An Open-Source Framework for Mass Calculation of Antibody-Based Therapeutic Molecules

Biotherapeutic masses are a means of verifying identity and structural integrity. Mass spectrometry (MS) of intact proteins or protein subunits provides an easy analytical tool for different stages of biopharmaceutical development. The protein's identity is confirmed when the experimental mass from MS is within a pre-defined mass error range of the theoretical mass. While several computational tools exist for the calculation of protein and peptide molecular weights, they either were not designed for direct application to biotherapeutic entities, have access limitations due to paid licenses, or require uploading protein sequences to host servers. We have developed a modular mass calculation routine that enables the easy determination of the average or monoisotopic masses and elemental compositions of therapeutic glycoproteins, including monoclonal antibodies (mAb), bispecific antibodies (bsAb), and antibody-drug conjugates (ADC). The modular nature of this Python-based calculation framework will allow the extension of this platform to other modalities such as vaccines, fusion proteins, and oligonucleotides in the future, and this framework could also be useful for the interrogation of top-down mass spectrometry data. By creating an open-source standalone desktop application with a graphical user interface (GUI), we hope to overcome the restrictions around use in environments where proprietary information cannot be uploaded to web-based tools. This article describes the algorithms and application of this tool, mAbScale, to different antibody-based therapeutic modalities.

A Phase 1B Trial in GBA1-Associated Parkinson's Disease of BIA-28-6156, a Glucocerebrosidase Activator

BACKGROUND

Loss-of-function mutations in the GBA1 gene are one of the most common genetic risk factors for onset of Parkinson's disease and subsequent progression (GBA-PD). GBA1 encodes the lysosomal enzyme glucocerebrosidase (GCase), a promising target for a possible first disease-modifying therapy. LTI-291 is an allosteric activator of GCase, which increases the activity of normal and mutant forms of GCase.

OBJECTIVES

This first-in-patient study evaluated the safety, tolerability, pharmacokinetics, and pharmacodynamics of 28 daily doses of LTI-291 in GBA-PD.

METHODS

This was a randomized, double-blind, placebo-controlled trial in 40 GBA-PD participants. Twenty-eight consecutive daily doses of 10, 30, or 60 mg of LTI-291 or placebo were administered (n = 10 per treatment allocation). Glycosphingolipid (glucosylceramide and lactosylceramide) levels were measured in peripheral blood mononuclear cells (PBMCs), plasma, and cerebrospinal fluid (CSF), and a test battery of neurocognitive tasks, the Movement Disorder Society-Unified Parkinson's Disease Rating Scale and the Mini-Mental State Exam, were performed.

RESULTS

LTI-291 was generally well tolerated, no deaths or treatment-related serious adverse events occurred, and no participants withdrew due to adverse events. C_max , and AUC_0-6 of LTI-291 increased in a dose-proportional manner, with free CSF concentrations equal to the free fraction in plasma. A treatment-related transient increase in intracellular glucosylceramide (GluCer) in PBMCs was measured.

CONCLUSION

These first-in-patient studies demonstrated that LTI-291 was well tolerated when administered orally for 28 consecutive days to patients with GBA-PD. Plasma and CSF concentrations that are considered pharmacologically active were reached (ie, sufficient to at least double GCase activity). Intracellular GluCer elevations were detected. Clinical benefit will be assessed in a larger long-term trial in GBA-PD. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

A Biomarker Study in Patients with GBA1-Parkinson's Disease and Healthy Controls

BACKGROUND

Molecules related to glucocerebrosidase (GCase) are potential biomarkers for development of compounds targeting GBA1-associated Parkinson's disease (GBA-PD).

OBJECTIVES

Assessing variability of various glycosphingolipids (GSLs) in plasma, peripheral blood mononuclear cells (PBMCs), and cerebrospinal fluid (CSF) across GBA-PD, idiopathic PD (iPD), and healthy volunteers (HVs).

METHODS

Data from five studies were combined. Variability was assessed of glucosylceramide (various isoforms), lactosylceramide (various isoforms), glucosylsphingosine, galactosylsphingosine, GCase activity (using fluorescent 4-methylumbeliferryl-β-glucoside), and GCase protein (using enzyme-linked immunosorbent assay) in plasma, PBMCs, and CSF if available, in GBA-PD, iPD, and HVs. GSLs in leukocyte subtypes were compared in HVs. Principal component analysis was used to explore global patterns in GSLs, clinical characteristics (Movement Disorder Society - Unified Parkinson's Disease Rating Scale Part 3 [MDS-UPDRS-3], Mini-Mental State Examination [MMSE], GBA1 mutation type), and participant status (GBA-PD, iPD, HVs).

