Endoscopic imaging modalities for diagnosing the invasion depth of superficial esophageal squamous cell carcinoma: a systematic review

Esophagus - Endoscopic diagnosis of the invasion depth of superficial esophageal squamous cell carcinoma (ESCC) is an important determinant of the treatment strategy. The three endoscopic imaging...     

Development of cyclic peptides with potent in vivo osteogenic activity through RaPID-based affinity maturation

Osteoporosis is caused by a disequilibrium between bone resorption and bone formation. Therapeutics for osteoporosis can be divided into antiresorptives that suppress bone resorption and anabolics which increase bone formation. Currently, the only anabolic treatment options are parathyroid hormone mimetics or an anti-sclerostin monoclonal antibody. With the current global increases in demographics at risk for osteoporosis, development of therapeutics that elicit anabolic activity through alternative mechanisms is imperative. Blockade of the PlexinB1 and Semaphorin4D interaction on osteoblasts has been shown to be a promising mechanism to increase bone formation. Here we report the discovery of cyclic peptides by a novel RaPID (Random nonstandard Peptides Integrated Discovery) system-based affinity maturation methodology that generated the peptide PB1m6A9 which binds with high affinity to both human and mouse PlexinB1. The chemically dimerized peptide, PB1d6A9, showed potent inhibition of PlexinB1 signaling in mouse primary osteoblast cultures, resulting in significant enhancement of bone formation even compared to non-Semaphorin4D–treated controls. This high anabolic activity was also observed in vivo when the lipidated PB1d6A9 (PB1d6A9-Pal) was intravenously administered once weekly to ovariectomized mice, leading to complete rescue of bone loss. The potent osteogenic properties of this peptide shows great promise as an addition to the current anabolic treatment options for bone diseases such as osteoporosis.

