A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions.

Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition, and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ∼380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a large and complex network of interactions both within and across biological systems. We identified new PPIs for receptors with well-characterized ligands and binding partners for "orphan" receptors. New PPIs include proteins expressed on multiple cell types and involved in diverse processes including immune and nervous system development and function, differentiation/proliferation, metabolism, vascularization, and reproduction. These PPIs provide a resource for further biological investigation into their functional relevance and may offer new therapeutic drug targets.

A High-Throughput System for Transient and Stable Protein Production in Mammalian Cells.

Recombinant protein expression and purification is an essential component of biomedical research and drug discovery. Advances in automation and laboratory robotics have enabled the development of highly parallel and rapid processes for cell culture and protein expression, purification, and analysis. Human embryonic kidney (HEK) cells and Chinese hamster ovary (CHO) cells have emerged as the standard host cell workhorses for producing recombinant secreted mammalian proteins by using both transient and stable production strategies. In this chapter we describe a fully automated custom platform, Protein Expression and Purification Platform (PEPP), used for transient protein production from HEK cells and stable protein production from CHO cells. Central to PEPP operation is a suite of custom robotic and instrumentation platforms designed and built at GNF, custom cell culture ware, and custom scheduling software referred to as Runtime. The PEPP platform enables cost-effective, facile, consistent production of proteins at quantities and quality useful for early stage drug discovery tasks such as screening, bioassays, protein engineering, and analytics.

Mammalian cell culture density determination using a laser through-beam sensor.

High-throughput protein expression platforms are increasingly used to produce proteins for many applications: to support studies in structure/function, regulation and proteomics, as well as for direct use as potential biotherapeutic agents for medical applications. Here we describe a device that we refer to as the flask density reader (FDR) consisting of a through-beam laser and sensor, and a customized culture flask-receiving nest. The FDR has been integrated onto GNF System™'s automated protein expression platform to enable rapid, noninvasive, fully automated spectrophotometric determination of cell densities in suspension mammalian cell cultures. The FDR reduces the risk of culture contamination from frequent flask sampling and greatly reduces the time and effort needed to count cells using off-line methods.

Eradication of Canine Diffuse Large B-Cell Lymphoma in a Murine Xenograft Model with CD47 Blockade and Anti-CD20.

Cancer immunotherapies hold much promise, but their potential in veterinary settings has not yet been fully appreciated. Canine lymphomas are among the most common tumors of dogs and bear remarkable similarity to human disease. In this study, we examined the combination of CD47 blockade with anti-CD20 passive immunotherapy for canine lymphoma. The CD47/SIRPα axis is an immune checkpoint that regulates macrophage activation. In humans, CD47 is expressed on cancer cells and enables evasion from phagocytosis. CD47-blocking therapies are now under investigation in clinical trials for a variety of human cancers. We found the canine CD47/SIRPα axis to be conserved biochemically and functionally. We identified high-affinity SIRPα variants that antagonize canine CD47 and stimulate phagocytosis of canine cancer cells in vitro When tested as Fc fusion proteins, these therapeutic agents exhibited single-agent efficacy in a mouse xenograft model of canine lymphoma. As robust synergy between CD47 blockade and tumor-specific antibodies has been demonstrated for human cancer, we evaluated the combination of CD47 blockade with 1E4-cIgGB, a canine-specific antibody to CD20. 1E4-cIgGB could elicit a therapeutic response against canine lymphoma in vivo as a single agent. However, augmented responses were observed when combined with CD47-blocking therapies, resulting in synergy in vitro and in vivo and eliciting cures in 100% of mice bearing canine lymphoma. Our findings support further testing of CD47-blocking therapies alone and in combination with CD20 antibodies in the veterinary setting. Cancer Immunol Res; 4(12); 1072-87. ©2016 AACR.

Identification of a candidate therapeutic antibody for treatment of canine B-cell lymphoma.

B-cell lymphoma is one of the most frequently observed non-cutaneous neoplasms in dogs. For both human and canine BCL, the standard of care treatment typically involves a combination chemotherapy, e.g. "CHOP" therapy. Treatment for human lymphoma greatly benefited from the addition of anti-CD20 targeted biological therapeutics to these chemotherapy protocols; this type of therapeutic has not been available to the veterinary oncologist. Here, we describe the generation and characterization of a rituximab-like anti-CD20 antibody intended as a candidate treatment for canine B-cell lymphoma. A panel of anti-canine CD20 monoclonal antibodies was generated using a mouse hybridoma approach. Mouse monoclonal antibody 1E4 was selected for construction of a canine chimeric molecule based on its rank ordering in a flow cytometry-based affinity assay. 1E4 binds to approximately the same location in the extracellular domain of CD20 as rituximab, and 1E4-based chimeric antibodies co-stain canine B cells in flow cytometric analysis of canine leukocytes using an anti-canine CD21 antibody. We show that two of the four reported canine IgG subclasses (cIgGB and cIgGC) can bind to canine CD16a, a receptor involved in antibody-dependent cellular cytotoxicity (ADCC). Chimeric monoclonal antibodies were assembled using canine heavy chain constant regions that incorporated the appropriate effector function along with the mouse monoclonal 1E4 anti-canine CD20 variable regions, and expressed in CHO cells. We observed that 1E4-cIgGB and 1E4-cIgGC significantly deplete B-cell levels in healthy beagle dogs. The in vivo half-life of 1E4-cIgGB in a healthy dog was ∼14 days. The antibody 1E4-cIgGB has been selected for further testing and development as an agent for the treatment of canine B-cell lymphoma.

