RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein composition that occur during biological processes

Motivation

Glycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically synthesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. Glycoproteins, accounting for approximately half of all proteins, require specialized proteomics data analysis methods due to micro- and macro-heterogeneities as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values. In conjunction with the low sample size inherent to glycoproteomics, a specialized toolset is needed to determine if observed changes in glycopeptide abundances are biologically significant or due to data quality limitations.

Results

We developed an R package, Relative Assessment of m/z Identifications by Similarity (RAMZIS), that uses similarity metrics to guide researchers to a more rigorous interpretation of glycoproteomics data. RAMZIS uses a permutation test to generate contextual similarity, which assesses the quality of mass spectral data and outputs a graphical demonstration of the likelihood of finding biologically significant differences in glycosylation abundance datasets. Investigators can assess dataset quality, holistically differentiate glycosites, and identify which glycopeptides are responsible for glycosylation pattern change. RAMZIS is validated by theoretical cases and a proof-of-concept application. RAMZIS enables comparison between datasets too stochastic, small, or sparse for interpolation while acknowledging these issues in its assessment. Using this tool, researchers will be able to rigorously define the role of glycosylation and the changes that occur during biological processes.

Availability and implementation

https://github.com/WillHackett22/RAMZIS.

[Research progress on biomarkers and detection methods for Alzheimer's disease diagnosis in vitro]

Alzheimer's disease (AD) is a neurodegenerative disease with insidious onset, posing a serious threat to human physical and mental health. The cognitive impairments caused by AD are generally diffuse and overlap symptomatically with other neurodegenerative diseases. Moreover, the symptoms of AD are often covert, leading to missed opportunities for optimal treatment after diagnosis. Therefore, early diagnosis of AD is crucial. In vitro diagnostic biomarkers not only contribute to the early clinical diagnosis of AD but also aid in further understanding the disease's pathogenesis, predicting disease progression, and observing the effects of novel candidate therapeutic drugs in clinical trials. Currently, although there are numerous biomarkers associated with AD diagnosis, the complex nature of AD pathogenesis, limitations of individual biomarkers, and constraints of clinical detection methods have hindered the development of efficient, cost-effective, and convenient diagnostic methods and standards. This article provides an overview of the research progress on in vitro diagnostic biomarkers and detection methods related to AD in recent years.

Retinal small vessel narrowing in women with gestational diabetes, pregnancy-associated hypertension, or small-for-gestational age babies

Background

Gestational diabetes, pregnancy-associated hypertension and small-for-gestational age babies are all associated with impaired placental vascularisation. This study compared the effects of these conditions the systemic small vessel calibre that was examined in the retina.

Methods

This was a cross-sectional observational study of consecutive pregnant women recruited from an antenatal clinic. Participants underwent a Glucose Tolerance Test, BP measurements, and were examined for small-for-gestational age babies as per national guidelines. They also underwent retinal photography with a non-mydriatic camera, and vessel calibres were measured with a validated semi-quantitative system at a retinal grading centre. Some participants also underwent testing of retinal vascular responsiveness to a flickering light.

Results

Women with gestational diabetes (n = 68) had a higher mean arterial pressure (85 ± 9 mm Hg) than normal pregnant women (n = 27, 80 ± 8 mmHg, p = 0.01). They also had smaller mean retinal arteriole (147.5 ± 13.6 μm and 159.7 ± 6.7 μm respectively, p < 0.01) and venular calibre (221.0 ± 13.4 μm and 232.8 ± 20.1 μm respectively, p < 0.01) than normal. However their babies' mean birth weights were not different from normal (3,311 ± 558 g and 3,401 ± 600 g respectively, p = 0.48). They also demonstrated a trend to reduced retinal arteriolar dilatation (3.5 ± 1.3%, n = 23) in response to vasodilatory stimuli (4.4 ± 1.8%) (n = 11) (p = 0.08) consistent with endothelial dysfunction. Women with pregnancy-associated hypertension (n = 35) had a higher mean arterial pressure (101 ± 12 mm Hg, p < 0.01), a smaller mean retinal arteriolar calibre (139.9 ± 10.6 μm, p < 0.0001), and a lower baby mean birth weight than for normal pregnancies (3,095 ± 443 g, p = 0.02). Likewise, women with small-for-gestational age babies (n = 31) had a higher mean arterial pressure (89 ± 19 mm Hg, p = 0.03), a smaller mean retinal arteriolar calibre (141.6 ± 12.8 μm, p < 0.01) and a lower baby mean birth weight than for normal pregnancies (2,468 ± 324 g, p < 0.0001).