RESULTS

Within-subject between-day variability ranged from 5.8% to 44.5% and was generally lower in plasma than in PBMCs. Extracellular glucosylceramide levels (plasma) were slightly higher in GBA-PD compared with both iPD and HVs, while intracellular levels were comparable. GSLs in the different matrices (plasma, PBMCs, CSF) did not correlate. Both lactosylceramide and glucosylsphingosine were more abundant in granulocytes compared with monocytes and lymphocytes. Absolute levels of GSL isoforms differed greatly. GBA1 mutation types could not be differentiated based on GSL data.

CONCLUSIONS

Glucosylceramide can stably be measured over days in both plasma and PBMCs and may be used as a biomarker in clinical trials targeting GBA-PD. Glucosylsphingosine and lactosylceramide are stable in plasma but are strongly affected by leukocyte subtypes in PBMCs. GBA-PD could be differentiated from iPD and HVs, primarily based on glucosylceramide levels in plasma. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Efficacy and safety of combined administration of erythropoietin and iron in comparison to iron therapy alone in orthopaedic surgery: systematic review and metanalysis

INTRODUCTION

Iron deficiency anaemia in orthopaedic surgery is common and there is increased risk of blood transfusion and associated adverse reactions. The management involves administration of iron (oral or intravenous) and erythropoietin stimulating agents.

MATERIAL AND METHODS

We searched for PubMed, Embase, Google Scholar and Cochrane database to identify the studies from inception to April 2021. Randomized controlled trials with adult patients undergoing orthopedic surgery were included. The metanalysis compared patients who were administered combination of erythropoietin stimulating agents and iron in one group and iron alone. The primary outcome was the rate of blood transfusion and the secondary outcome studied were postoperative hemoglobin concentration, after treatment hemoglobin levels, and complications like mortality, stroke, myocardial infarction, deep vein thrombosis, pulmonary embolism and renal dysfunction.

RESULTS

Eleven studies were included. The combination of ESA and iron decreased number of patients who required blood transfusion in comparison to patients treated with iron therapy alone (RR, 0.73; 95% CI, 0.59 to 0.91, I.

CONCLUSION

<ref id="2">2</ref> = 65%; p = 0.005). In subgroup analysis with oral and intravenous iron, the difference was not statistically significant (p = 0.24). Administration of erythropoietin either in high ( 80,000 IU) or low dose ( 80,000 IU) resulted in lower blood transfusion rates (p = 0.0007) with no significant difference between groups. The risk of mortality, myocardial infarction, stroke, deep vein thrombosis or pulmonary embolism did not significantly increase. Combined administration of ESA and iron versus iron only reduces the number of red blood cell transfusions in the postoperative period in orthopedic procedures with minimal risk of complications.

Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry

Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.

Efficacy of metam potassium on Fusarium oxysporum, Macrophomina phaseolina, Meloidogyne javanica, and seven weed species in microcosm experiments

BACKGROUND

Metam potassium (metam-K) is a soil fumigant widely used to control plant pathogens, nematodes, and weeds in Florida plasticulture production. The objective of the study was to determine the efficacy of metam-K against Fusarium oxysporum, Macrophomina phaseolina, Meloidogyne javanica, and seven important weed species under controlled conditions. The optimal rates generated in this study provide insight into the efficacy of metam-K for field application.

RESULTS

F. oxysporum and M. phaseolina were similarly sensitive toward metam-K with a 90% effective concentration (EC₉₀ ) of 478 and 493 μmol kg^-1 soil, respectively. Meloidogyne javanica was the most sensitive pest with an EC₉₀ of 25 μmol kg^-1 which is similar to previous studies. Chenopodium album was the most sensitive weed seed with an EC₉₀ of 260 μmol kg^-1 . Geranium carolinianum and Medicago lupulina were the least sensitive weed species with EC₉₀ values of 786 and 567 μmol kg^-1 , respectively.

CONCLUSION

It is apparent from these results that metam-K can effectively control important pests in Florida plasticulture production systems with the correct application rate and adequate exposure of pest to the fumigant.

Imaging specific cellular glycan structures using glycosyltransferases via click chemistry

Heparan sulfate (HS) is a polysaccharide fundamentally important for biologically activities. T/Tn antigens are universal carbohydrate cancer markers. Here, we report the specific imaging of these carbohydrates using a mesenchymal stem cell line and human umbilical vein endothelial cells (HUVEC). The staining specificities were demonstrated by comparing imaging of different glycans and validated by either removal of target glycans, which results in loss of signal, or installation of target glycans, which results in gain of signal. As controls, representative key glycans including O-GlcNAc, lactosaminyl glycans and hyaluronan were also imaged. HS staining revealed novel architectural features of the extracellular matrix (ECM) of HUVEC cells. Results from T/Tn antigen staining suggest that O-GalNAcylation is a rate-limiting step for O-glycan synthesis. Overall, these highly specific approaches for HS and T/Tn antigen imaging should greatly facilitate the detection and functional characterization of these biologically important glycans.