Activating Fc γ receptors contribute to the antitumor activities of immunoregulatory receptor-targeting antibodies.

Fc γ receptor (FcγR) coengagement can facilitate antibody-mediated receptor activation in target cells. In particular, agonistic antibodies that target tumor necrosis factor receptor (TNFR) family members have shown dependence on expression of the inhibitory FcγR, FcγRIIB. It remains unclear if engagement of FcγRIIB also extends to the activities of antibodies targeting immunoregulatory TNFRs expressed by T cells. We have explored the requirement for activating and inhibitory FcγRs for the antitumor effects of antibodies targeting the TNFR glucocorticoid-induced TNFR-related protein (GITR; TNFRSF18; CD357) expressed on activated and regulatory T cells (T reg cells). We found that although FcγRIIB was dispensable for the in vivo efficacy of anti-GITR antibodies, in contrast, activating FcγRs were essential. Surprisingly, the dependence on activating FcγRs extended to an antibody targeting the non-TNFR receptor CTLA-4 (CD152) that acts as a negative regulator of T cell immunity. We define a common mechanism that correlated with tumor efficacy, whereby antibodies that coengaged activating FcγRs expressed by tumor-associated leukocytes facilitated the selective elimination of intratumoral T cell populations, particularly T reg cells. These findings may have broad implications for antibody engineering efforts aimed at enhancing the therapeutic activity of immunomodulatory antibodies.

Higher altitude and risk of bronchopulmonary dysplasia among preterm infants.

OBJECTIVE: To assess the association between altitudes of neonatal intensive care units (NICU) and the rate of bronchopulmonary dysplasia (BPD) and BPD/death in very preterm infants. STUDY DESIGN: Data from infants born at <33 weeks' gestation admitted to Canadian Neonatal Network during 2008 and 2009 were analyzed. The associations between the altitude of NICU and the BPD and altitude and BPD/death were determined using logistic regression models. RESULTS: Of 7551 eligible infants, 1540 (20%) were admitted to NICUs at an altitude > 400 m, 3661 (48%) between 86 and 400 m, 2350 (31%) at ≤85 m. The incidences of BPD (21.7% versus 17.2%) and BPD/death (26.2% versus 23.0%) were significantly higher in the infants admitted to NICUs at >400 m altitude versus those ≤400 m altitude (p < 0.01). In multivariable analyses, the adjusted odds ratio was 1.81 (95% confidence interval [CI] 1.05 to 3.12) for BPD and 1.79 (95% CI 1.12 to 2.85) for BPD/death among infants admitted to NICUs at altitude > 400 m compared with NICUs at altitude ≤ 400 m. For each 100-m increase in altitude, the odds increased by 8% for BPD (95% CI 4 to 13%) and 9% for BPD/death (95% CI 5 to 13%); however, the increase was mainly due to increase in BPD. CONCLUSION: For very preterm infants, higher altitude of NICUs increased the risk of BPD.

Two novel WD40 domain-containing proteins, Ere1 and Ere2, function in the retromer-mediated endosomal recycling pathway.

Regulated secretion, nutrient uptake, and responses to extracellular signals depend on cell-surface proteins that are internalized and recycled back to the plasma membrane. However, the underlying mechanisms that govern membrane protein recycling to the cell surface are not fully known. Using a chemical-genetic screen in yeast, we show that the arginine transporter Can1 is recycled back to the cell surface via two independent pathways mediated by the sorting nexins Snx4/41/42 and the retromer complex, respectively. In addition, we identify two novel WD40-domain endosomal recycling proteins, Ere1 and Ere2, that function in the retromer pathway. Ere1 is required for Can1 recycling via the retromer-mediated pathway, but it is not required for the transport of other retromer cargoes, such as Vps10 and Ftr1. Biochemical studies reveal that Ere1 physically interacts with internalized Can1. Ere2 is present in a complex containing Ere1 on endosomes and functions as a regulator of Ere1. Taken together, our results suggest that Snx4/41/42 and the retromer comprise two independent pathways for the recycling of internalized cell-surface proteins. Moreover, a complex containing the two novel proteins Ere1 and Ere2 mediates cargo-specific recognition by the retromer pathway.

