depression (ACT-D) is a promising depression treatment which has not been evaluated on a large scale within VA. This study aimed to evaluate ACT-D's effectiveness in a national, treatment-seeking sample of Veterans. METHODS: The sample comprised 831 Veterans who received a primary depression diagnosis and received at least two sessions of ACT-D during fiscal years 2015-2020. We used GLM to measure predictors of symptom change, treatment response (50 % reduction in PHQ-9 and AAQ-II scores), subthreshold depression symptoms (PHQ-9 < 10; AAQ-II < 27), and treatment completion. RESULTS: Veterans experienced an average reduction of 3.39 points on the PHQ-9 (Cohen's d = 0.56) and 3.76 points on the AAQ-II (Cohen's d = 0.43). On the PHQ-9, 40 % achieved subthreshold depression symptoms. On the AAQ-II, 36 % of Veterans achieved subthreshold psychological inflexibility scores. Service-connected disability rating for depression and higher levels of medical comorbidity were both related to lower levels of overall depression symptom change and treatment response. Substance use disorder and bipolar/psychosis diagnoses were associated with greater reductions in psychological inflexibility. LIMITATIONS: This is an observational study without a control group, so we were unable to compare the effectiveness of ACT-D to other usual care for depression. We were also unable to assess variables that can influence treatment success, such as therapist fidelity and patient engagement. CONCLUSIONS: ACT-D achieved similar improvements in depression as reported in controlled trials. Adaptations to ACT-D may be needed to improve outcomes for Veterans with depression and comorbid PTSD.

The Impact of Community-Based Testing Sites and Gift Incentives on COVID-19 Testing Uptake in Maryland, April 29 - May 9, 2021.

PURPOSE: Information on incentives for COVID-19 testing is needed to understand effective practices that encourage testing uptake. We describe characteristics of those who received an incentive after performing a rapid antigen test. DESIGN: Cross-sectional descriptive analysis of survey data. SETTING: During April 29-May 9, 2021, COVID-19 rapid antigen testing was offered in 2 Maryland cities. SAMPLE: Convenience sample of 553 adults (≥18 years) who tested and received an incentive; 93% consented to survey. MEASURES: Survey questions assessed reasons for testing, testing history, barriers, and demographics. ANALYSIS: Robust Poisson regressions were used to determine characteristic differences based on testing history and between participants who would re-test in the future without an incentive vs participants who would not. RESULTS: The most common reasons for testing were the desire to be tested (n = 280; 54%) and convenience of location (n = 146; 28%). Those motivated by an incentive to test (n = 110; 21%) were 5.83 times as likely to state they would not test again without an incentive, compared to those with other reasons for testing (95% CI: 2.67-12.72, P < .001). CRITICAL LIMITATIONS: No comparative study group. CONCLUSION: Results indicate internal motivation and convenience were prominent factors supporting testing uptake. Incentives may increase community testing participation, particularly among people who have never tested. Keywords COVID-19, pandemic, incentives, health behavior, community testing.

Posttreatment Exposure Rates for 90Y-Microsphere Patients: A Comparison of Products.

There has been a significant increase in the use of 90Y-microspheres in treating liver malignancies. This increase could be seen over the last 30 y, and Food and Drug Administration approval of 2 products-Sirtex SIR-Spheres and Boston Scientific TheraSphere-has helped in the proliferation of these treatments. As the increase in use of both products rose at our institution, there was a need to determine whether there should be special considerations for patients who receive one product compared with patients who receive the other product. This determination was made by measuring exposure rates for several regions of the patient before and after implantation. An independent-samples t test analysis (ɑ = 0.05) was performed for 50 patients (25 TheraSphere and 25 SIR-Spheres) to determine whether the products behaved similarly to the extent that exposure to others was minimized and that as-low-as-reasonably-achievable principles were kept. The results showed that the products exhibited no significant differences in exposure rates, suggesting that no special considerations are needed for the procedure for one product compared with the other.