Glycomic and Proteomic Changes in Aging Brain Nigrostriatal Pathway

Parkinson's disease (PD) is a neurological disorder characterized by the progressive loss of functional dopaminergic neurons in the nigrostriatal pathway in the brain. Although current treatments provide only symptomatic relief, gene therapy has the potential to slow or halt the degeneration of nigrostriatal dopamine neurons in PD patients. Adeno-associated viruses (AAV) are vectors of choice in gene therapy because of their well-characterized safety and efficacy profiles; however, although gene therapy has been successful in preclinical models of the disease, clinical trials in humans have failed to demonstrate efficacy. Significantly, all primary AAV receptors of the virus are glycans. We thus hypothesize that age related changes in glycan receptors of heparan sulfate (HS) proteoglycans (receptor for rAAV2), and/or N-glycans with terminal galactose (receptor for rAAV9) results in poor adeno-associated virus binding in either the striatum or substantia nigra, or both, affecting transduction and gene delivery. To test our hypothesis we analyzed the striatum and substantia nigra for changes in HS, N-glycans and proteomic signatures in young versus aged rat brain striatum and substantia nigra. We observed different brain region-specific HS disaccharide profiles in aged compared with young adult rats for brain region-specific profiles in striatum versus substantia nigra. We observed brain region- and age-specific N-glycan compositional profiles with respect to the terminal galactose units that serve as receptors for AAV9. We also observed brain region-specific changes in protein expression in the aging nigrostriatal pathway. These studies provide insight into age- and brain region-specific changes in glycan receptors and proteome that will inform design of improved viral vectors for Parkinson Disease (PD) gene therapy.

Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides

Analysis of singly glycosylated peptides has evolved to a point where large-scale LC-MS analyses can be performed at almost the same scale as proteomics experiments. While collisionally activated dissociation (CAD) remains the mainstay of bottom-up analyses, it performs poorly for the middle-down analysis of multiply glycosylated peptides. With improvements in instrumentation, electron-activated dissociation (ExD) modes are becoming increasingly prevalent for proteomics experiments and for the analysis of fragile modifications such as glycosylation. While these methods have been applied for glycopeptide analysis in isolated studies, an organized effort to compare their efficiencies, particularly for analysis of multiply glycosylated peptides (termed here middle-down glycoproteomics), has not been made. We therefore compared the performance of different ExD modes for middle-down glycopeptide analyses. We identified key features among the different dissociation modes and show that increased electron energy and supplemental activation provide the most useful data for middle-down glycopeptide analysis. Graphical Abstract.

Lectin-mediated binding and sialoglycans of porcine surfactant protein D synergistically neutralize influenza A virus

Innate immunity is critical in the early containment of influenza A virus (IAV) infection, and surfactant protein D (SP-D) plays a crucial role in the pulmonary defense against IAV. In pigs, which are important intermediate hosts during the generation of pandemic IAVs, SP-D uses its unique carbohydrate recognition domain (CRD) to interact with IAV. An N-linked CRD glycosylation provides interactions with the sialic acid-binding site of IAV, and a tripeptide loop at the lectin-binding site facilitates enhanced interactions with IAV glycans. Here, to investigate both mechanisms of IAV neutralization in greater detail, we produced an N-glycosylated neck-CRD fragment of porcine SP-D (RpNCRD) in HEK293 cells. X-ray crystallography disclosed that the N-glycan did not alter the CRD backbone structure, including the lectin site conformation, but revealed a potential second nonlectin-binding site for glycans. IAV hemagglutination inhibition, IAV aggregation, and neutralization of IAV infection studies showed that RpNCRD, unlike the human analogue RhNCRD, exhibits potent neutralizing activity against pandemic A/Aichi/68 (H3N2), enabled by both porcine-specific structural features of its CRD. MS analysis revealed an N-glycan site-occupancy of >98% at Asn-303 of RpNCRD with complex-type, heterogeneously branched and predominantly α(2,3)-sialylated oligosaccharides. Glycan-binding array data characterized both RpNCRD and RhNCRD as mannose-type lectins. RpNCRD also bound Lewis^Y structures, whereas RhNCRD bound polylactosamine-containing glycans. The presence of the N-glycan in the CRD increases the glycan-binding specificity of RpNCRD. These insights increase our understanding of porcine-specific innate defense against pandemic IAV and may inform the design of recombinant SP-D-based antiviral drugs.

GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. Graphical Abstract ᅟ.