Anti-adhesion molecule therapies in inflammatory bowel disease: touch and go.

Exploration of the mechanisms underlying the inflammatory bowel diseases [N. Mori, Y. Horie, M.E. Gerritsen, D.C. Anderson, D.N. Granger, Anti-inflammatory drugs and endothelial cell adhesion molecule expression in murine vascular beds. Gut 1999;44:186-95] is a leading field of medical research that drives the application of biological therapies to human diseases. Indeed, many inflammatory mediators can be targeted in the gut by monoclonal antibodies. A recent direction for these therapeutics is targeting of the adhesion molecule family. This molecule family mediates the adhesion and extravasation of leukocytes through the endothelium at sites of inflammation. This is a complex multistep process that has been extensively investigated in recent years; thanks to these studies some adhesion molecules have been identified to specifically mediate leukocyte migration to gut inflammatory sites, like alpha(4)beta(7) integrin. This review outlines the scientific basis behind this therapeutic approach, and describes the principal clinical studies that have been carried out on these new molecules in patients with IBD.

Temporary placement of covered self-expandable metal stents in benign biliary strictures: a new paradigm? (with video).

BACKGROUND: Benign biliary strictures (BBS) are usually managed with plastic stents, whereas placement of uncovered metallic stents has been associated with failure related to mucosal hyperplasia. OBJECTIVE: We analyzed the efficacy and safety of temporary placement of a covered self-expanding metal stent (CSEMS) in BBS. DESIGN: Patients with BBS received temporary placement of CSEMSs until adequate drainage was achieved; confirmed by resolution of symptoms, normalization of liver function tests, and imaging. SETTING: Tertiary-care center with long-standing experience with CSEMSs. PATIENTS: Seventy-nine patients with BBS secondary to chronic pancreatitis (32), calculi (24), liver transplant (16), postoperative biliary repair (3), autoimmune pancreatitis (3), and primary sclerosing cholangitis (1). INTERVENTION: ERCP with temporary CSEMS placement. Removal of CSEMSs was performed with a snare or a rat-tooth forceps. MAIN OUTCOME MEASUREMENTS: End points were efficacy, morbidity, and clinical response. RESULTS: CSEMSs were removed from 65 patients. Resolution of the BBS was confirmed in 59 of 65 patients (90%) after a median follow-up of 12 months after removal (range 3-26 months). If patients who were lost to follow-up, developed cancer, or expired were considered failures, then an intent-to-treat global success rate of 59 of 79 (75%) was obtained. Complications associated with placement included 3 post-ERCP pancreatitis (4%), 1 postsphincterotomy bleed (1%), and 2 pain that required CSEMS removal (2%). In 11 patients (14%), the CSEMS migrated. In 1 patient, CSEMS removal was complicated by a bile leak that was successfully managed with plastic stents. LIMITATION: Pilot study from a single center. CONCLUSIONS: Temporary CSEMS placement in patients with BBS offers a potential alternative to surgery.

Novel Ist1-Did2 complex functions at a late step in multivesicular body sorting.

In Saccharomyces cerevisiae, integral plasma membrane proteins destined for degradation and certain vacuolar membrane proteins are sorted into the lumen of the vacuole via the multivesicular body (MVB) sorting pathway, which depends on the sequential action of three endosomal sorting complexes required for transport. Here, we report the characterization of a new positive modulator of MVB sorting, Ist1. We show that endosomal recruitment of Ist1 depends on ESCRT-III. Deletion of IST1 alone does not cause cargo-sorting defects. However, synthetic genetic analysis of double mutants of IST1 and positive modulators of MVB sorting showed that ist1Delta is synthetic with vta1Delta and vps60Delta, indicating that Ist1 is also a positive component of the MVB-sorting pathway. Moreover, this approach revealed that Ist1-Did2 and Vta1-Vps60 compose two functional units. Ist1-Did2 and Vta1-Vps60 form specific physical complexes, and, like Did2 and Vta1, Ist1 binds to the AAA-ATPase Vps4. We provide evidence that the ist1Delta mutation exhibits a synthetic interaction with mutations in VPS2 (DID4) that compromise the Vps2-Vps4 interaction. We propose a model in which the Ist1-Did2 and Vta1-Vps60 complexes independently modulate late steps in the MVB-sorting pathway.

Temporary placement of covered self-expandable metallic stents in patients with biliary leak: midterm evaluation of a pilot study.