Osteoporosis is a common cause of bone fracture in the elderly, costing billions globally due to fractures leading to long-term disability and subsequent exit from the working population (1, 2). Several treatment options are available for osteoporosis which can be divided into antiresorptives and anabolics ranging from orally dosed small molecules to injectable peptides and biologics (2, 3). Antiresorptive and anabolic agents differ in that antiresorptives inhibit or reduce bone resorption, thereby suppressing bone remodeling, whereas anabolics enhance the rate of bone formation while allowing continued resorption and remodeling of bone tissue. Although both treatments result in increased bone mass, resorption and remodeling are key to the microstructural integrity of bone, and emerging evidence points toward anabolics being more effective in reducing fracture (4–6). Currently, the only anabolics in the clinic are the parathyroid hormone and parathyroid hormone-related peptide mimetics (teriparatide and abaloparatide, respectively) and the sclerostin inhibitor monoclonal antibody (romosozumab). Teriparatide and abaloparatide both cannot be administered over 24 mo in a patient’s lifetime due to the risk for developing osteosarcomas, and romosozumab treatment is recommended for 12 mo due to waning efficacy beyond this duration (7, 8). Therefore, with the ever increasing global median age and associated osteoporosis cases, the development of additional anabolic treatment options are of high importance.Bone resorption and bone formation are regulated through communications between osteoclasts and osteoblasts, respectively (9). Among the paracrine factors involved in this process, axon guidance molecules, such as Semaphorin4D (Sema4D) and Semaphorin3A, mediate the regulation of bone cell differentiation. Sema4D, which is expressed and secreted by mature osteoclasts, inhibits osteoblast differentiation through its receptor PlexinB1 (PlxnB1) expressed on osteoblast surfaces. Binding of Sema4D to PlxnB1 leads to the inhibition of the activation of insulin receptor substrate-1 which is downstream of insulin-like growth factor-1 signaling. In addition, Sema4D controls the spatial distribution of bone-forming osteoblasts through PlxnB1-RhoA signaling (10). Mice with genetic deletion of Sema4D or PlxnB1 as well as mice expressing a dominant-negative form of RhoA in osteoblasts exhibit a high bone mass phenotype due to increased bone formation (11). These findings suggest that inhibiting PlxnB1-Sema4D signaling would lead to a bone anabolic effect through enhancement of osteoblastic differentiation while keeping osteoblasts away from osteoclasts to enable efficient osteoclastic bone resorption.We have previously reported a macrocyclic peptide discovery campaign to identify binding sites on PlxnB1 that inhibit its interaction with Sema4D by means of messenger RNA (mRNA) display in combination with genetic code reprogramming, referred to as the RaPID (Random nonstandard Peptides Integrated Discovery) system (12). We successfully identified a 16-mer thioether-macrocyclic peptide, PB1m6, capable of binding human PlxnB1 (hPlxnB1) with single-digit nanomolar-binding affinity and inhibiting its interaction with Sema4D (13). X-ray structural analysis of cocrystals of PB1m6 and hPlxnB1 revealed that PB1m6 is a negative allosteric modulator of the hPlxnB1-Sema4D interaction by binding a cleft distal to the Sema4D-binding interface of hPlxnB1 while still able to inhibit the hPlxnB1-Sema4D interaction. However, PB1m6 was shown to be selective toward hPlxnB1 over mouse PlxnB1 (mPlxnB1) displaying no detectable affinity (dissociation constant (K_D) over 1 µM) regardless of having 88% sequence identity in the N-terminal sema domains of hPlxnB1 and mPlxnB1. Modeling efforts based on the three-dimensional (3D) structure to rationally increase the species cross-reactivity were unsuccessful in our hands. This high selectivity is often observed with RaPID-derived macrocyclic peptides and is generally considered beneficial (13–18). However, in this instance, the high selectivity of PB1m6 hinders its ability to validate the inhibitory mechanism in mouse models. In this study, we used a fragmented saturation mutagenesis approach to create an mRNA library of PB1m6 analogs to be utilized in a RaPID selection campaign against mouse PlxnB1. After five iterative rounds of selection, we discovered a PB1m6 analog, referred to as PB1m6A9, exhibiting enhanced cross-reactivity with 44 nM K_D against mouse PlxnB1 and which, remarkably, also showed 10-fold stronger binding affinity against human PlxnB1 (0.28 nM K_D). To further improve apparent affinity and inhibitory activity, a homodimer of PB1m6A9 was chemically synthesized (PB1d6A9), and it was shown to exhibit potent mPlxnB1-Sema4D inhibitory activity in mouse primary osteoblasts as well as enhanced osteogenesis even when compared to cells not treated with Sema4D. Moreover, once-weekly intravenous (i.v.) administration of palmitoylated PB1d6A9 (PB1d6A9-Pal) in a mouse model of postmenopausal osteoporosis showed significant enhancement of bone formation compared to both vehicle and sham-operated (Sham) control mice. This work presents the facile development of a novel bone anabolic modality which shows promise as an addition to the current repertoire of anabolic agents used to address osteoporosis.     

Antagonistic regulation of myogenesis by two deubiquitinating enzymes,UBP45 and UBP69

Protein modification by ubiquitin is a dynamic and reversible process that is involved in the regulation of a variety of cellular processes. Here, we show that myogenic differentiation of embryonic muscle cells is antagonistically regulated by two deubiquitinating enzymes, UBP45 and UBP69, that are generated by alternative splicing. Both enzymes cleaved off ubiquitin from polyubiquitinated protein conjugates in vivo as well as from linear ubiquitin-protein fusions in vitro. In cultured myoblasts, the level of UBP69 mRNA markedly but transiently increased before membrane fusion, whereas that of UBP45 mRNA increased as the cells fused to form myotubes. Both myoblast fusion and accumulation of myosin heavy chain were dramatically stimulated by the stable expression of UBP69 but strongly attenuated by that of the catalytically inactive form of the protease, suggesting that the mutant enzyme acts dominant negatively on the function of the wild-type protease. In contrast, stable expression of UBP45 completely blocked both of the myogenic processes but that of inactive enzyme did not, indicating that the catalytic activity of the enzyme is essential for its inhibitory effects. These results indicate that differential expression of UBP45 and UBP69 is involved in the regulation of muscle cell differentiation.     