Algorithms and design strategies towards automated glycoproteomics analysis

Glycoproteomics involves the study of glycosylation events on protein sequences ranging from purified proteins to whole proteome scales. Understanding these complex post-translational modification (PTM) events requires elucidation of the glycan moieties (monosaccharide sequences and glycosidic linkages between residues), protein sequences, as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts. Compared with proteomics, bioinformatics for glycoproteomics is immature and many researchers still rely on tedious manual interpretation of glycoproteomics data. As sample preparation protocols and analysis techniques have matured, the number of publications on glycoproteomics and bioinformatics has increased substantially; however, the lack of consensus on tool development and code reuse limits the dissemination of bioinformatics tools because it requires significant effort to migrate a computational tool tailored for one method design to alternative methods. This review discusses algorithms and methods in glycoproteomics, and refers to the general proteomics field for potential solutions. It also introduces general strategies for tool integration and pipeline construction in order to better serve the glycoproteomics community. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:475-498, 2017.

Microfluidic Capillary Electrophoresis-Mass Spectrometry for Analysis of Monosaccharides, Oligosaccharides, and Glycopeptides

Glycomics and glycoproteomics analyses by mass spectrometry require efficient front-end separation methods to enable deep characterization of heterogeneous glycoform populations. Chromatography methods are generally limited in their ability to resolve glycoforms using mobile phases that are compatible with online liquid chromatography-mass spectrometry (LC-MS). The adoption of capillary electrophoresis-mass spectrometry methods (CE-MS) for glycomics and glycoproteomics is limited by the lack of convenient interfaces for coupling the CE devices to mass spectrometers. Here, we describe the application of a microfluidics-based CE-MS system for analysis of released glycans, glycopeptides and monosaccharides. We demonstrate a single CE method for three different modalities, thus contributing to comprehensive glycoproteomics analyses. In addition, we explored compatible sample derivatization methods. We used glycan TMT-labeling to improve electrophoretic migration and enable multiplexed quantitation by tandem MS. We used sialic acid linkage-specific derivatization methods to improve separation and the level of information obtained from a single analytical step. Capillary electrophoresis greatly improved glycoform separation for both released glycans and glycopeptides over that reported for chromatography modes more frequently employed for such analyses. Overall, the CE-MS method described here enables rapid setup and analysis of glycans and glycopeptides using mass spectrometry.

Construction of a Database of Collision Cross Section Values for Glycopeptides, Glycans, and Peptides Determined by IM-MS

An ion mobility quadrupole time-of-flight mass spectrometer was used to examine the gas-phase structures of a set of glycopeptides resulting from proteolytic digestion of the well-characterized glycoproteins bovine ribonuclease B, human transferrin, bovine fetuin and human α1-acid glycoprotein, the corresponding deglycosylated peptides, and the glycans released by the endoglycosidase PNGase F. When closely related glycoforms did not occur naturally, exoglycosidases were used to achieve stepwise removal of individual saccharide units from the nonreducing termini of the multiantennary structures. Collision cross sections (CCS) were calculated and plotted as a function of mass-to-charge ratio. Linear trendlines were observed for the glycoforms of individual N-linked glycopeptides, the deglycosylated peptides, and the released, deutero-reduced permethylated glycans. For the glycoforms of a given glycopeptide or set of derivatized glycans, the slope of the line connecting CCS values remained similar for the [M+3H]3+ ions observed as the glycan antennae were shortened by stepwise exoglycosidase treatments; this trend was consistent regardless of the peptide length or the saccharide removed. The results form the basis for a database of CCS values and the CCS increments that correspond to changes in glycoform compositions.

Complete Molecular Weight Profiling of Low-Molecular Weight Heparins Using Size Exclusion Chromatography-Ion Suppressor-High-Resolution Mass Spectrometry

Low-molecular weight heparins (LMWH) prepared by partial depolymerization of unfractionated heparin are used globally to treat coagulation disorders on an outpatient basis. Patent protection for several LMWH has expired and abbreviated new drug applications have been approved by the Food and Drug Administration. As a result, reverse engineering of LMWH for biosimilar LMWH has become an active global endeavor. Traditionally, the molecular weight distributions of LMWH preparations have been determined using size exclusion chromatography (SEC) with optical detection. Recent advances in liquid chromatography-mass spectrometry methods have enabled exact mass measurements of heparin saccharides roughly up to degree-of-polymerization 20, leaving the high molecular weight half of the LMWH preparation unassigned. We demonstrate a new LC-MS system capable of determining the exact masses of complete LMWH preparations, up to dp30. This system employed an ion suppressor cell to desalt the chromatographic effluent online prior to the electrospray mass spectrometry source. We expect this new capability will impact the ability to define LMWH mixtures favorably.

Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions

Despite sustained biomedical research effort, influenza A virus remains an imminent threat to the world population and a major healthcare burden. The challenge in developing vaccines against influenza is the ability of the virus to mutate rapidly in response to selective immune pressure. Hemagglutinin is the predominant surface glycoprotein and the primary determinant of antigenicity, virulence and zoonotic potential. Mutations leading to changes in the number of HA glycosylation sites are often reported. Such genetic sequencing studies predict at best the disruption or creation of sequons for N-linked glycosylation; they do not reflect actual phenotypic changes in HA structure. Therefore, combined analysis of glycan micro and macro-heterogeneity and bioassays will better define the relationships among glycosylation, viral bioactivity and evolution. We present a study that integrates proteomics, glycomics and glycoproteomics of HA before and after adaptation to innate immune system pressure. We combined this information with glycan array and immune lectin binding data to correlate the phenotypic changes with biological activity. Underprocessed glycoforms predominated at the glycosylation sites found to be involved in viral evolution in response to selection pressures and interactions with innate immune-lectins. To understand the structural basis for site-specific glycan microheterogeneity at these sites, we performed structural modeling and molecular dynamics simulations. We observed that the presence of immature, high-mannose type glycans at a particular site correlated with reduced accessibility to glycan remodeling enzymes. Further, the high mannose glycans at sites implicated in immune lectin recognition were predicted to be capable of forming trimeric interactions with the immune-lectin surfactant protein-D.

Posterior Cruciate Ligament Tibial Avulsion treated with Open Reduction and Internal Fixation through the Burks and Schaffer Approach

Objective: To report functional outcome in Posterior Cruciate Ligament (PCL) tibial avulsion fractures treated with open reduction and internal fixation through Burks and Schaffer approach. The patient specific functional outcome measures like IKDC grading together with objective grading with stress radiographs have rarely been used -to assess PCL tibial avulsion fractures.

Material and Methods: Twenty seven patients (21 males and 6 females) were included in the study. The mean follow up duration was 22.30±6.82 months. They were assessed using international knee documentation committee (IKDC) grades, Lysholm scoring and stress radiography. The injury severity scores (ISS) of the patients were also recorded.

Results: The mean Lysholm scores at the time of last follow up was 90.85±5.58. The IKDC grades achieved were normal in 20 patients, near normal in five and abnormal in two. The PCL laxity determined on active hamstring contraction stress radiography was grade I in 20 cases and grade II in seven cases. All patients had achieved bony union of tibial avulsion fractures at the time of last follow up. Statistically significant association was found between higher ISS and lower Lysholm scores. (t=3.455, p=0.0019). Good IKDC grades were associated with higher Lysholm scores (analysis of variance, F=32.51, p<.0001). There was no correlation between PCL laxity and functional outcome (t=.857, p = 0.399).

Conclusion: PCL tibial avulsion fractures treated through Burk and Schaffer approach with open reduction and internal fixation produces good results. The early rehabilitation without cast immobilisation prevents arthrofibrosis.

Confident assignment of site-specific glycosylation in complex glycoproteins in a single step

A glycoprotein may contain several sites of glycosylation, each of which is heterogeneous. As a consequence of glycoform diversity and signal suppression from nonglycosylated peptides that ionize more efficiently, typical reversed-phase LC-MS and bottom-up proteomics database searching workflows do not perform well for identification of site-specific glycosylation for complex glycoproteins. We present an LC-MS system for enrichment, separation, and analysis of glycopeptides from complex glycoproteins (>4 N-glycosylation sequons) in a single step. This system uses an online HILIC enrichment trap prior to reversed-phase C18-MS analysis. We demonstrated the effectiveness of the system using a set of glycoproteins including human transferrin (2 sequons), human alpha-1-acid glycoprotein (5 sequons), and influenza A virus hemagglutinin (9 sequons). The online enrichment renders glycopeptides the most abundant ions detected, thereby facilitating the generation of high-quality data-dependent tandem mass spectra. The tandem mass spectra exhibited product ions from both glycan and peptide backbone dissociation for a majority of the glycopeptides tested using collisionally activated dissociation that served to confidently assign site-specific glycosylation. We demonstrated the value of our system to define site-specific glycosylation using a hemagglutinin containing 9 N-glycosylation sequons from a single HILIC-C18-MS acquisition.

Workflow for combined proteomics and glycomics profiling from histological tissues

Extracellular matrixes comprise glycoproteins, glycosaminoglycans and proteoglycans that order the environment through which cells receive signals and communicate. Proteomic and glycomic molecular signatures from tissue surfaces can add diagnostic power to the immunohistochemistry workflows. Acquired in a spatially resolved manner, such proteomic and glycomic information can help characterize disease processes and be easily applied in a clinical setting. Our aim toward obtaining integrated omics datasets was to develop the first workflow applicable for simultaneous analysis of glycosaminoglycans, N-glycans and proteins/peptides from tissue surface areas as small as 1.5 mm in diameter. Targeting small areas is especially important in the case of glycans, as their distribution can be very heterogeneous between different tissue regions. We first established reliable and reproducible digestion protocols for the individual compound classes by applying standards on the tissue using microwave irradiation to achieve reduced digestion times. Next, we developed a multienzyme workflow suitable for analysis of the different compound classes. Applicability of the workflow was demonstrated on serial mouse brain and liver sections, both fresh frozen and formalin-fixed. The glycomics data from the 1.5 mm diameter tissue surface area was consistent with data published on bulk mouse liver and brain tissues, which demonstrates the power of the workflow in obtaining combined molecular signatures from very small tissue regions.