BACKGROUND: Management of biliary leaks includes ERCP and stent placement. The ability to temporarily place a partially covered self-expandable metallic stent (CSEMS) might offer an advantage in the treatment of biliary leaks. OBJECTIVE: We analyzed our 2 years' experience when using this innovative technique. DESIGN: Patients in whom a previous ERCP had failed to resolve a bile leak or patients with severe comorbidities were offered CSEMS and were followed prospectively for clinical and radiologic responses. SETTING: Tertiary-care center with long-standing experience of using CSEMS. PATIENTS: A total of 16 patients were included. Of these, 7 had previously undergone unsuccessful plastic stent placement, 3 had previously failed ERCP, and 7 had severe comorbidities that prevented multiple interventions. INTERVENTION: ERCP with placement of a CSEMS covering the cystic duct take-off in the case of a cystic-stump leak. CSEMS were removed after resolution of the leak. MAIN OUTCOME MEASUREMENTS: Efficacy and safety of the CSEMS in bile leaks; complications were also evaluated. RESULTS: Of the patients studied, 15 responded to CSEMS placement with complete resolution of the leak on imaging. One patient with partial cholecystectomy relapsed and underwent drainage; another patient responded to the treatment but required revision because of migration. CSEMS were left in place for a median time of 3 months (range, 1-17 months). Complications included 1 proximal and 1 distal migration. LIMITATIONS: Pilot study from a single center. CONCLUSIONS: CSEMS is an excellent option in this subgroup of patients not responding to plastic stent placement or with severe comorbidities.

Commensal bacteria exacerbate intestinal inflammation but are not essential for the development of murine ileitis.

The pathogenesis of Crohn's disease has been associated with a dysregulated response of the mucosal immune system against intraluminal Ags of bacterial origin. In this study, we have investigated the effects of germfree (GF) conditions in the SAMP1/YitFc murine model of Crohn's disease-like ileitis. We show that the bacterial flora is not essential for ileitis induction, because GF SAMP1/YitFc mice develop chronic ileitis. However, compared with disease in specific pathogen-free (SPF) mice, ileitis in GF mice is significantly attenuated, and is associated with delayed lymphocytic infiltration and defective mucosal expression of Th2 cytokines. In addition, we demonstrate that stimulation with purified fecal Ags from SPF, but not GF mice leads to the generation of IL-4-secreting effector lymphocytes. This result suggests that commensal bacteria drive Th2 responses characteristic of the chronic phase of SAMP1/YitFc ileitis. Finally, adoptive transfer of CD4-positive cells from GF, but not SPF mice induces severe colitis in SCID recipients. These effects were associated with a decreased frequency of CD4(+)CD25(+)Foxp3(+) T cells in the mesenteric lymph nodes of GF mice compared with SPF mice, as well as lower relative gene expression of Foxp3 in CD4(+)CD25(+) T cells in GF mice. It is therefore apparent that, in the absence of live intraluminal bacteria, the regulatory component of the mucosal immune system is compromised. All together, our results indicate that in SAMP1/YitFc mice, bacterial flora exacerbates intestinal inflammation, but is not essential for the generation of the chronic ileitis that is characteristic of these mice.

Evidence-based medications for the treatment of the inflammatory bowel diseases.

PURPOSE OF REVIEW: Evidence-based medicine is an increasingly important tool to aid the clinician in the treatment of patients. This is particularly true for diseases such as the inflammatory bowel diseases, for which the pathogenesis is unknown and an extensive range of treatment options is available. High quality data may not be available for all decisions, but it is essential that clinicians are aware of well-grounded data that are available. RECENT FINDINGS: The body of data supporting the use of biological therapies in inflammatory bowel disease continues to grow and diversify. Regulatory requirements and academic expectations are evolutionary forces that are resulting in continuous improvement in the quality of studies. SUMMARY: This review will update the reader on several significant analyses that have been published recently. It is intended to raise awareness of the data, helping clinicians to evaluate new treatments and to revisit older treatments with a critical eye.

An internal ribosome entry site promotes translation of a novel SIV Pr55(Gag) isoform.

In complex retroviruses including simian immunodeficiency virus (SIV) and human immunodeficiency virus type 1 (HIV-1), the major structural proteins are encoded by the gag gene and translated as a precursor polyprotein, Pr55(Gag). An internal ribosome entry site (IRES) within the coding region of HIV-1 and HIV type 2 (HIV-2) gag RNA mediates expression of N-terminally truncated isoforms of the precursor polyprotein. In this study, we identify an N-terminally truncated SIV Pr55(Gag) isoform expressed from the SIV gag gene SIV p43. We demonstrate that translation of p43 occurs independently of Pr55(Gag) translation and initiates at an in-frame AUG within the gag transcript. We test several mechanisms that could mediate translation of p43 and report that translation of SIV p43 is driven by an IRES located entirely within the coding region of gag mRNA. Additionally, we present data that suggest SIV p43 affects viral replication in cell culture.