A case of amebic liver abscess complicated by hemobilia due to rupture of hepatic artery aneurysm

We report the case of a 51-year-old man with hepatic amebic abscess complicated by hepatic artery aneurysm. The patient first presented with peritonitis caused by perforating appendicitis. Surgical treatment resolved peritonitis but Entamoeba histolytica was detected in the colonic mucosa. Subsequently, liver abscess developed and the size of the abscess increased gradually after surgery in spite of continued treatment with metronidazole. Brown pus was drained from the abscess but 13 days after the drainage process the patient complained of right upper abdominal pain and the drained fluid became blood-colored and stool became tarry in color. Enhanced computed tomography showed a hepatic artery aneurysm that had ruptured into the liver abscess and duodenoscopy revealed bleeding from the ampulla of Vater. Transcatheter arterial embolization with several steel coils was successfully performed which resulted in cessation of bleeding from the ampulla of Vater. The patient was discharged without any complications five weeks after rupture of the aneurysm. Our case demonstrates rupture of the hepatic artery aneurysm as a rare complication of amebic liver abscess and the effectiveness of interventional embolotherapy in this condition.     

The impact of anti-inflammatory cytokines provoked by CD163 positive macrophages on ventricular functional recovery after myocardial infarction

Present study aimed to investigate the impact of anti-inflammatory cytokines provoked by the hemoglobin scavenger receptor, CD163, on left ventricular (LV) functional recovery after successful reperfusion in patients with acute myocardial infarction (AMI). Intraplaque hemorrhage accelerates plaque destabilization. Extracellular hemoglobin is cleared by CD163, a macrophage scavenger receptor. This process provokes secretion of anti-inflammatory atheroprotective cytokine, interleukin (IL)-10. In 40 patients with the first AMI, coronary atherothrombotic debris was retrieved during percutaneous coronary intervention (PCI), stained with antibodies to CD163 and IL-10. LV function was determined by echocardiography before PCI and 6 months after PCI. %CD163 was defined as ratio of CD163 (+)-cells to whole cells. %IL-10 was expressed as the ratio of positively stained areas per total tissue. Patients were divided into two groups depending on the amount of CD163 (+)-cells: CD163 > 10 % (CD_163high, n = 20) and CD163 ≤ 10 % (CD_163low, n = 20). CD_163high group had significantly higher %IL-10. Final thrombolysis in myocardial infarction (TIMI) flow grade was significantly lower in CD_163high group. In subgroups with the final TIMI-3 flow (CD_163high-Reflow, n = 15 and CD_163low-Reflow, n = 20), the time to reperfusion, infarct size, LV dimensions and fractional shortening (%FS) before PCI were similar. Significant correlation was observed between %IL10 and changes in LV dimensions (diastole, r = ?0.49, P = 0.01; systole, r = ?0.65, P < 0.01) or %FS (r = 0.51, P < 0.01) at 6 months after PCI. Plaque with CD163(+)-macrophages could impair distal flow after primary PCI. However, CD163(+)-macrophages enhance the anti-inflammatory cytokine expression that aids in ventricular functional recovery if distal flow can be achieved by successful reperfusion.     

From the Cover: Folding pathway of a multidomain protein depends on its topology of domain connectivity