Lithotomy-related neurovascular complications in the lower limbs after colorectal surgery

AIM

To review the literature on lithotomy-related neurovascular complications (LRNVC) of the lower limbs after colorectal surgery.

METHOD

Electronic databases were searched for relevant articles, including Medline, EMBASE, Pubmed, CENTRAL and CINHL.

RESULTS

LRNVC after prolonged lithotomy position during colorectal surgery can be classified into vascular, neurological and neurovascular combined. Compartment syndrome (CS) is the most common clinical presentation. Seven case reports and 10 case series on 34 patients (27 men, 6 women) with CS have been reported. Risk factors included the lithotomy position and duration of surgery of more than 4 h.

CONCLUSION

In colorectal surgery, lower limb LRNCVs, and CS are rare. A high index of clinical suspicion and early decompression may reduce morbidity.

Endo-anal ultrasound versus endo-anal magnetic resonance imaging for the depiction of external anal sphincter pathology in patients with faecal incontinence: a systematic review

Objective: To evaluate the endo-anal ultrasound (EAUS) versus endo-anal magnetic resonance imaging (EAMRI) in the diagnosis of external anal sphincter defects (EAS) in patients with faecal incontinence (FI). Methods: Studies on EAUS and EAMRI were selected and analyzed to generate summative data. Results: Five studies encompassing 347 patients of FI were included in this review. Three studies validated the results of EAUS and EAMRI by surgery (61 patients). In the fixed effect model, EAUS was superior to EAMRI in the depiction of EAS defects. On combined analysis of five studies using fixed effect model, both EAUS and EAMRI were equally effective. However, there was a significant heterogeneity between studies. Conclusion: EAUS and EAMRI are comparable in the diagnosis of EAS defects in patients of FI. Since EAUS is an economical, quicker and easily available imaging modality, it may be used a preferable investigation for the diagnosis of EAS defects in patients of FI.

Mini-open reduction and intramedullary interlocking nailing of fracture shaft of tibia without an image intensifier

Intramedullary interlocking tibial nailing is usually performed using an image intensifier. But being expensive, it is not available in the most of the hospitals of resource-poor countries of the world. The purpose of this study is to analyze the results of interlocking nailing without the use of an image intensifier. This is the retrospective study of 55 diaphyseal tibial fractures treated with minimally open reduction and internal fixation with interlocked intramedullary nail fixation. The proximal locking of the nail with the screws was made using external jig and for the distal locking direct visualization of the hole was carried out. There were 15 females and 40 males. The average age in years was 32 with a range of 18 to 64 years. The surgical approach was medial parapatellar. The average follow up period was 4 months. This period ranged from 3 months to 14 months. The union time in an average was 4 months. The complication mainly was distal screw loosening leading to valgus deformity and shortening in 1 case. It is, therefore, concluded that interlocking intramedullary nailing can be performed with proximal and distal locking accurately without the use of an image intensifier.

Targeted intracellular delivery of therapeutics: an overview

During the last decade, intracellular drug delivery has become an emerging area of research in the medical and pharmaceutical field. Many therapeutic agents such as drugs and DNA/oligonucleotides can be delivered not just to the cell but also to a particular compartment of that cell to achieve better activity e.g. proapoptotic drugs to the mitochondria, antibiotics and enzymes to the lysosomes and various anticancer drugs and gene to the nucleus. The lipidic nature of biological membrans is the major obstacle to the intracellular delivery of macromolecular and ionic drugs. Additionally, after endocytosis, the lysosome, the major degradation compartment, needs to be avoided for better activity. To avoid these problems, various carriers have been investigated for efficient intracellular delivery, either by direct entry to cytoplasm or by escaping the endosomal compartment. These include cell penetrating peptides, and carrier systems such as liposomes, cationic lipids and polymers, polymeric nanoparticles, etc. Various properties of these carriers, including size, surface charge, composition and the presence of cell specific ligands, alter their efficacy and specificity towards particular cells. This review summarizes various aspects of targeted intracellular delivery of therapeutics including pathways, mechanisms and approaches. Various carrier constructs having potential for targeted intracellular delivery are also been discussed.