Pathogenesis to management of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is the most common primary liver cancer whose incidence continues to rise in many parts of the world due to a concomitant rise in many associated risk factors, such as alcohol use and obesity. Although early-stage HCC can be potentially curable through liver resection, liver-directed therapies, or transplantation, patients usually present with intermediate to advanced disease, which continues to be associated with a poor prognosis. This is because HCC is a cancer with significant complexities, including substantial clinical, histopathologic, and genomic heterogeneity. However, the scientific community has made a major effort to better characterize HCC in those aspects via utilizing tissue sampling and histological classification, whole genome sequencing, and developing viable animal models. These efforts ultimately aim to develop clinically relevant biomarkers and discover molecular targets for new therapies. For example, until recently, there was only one approved systemic therapy for advanced or metastatic HCC in the form of sorafenib. Through these efforts, several additional targeted therapies have gained approval in the United States, although much progress remains to be desired. This review will focus on the link between characterizing the pathogenesis of HCC with current and future HCC management.

Anti-SARS-CoV-2 immunoadhesin remains effective against Omicron and other emerging variants of concern.

Blocking the interaction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with its angiotensin-converting enzyme 2 (ACE2) receptor was proved to be an effective therapeutic option. Various protein binders as well as monoclonal antibodies that effectively target the receptor-binding domain (RBD) of SARS-CoV-2 to prevent interaction with ACE2 were developed. The emergence of SARS-CoV-2 variants that accumulate alterations in the RBD can severely affect the efficacy of such immunotherapeutic agents, as is indeed the case with Omicron that resists many of the previously isolated monoclonal antibodies. Here, we evaluate an ACE2-based immunoadhesin that we have developed early in the pandemic against some of the recent variants of concern (VoCs), including the Delta and the Omicron variants. We show that our ACE2-immunoadhesin remains effective in neutralizing these variants, suggesting that immunoadhesin-based immunotherapy is less prone to escape by the virus and has a potential to remain effective against future VoCs.

De novo-designed transmembrane domains tune engineered receptor functions.

De novo-designed receptor transmembrane domains (TMDs) present opportunities for precise control of cellular receptor functions. We developed a de novo design strategy for generating programmed membrane proteins (proMPs): single-pass α-helical TMDs that self-assemble through computationally defined and crystallographically validated interfaces. We used these proMPs to program specific oligomeric interactions into a chimeric antigen receptor (CAR) that we expressed in mouse primary T cells and found that both in vitro CAR T cell cytokine release and in vivo antitumor activity scaled linearly with the oligomeric state encoded by the receptor TMD, from monomers up to tetramers. All programmed CARs stimulated substantially lower T cell cytokine release relative to the commonly used CD28 TMD, which we show elevated cytokine release through lateral recruitment of the endogenous T cell costimulatory receptor CD28. Precise design using orthogonal and modular TMDs thus provides a new way to program receptor structure and predictably tune activity for basic or applied synthetic biology.

Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning.

Stabilizing antigenic proteins as vaccine immunogens or diagnostic reagents is a stringent case of protein engineering and design as the exterior surface must maintain recognition by receptor(s) and antigen-specific antibodies at multiple distinct epitopes. This is a challenge, as stability enhancing mutations must be focused on the protein core, whereas successful computational stabilization algorithms typically select mutations at solvent-facing positions. In this study, we report the stabilization of SARS-CoV-2 Wuhan Hu-1 Spike receptor binding domain using a combination of deep mutational scanning and computational design, including the FuncLib algorithm. Our most successful design encodes I358F, Y365W, T430I, and I513L receptor binding domain mutations, maintains recognition by the receptor ACE2 and a panel of different anti-receptor binding domain monoclonal antibodies, is between 1 and 2°C more thermally stable than the original receptor binding domain using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original receptor binding domain. Our approach could be applied to the computational stabilization of a wide range of proteins without requiring detailed knowledge of active sites or binding epitopes. We envision that this strategy may be particularly powerful for cases when there are multiple or unknown binding sites.

Structure and receptor recognition by the Lassa virus spike complex.

Lassa virus (LASV) is a human pathogen, causing substantial morbidity and mortality1,2. Similar to other Arenaviridae, it presents a class-I spike complex on its surface that facilitates cell entry. The virus's cellular receptor is matriglycan, a linear carbohydrate that is present on α-dystroglycan3,4, but the molecular mechanism that LASV uses to recognize this glycan is unknown. In addition, LASV and other arenaviruses have a unique signal peptide that forms an integral and functionally important part of the mature spike5-8; yet the structure, function and topology of the signal peptide in the membrane remain uncertain9-11. Here we solve the structure of a complete native LASV spike complex, finding that the signal peptide crosses the membrane once and that its amino terminus is located in the extracellular region. Together with a double-sided domain-switching mechanism, the signal peptide helps to stabilize the spike complex in its native conformation. This structure reveals that the LASV spike complex is preloaded with matriglycan, suggesting the mechanism of binding and rationalizing receptor recognition by α-dystroglycan-tropic arenaviruses. This discovery further informs us about the mechanism of viral egress and may facilitate the rational design of novel therapeutics that exploit this binding site.

Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences.

White-rot fungi secrete a repertoire of high-redox potential oxidoreductases to efficiently decompose lignin. Of these enzymes, versatile peroxidases (VPs) are the most promiscuous biocatalysts. VPs are attractive enzymes for research and industrial use but their recombinant production is extremely challenging. To date, only a single VP has been structurally characterized and optimized for recombinant functional expression, stability, and activity. Computational enzyme optimization methods can be applied to many enzymes in parallel but they require accurate structures. Here, we demonstrate that model structures computed by deep-learning-based ab initio structure prediction methods are reliable starting points for one-shot PROSS stability-design calculations. Four designed VPs encoding as many as 43 mutations relative to the wildtype enzymes are functionally expressed in yeast, whereas their wildtype parents are not. Three of these designs exhibit substantial and useful diversity in their reactivity profiles and tolerance to environmental conditions. The reliability of the new generation of structure predictors and design methods increases the scale and scope of computational enzyme optimization, enabling efficient discovery and exploitation of the functional diversity in natural enzyme families directly from genomic databases.

Microglial depletion abolishes ischemic preconditioning in white matter.

Ischemic preconditioning (IPC) is a phenomenon whereby a brief, non-injurious ischemic exposure enhances tolerance to a subsequent ischemic challenge. The mechanism of IPC has mainly been studied in rodent stroke models where gray matter (GM) constitutes about 85% of the cerebrum. In humans, white matter (WM) is 50% of cerebral volume and is a critical component of stroke damage. We developed a novel CNS WM IPC model using the mouse optic nerve (MON) and identified the involved immune signaling pathways. Here we tested the hypothesis that microglia are necessary for WM IPC. Microglia were depleted by treatment with the colony stimulating factor 1 receptor (CSF1R) inhibitor PLX5622. MONs were exposed to transient ischemia in vivo, acutely isolated 72 h later, and subjected to oxygen-glucose deprivation (OGD) to simulate a severe ischemic injury (i.e., stroke). Functional and structural axonal recovery was assessed by recording compound action potentials (CAPs) and by microscopy using quantitative stereology. Microglia depletion eliminated IPC-mediated protection. In control mice, CAP recovery was improved in preconditioned MONs compared with non-preconditioned MONs, however, in PLX5622-treated mice, we observed no difference in CAP recovery between preconditioned and non-preconditioned MONs. Microgliadepletion also abolished IPC protective effects on axonal integrity and survival of mature (APC+ ) oligodendrocytes after OGD. IPC-mediated protection was independent of retinal injury suggesting it results from mechanistic processes intrinsic to ischemia-exposed WM. We conclude that preconditioned microglia are critical for IPC in WM. The "preconditioned microglia" phenotype might protect against other CNS pathologies and is a neurotherapeutic horizon worth exploring.

Therapeutic Lymphangiography for Persistent Lymphatic Leak After Kidney Transplant: A Novel Technique.

Lymphatic leakage is a common and well-described complication after kidney transplantation, occurring in up to 25% of patients. Accumulation of lymph is due to the surgical disruption of recipient lymphatic channels accompanying the external iliac vessels, complicated by lower extremity edema, wound breakdown, infection, and, if unresolved, graft loss due to extrinsic compression. In this report, we describe the novel use of diagnostic and therapeutic lymphangiography to successfully treat lymphatic leak after renal transplant that was resistant to drain placement, sclerotherapy, and laparoscopic peritoneal window creation. We also describe the methodology, indications, and contraindications and conclude that this technique is well-tolerated and offers a good option for complex lymph leaks that do not respond to conventional treatment. Further studies are required to compare its efficacy with other standard methods, including sclerotherapy and laparoscopic peritoneal fenestration, as the primary treatment modality.