How do the folding mechanisms of multidomain proteins depend on protein topology? We addressed this question by developing an Ising-like structure-based model and applying it for the analysis of free-energy landscapes and folding kinetics of an example protein, Escherichia coli dihydrofolate reductase (DHFR). DHFR has two domains, one comprising discontinuous N- and C-terminal parts and the other comprising a continuous middle part of the chain. The simulated folding pathway of DHFR is a sequential process during which the continuous domain folds first, followed by the discontinuous domain, thereby avoiding the rapid decrease in conformation entropy caused by the association of the N- and C-terminal parts during the early phase of folding. Our simulated results consistently explain the observed experimental data on folding kinetics and predict an off-pathway structural fluctuation at equilibrium. For a circular permutant for which the topological complexity of wild-type DHFR is resolved, the balance between energy and entropy is modulated, resulting in the coexistence of the two folding pathways. This coexistence of pathways should account for the experimentally observed complex folding behavior of the circular permutant.Topology of protein conformation, or the spatial arrangement of structural units and the chain connectivity among them, is a key determinant of the folding mechanisms of proteins (1–5). However, predicting a folding pathway is a subtle problem when a protein comprises multiple regions of cooperative structure formation (i.e., foldons or domains). Given that a protein has n such cooperative regions and each region tends to show a two-state–like structural transition between ordered and disordered states, the protein as a whole can have 2ⁿ conformation states and multiple folding routes passing through them are allowed. The statistical weights of these folding routes should be determined both by the interactions among structural regions and the strength of cooperativity within individual regions (6). When multiple competitive routes coexist, the observed folding pathway of an ensemble of molecules should be a superposition of these routes, and the dominant folding pathway should be flexibly changed by changing the solution conditions or by mutations. The multiplicity and flexibility of pathways are important, even for small single-domain proteins like ribosomal protein S6 (7, 8), and are evident for proteins that have repeating structures (9–13). For proteins comprising multiple domains (14), the multiplicity of possible folding pathways is significant. The relative importance among 2ⁿ conformation states in the folding process in proteins with n independently foldable domains should be determined by length, structure (13), the topological connectivity of linkers between domains (3), and the interactions at the interface between domains (3, 15, 16). Fig. 1A shows an example protein for the case n = 2.Open in a separate windowFig. 1.Examples of two-domain proteins with different topological complexities. (A) Human γD-crystallin (PDB ID: 1HK0), which has two independently foldable domains connected by a single linker. (B) DHFR (PDB ID: 1rx1), which is topologically more complex, comprising two domains, DLD (blue) and ABD (pink). DLD is a discontinuous domain comprising the N- and C-terminal parts of the chain, and ABD and DLD are connected by two linkers. The positions of linkers are designated by red arrows.The above mechanism for determining folding intermediates and pathways of multidomain proteins is not applicable when domains have mutually correlated folding tendencies. In particular, the correlation between domains may be significant in a topologically complex protein, which has a domain comprising multiple discontinuous parts of a chain. For example, consider one domain, a discontinuous domain, consisting of residues 1 ≤ i ≤ N₁ and N₂ ≤ i ≤ N, and another domain, a continuous domain, consisting of residues N₁ < i < N₂. Because there is a tendency that the continuous parts of the chain form “islands” of ordered structures (17, 18) and that these continuous parts of a sequence can be the nuclei for folding, the discontinuous domain may not be an independent folding unit, but may depend on the continuous domain. In this paper, we theoretically analyze the problem of how a folding pathway is selected in multidomain proteins that have a discontinuous domain by using Escherichia coli dihydrofolate reductase (DHFR) as an example and compare it with its circular permutant that consists only of continuous domains.As shown in Fig. 1B, DHFR is a 159-residue α/β protein consisting of two domains: a discontinuous loop domain (DLD) (residues 1–37 and 107–159) and an adenosine-binding domain (ABD) (residues 38–106). Because DLD does not include a single contiguous region of the chain, but rather includes separate N- and C-terminal parts, the structural ordering of DLD can be correlated with the structural ordering of ABD. As a model protein, DHFR has been intensively investigated (19–29), which has resulted in a picture that DHFR folds along the following pathway:U→τ7I6→τ6I5→τ5IHF→τ1,…,τ4{N}.[1]Here I₆ is an intermediate exhibiting heterogeneous compactness with DLD being only partially compacted but ABD attaining a native-like compactness (19). I₆ appeared in τ₇ < 35?μs after folding was initiated from the unfolded state (U). During τ₆ ～ 550?μs, further structural development was observed both in ABD and in DLD (19), which led to I₅ in which the secondary structures were reasonably formed (20–22) and two subsets of hydrogen-bonding networks were formed in ABD and DLD (23). During τ₅ ～ 200 ms, structures of ABD and DLD were further organized, which led to the hyperfluorescent intermediate state, I_HF, consisting of four substates, I₁, …, I₄, which matured through four parallel pathways on timescales of τ₁, …, τ₄ = 1 ? 100 s to reach the four native conformers, collectively denoted by {N} in Eq. 1 (24–27). It is plausible that the slow process (several hundred seconds) during the τ₁ ? τ₄ phases is due to intense “internal friction” (30–32) in the glassy dynamics of conformation (33), including formation/disruption of nonnative contacts, the effects of proline isomerization, and the cis–trans isomerization of Gly95 and Gly96. Apart from this complexity during the last phase, the folding scheme in Eq. 1 can be regarded as a hierarchical assembly of structures that begins from the ordering of each domain at the early phase of τ₇ and proceeds to the formation of the whole protein during the later phase of τ₅ (19). Therefore, the questions are the mechanisms for how such a sequential pathway is realized in DHFR and how the topological complexity of DHFR affects the pathway selection.