Vascularization of developing human olfactory neuroepithelium - a morphometric study

The present study reveals intraepithelial capillaries in the olfactory neuroepithelium of human fetuses aged between 12 and 24 weeks of gestation, which disappear at birth. The area occupied by the intraepithelial capillaries increases significantly with fetal age (0.047 +/- 0.014 microm(2)/microm(2) at 12 weeks and 0.101 +/- 0. 025 microm(2)/microm(2) at 24 weeks) and with the thickness of the epithelium (45.00 +/- 6.74 microm at 8 weeks and 64.10 +/- 8.51 microm at 24 weeks). The vascularization of the developing neuroepithelium may suggest increased metabolic demand during development and maturation of the olfactory neuroepithelium, and postnatal retreat of capillaries to the underlying lamina propria may suggest diffusion of nutrients and gases from blood vessels into the lamina propria and direct gaseous exchange from the atmosphere.

Sensory innervation of the suprarenal gland in the albino rat: a fluorescent tract tracer study

The afferent innervation of the suprarenal gland was studied by using a fluorescent tract tracer in the adult albino rat. The left suprarenal gland was injected slowly with 5 microl of 2% aqueous suspension of Fast blue. After a survival period of 4-5 days, the dorsal root ganglia were dissected out and 15-microm-thick plastic (JB 4) sections were examined under the fluorescent microscope. The labelled neurons were seen from the third thoracic to second lumbar dorsal root ganglia, ipsilateral to the site of injection with maximum concentration from T6 to T11. These primary sensory neurons were round to oval in shape, varied from 7 microm to 40 microm in size, and were distributed randomly in the dorsal root ganglia. The labelling of the primary sensory neurons in the dorsal root ganglia confirms the presence of sensory nerve endings in the suprarenal gland that may be responsible for the vascular distension and hormonal release.

Comparative clinical trial of 2 carbon dioxide resurfacing lasers with varying pulse durations. 100 microseconds vs 1 millisecond

OBJECTIVES

To compare the clinical and histological effects of 2 carbon dioxide lasers with different pulse durations and to evaluate the effect of carbon dioxide laser pulse duration on postprocedure erythema, wound healing, and efficacy of wrinkle treatment.

DESIGN

Prospective, randomized, comparative clinical trial.

SETTING

A university-affiliated hospital-based laser center.

PATIENTS

Thirty-five patients with facial wrinkles were enrolled in the study. Treatment sites included 15 perioral, 14 periorbital areas, and 6 full face.

INTERVENTION

A 2-sided comparison was performed. One side of the study site was treated with the TruPulse laser (Tissue Technologies, Palomar Medical Products Inc, Lexington, Mass). The other side of the study site was treated with the UltraPulse 5000 laser (Coherent Medical Inc, Palo Alto, Calif). The 2 sides were treated to equivalent tissue effects rather than maintaining the number of passes.

MAIN OUTCOME MEASURES

Photographs of the treatment areas at baseline, week 1, week 2, month 2, and month 6 were evaluated by a 5-member panel for degree of erythema, amount of edema, and percentage of wrinkle improvement. Silicon skin casts for profilometry measurements before and after the treatment were compared. To evaluate skin shrinkage, surface area before and after treatment of square tattoos on both cheeks of the full-face patients were computed using a digital imaging system. Histological sections before and after the procedure were analyzed.

RESULTS

At week 1, 75% of the patients had more erythema on the UltraPulse than TruPulse sides. The difference in erythema (TruPulse less than UltraPulse) between the 2 treatment sides was clinically mild yet statistically significant for weeks 1 (P = .05) and 2 (P = .05). Although observed results favored the UltraPulse over the TruPulse, the difference in efficacy between the 2 lasers did not reach statistical significance.

CONCLUSIONS

Compared with the longer pulse-duration carbon dioxide laser, the shorter pulse-duration carbon dioxide laser, used with higher energy and more passes, caused slightly less erythema while maintaining efficacy. The longer pulse-duration laser required lower energy and fewer number of passes to achieve an equivalent depth of ablation, level of residual thermal damage, and degree of efficacy. The shorter TruPulse allows for more superficial tissue damage per pass and therefore is best suited for situations requiring superficial or more controlled ablation. The longer UltraPulse achieves a desirable depth of tissue damage with fewer passes. The data did not support the long-term presence of tissue collagen shrinkage in the treated areas.

Utilization of pulmonary function tests by primary care internists in a community hospital

OBJECTIVE

A quality assurance effort to evaluate the use of pulmonary function tests by primary care physicians. Specifically, to examine the patient's understanding of the test, the types of tests physicians order, and the appropriateness of the ordered tests for answering questions posed by physicians.

DESIGN

Concurrent chart review, clinical interviews, and patient interviews.

SETTING

Community teaching hospital.

PATIENTS

101 consecutive inpatients and outpatients, referred to the Pulmonary Function Laboratory over a consecutive 5-month period.

MEASUREMENTS

Interview of the patient by a pulmonary technician. Interview of the primary care physician by a pulmonary physician. Interview, where applicable, with the house staff. Final assessment by a pulmonary physician.

MAIN RESULTS

64% of the patients understood the purpose of the test and 49% of the patients felt there was some potential benefit to be derived from participating in the testing. Sixty-five percent of the physicians ordered specific tests on their patients. Seventy-two percent of physicians planned on using the data obtained from testing to formulate treatment decisions. Fifty percent of the interviewed physicians said they were using the results for decisions regarding further diagnostic evaluation and/or treatment. The reviewing pulmonary physician considered that 31% of the pulmonary function tests ordered were appropriate for the goals defined by the requesting physician. Sixty-eight percent of the ordered tests could have had some aspects of ordering improved, and 1% of the testing was unnecessary.

CONCLUSIONS

1) There is a need to increase patient understanding of the indications and potential benefits of participating in pulmonary function testing. 2) When physicians-in-training are involved in the process of requesting pulmonary function tests, greater staff-level supervision and involvement should be present. 3) There is a need to increase physician knowledge regarding the appropriate pulmonary function tests that should be requested for specific clinical questions and situations. 4) The requesting form for pulmonary function testing may serve to remind and educate the physician, while documenting the indications for the testing and the physician's efforts. 5) Quality assurance/utilization-review efforts can be combined with educational efforts that could result in a diminution of the deficiencies.

Major histocompatibility complex haplotypes and class II genes in non-Jewish patients with pemphigus vulgaris

Previous studies demonstrated that HLA-DR4 was markedly increased among Ashkenazi Jewish patients with pemphigus vulgaris (PV), almost entirely as the common Jewish extended haplotype [HLA-B38, SC21, DR4, DQw8] or as the haplotype HLA-B35, SC31, DR4, DQw8, and that HLA-DR4, DQw8 was distributed among patients in a manner consistent with dominant expression of a class II (D-region or D-region-linked) susceptibility gene. In the present study of major histocompatibility complex (MHC) haplotypes in 25 non-Jewish PV patients, DR4, DQw8 was found in 12 of the patients and DRw6, DQw5 was found in 15. Only 3 patients had neither. Only 1 of the DR4, DQw8 haplotypes was [HLA-B38, SC21, DR4, DQw8] and 2 were HLA-B35, SC31, DR4, DQw8; most were the presumed fragments (SC31, DR4, DQw8) or (SC21, DR4, DQw8) or DR4, DQw8 with some other complotype. Of the patients with DRw6, DQw5, all were DRw14, DQw5, and 6 had a rare Caucasian haplotype, HLA-Bw55, SB45, DRw14, DQw5. Four of 6 of these were found in patients of Italian extraction, as was the 1 normal example. The non-Jewish patients were of more Southern European extraction than our controls. This suggests that there are two major MHC susceptibility alleles in American patients with PV. The more ancient apparently arose on a haplotype in the Jews, HLA-B38(35), SC21(SC31), DR4, DQw8, and spread to other populations largely as D-region segments. The other arose in or near Italy on the haplotype HLA-Bw55, SB45, DRw14, DQw5 and has also partially fragmented so that many patients carry only DRw14, DQw5. The available data do not permit the specific localization of either the DR4, DQw8- or the DRw14, DQw5-linked susceptibility genes.

Major histocompatibility complex haplotype studies in Ashkenazi Jewish patients with pemphigus vulgaris

Of 26 Ashkenazi Jewish patients with pemphigus vulgaris, 24 (92.3%) carried the major histocompatibility complex (MHC) class II alleles HLA-DR4, DQw3, of which all were of the subtype DR4, DQw8. From studies of the patients and their families, haplotypes were defined. It was found that, of the patients who carried HLA-DR4, DQw8, 75% carried one or the other (and in one case, both) of two haplotypes [HLA-B38, SC21, DR4] or HLA-B35, SC31, DR4. The former is a known extended haplotype among normal Jews, with a frequency of 0.102, and the latter may also be an extended haplotype in this ethnic group, with a frequency of 0.017 among normal haplotypes from Jews. Of the remaining DR4-positive patients, all but one had a presumed D-region segment (defined as SC21, DR4, DQw8 or SC31, DR4, DQw8 with variable HLA-B) of these haplotypes. Only one patient had DR4, DQw8 without any other markers of the extended haplotypes. The number of homozygotes and heterozygotes for DR4, DQw8 was consistent with dominant but not recessive (P less than 0.01) inheritance of a class II or a class II-linked susceptibility gene for the disease. Since the disease is entirely attributable to the presence of an antibody to an intraepidermal intercellular cement substance, it is likely that the class II susceptibility gene (on [HLA-B38, SC21, DR4, DQw8], HLA-B35, SC31, DR4, DQw8, or their segments, in Jewish patients) controls the production of the antibody as a dominantly expressed immune response gene.