Conclusion

Mean retinal arterial calibre was reduced in women with gestational diabetes, pregnancy-associated hypertension or small-for-gestational age babies. The reduction in calibre was greatest in pregnancy-associated hypertension and small-for-gestational age babies. Systemic arteriole narrowing may contribute to the pathogenesis of placental vascular dysfunction in these conditions.

SKIN REINNERVATION BY COLLATERAL SPROUTING FOLLOWING SPARED NERVE INJURY IN MICE

Following peripheral nerve injury, denervated tissues can be reinnervated via regeneration of injured neurons or via collateral sprouting of neighboring uninjured afferents into the denervated territory. While there has been substantial focus on mechanisms underlying regeneration, collateral sprouting has received relatively less attention. In this study, we used immunohistochemistry and genetic neuronal labeling to define the subtype specificity of sprouting-mediated reinnervation of plantar hind paw skin in the mouse spared nerve injury (SNI) model, in which productive regeneration cannot occur. Following an initial loss of cutaneous afferents in the tibial nerve territory, we observed progressive centripetal reinnervation by multiple subtypes of neighboring uninjured fibers into denervated glabrous and hairy plantar skin. In addition to dermal reinnervation, CGRP-expressing peptidergic fibers slowly but continuously repopulated the denervated epidermis, Interestingly, GFRα2-expressing nonpeptidergic fibers exhibited a transient burst of epidermal reinnervation, followed by trend towards regression. Presumptive sympathetic nerve fibers also sprouted into the denervated territory, as did a population of myelinated TrkC lineage fibers, though the latter did so less efficiently. Conversely, rapidly adapting Aβ fiber and C fiber low threshold mechanoreceptor (LTMR) subtypes failed to exhibit convincing collateral sprouting up to 8 weeks after nerve injury. Optogenetics and behavioral assays further demonstrated the functionality of collaterally sprouted fibers in hairy plantar skin with restoration of punctate mechanosensation without hypersensitivity. Our findings advance understanding of differential collateral sprouting among sensory neuron subpopulations and may guide strategies to promote the progression of sensory recovery or limit maladaptive sensory phenomena after peripheral nerve injury.

Significance Statement

Following nerve injury, whereas one mechanism for tissue reinnervation is regeneration of injured neurons, another, less well studied mechanism is collateral sprouting of nearby uninjured neurons. In this study, we examined collateral sprouting in denervated mouse skin and showed that it involves some, but not all neuronal subtypes. Despite such heterogeneity, a significant degree of restoration of punctate mechanical sensitivity is achieved. These findings highlight the diversity of collateral sprouting among peripheral neuron subtypes and reveal important differences between pre- and post-denervation skin that might be appealing targets for therapeutic correction to enhance functional recovery from denervation and prevent unwanted sensory phenomena such as pain or numbness.

[The incidence of artificial stone-related silicosis among interior decoration workers in different countries]

In this paper, 177 cases of artificial stone-related silicosis in interior decoration workers from Israel, Spain, USA, Italy and Australia were analyzed. Interior decoration workers were from small businesses (or workshops), engaged in kitchen and/or bathroom artificial stone countertops cutting, grinding, polishing and other reprocessing. In the working environment, the content of crystalline silica in artificial stone was more than 70%, and the concentration of silica dust exceeded the relevant standards. Most workplaces used dry cutting without ventilation and dust removal and other dust-proof measures, and most workers did not wear qualified respiratory protective equipment. Taking comprehensive measures such as wet operation, ventilation and dust removal, and individual protection can effectively prevent the occurrence of artificial stone-related silicosis.

RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein structure that occur during biological processes

Motivation

Glycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically syn-thesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. While glycoproteins account for approximately half of all proteins, their macro- and micro-heterogeneity requires specialized proteomics data analysis methods as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values. In conjunction with the low sample size inherent to glycoproteomics, this necessitated specialized statistical metrics to identify if observed changes in glycopeptide abundances are biologically significant or due to data quality limitations.

Results

We developed an R package, Relative Assessment of m/z Identifications by Similarity (RAMZIS), that uses similarity metrics to guide biomedical researchers to a more rigorous interpretation of glycoproteomics data. RAMZIS uses contextual similarity to assess the quality of mass spectral data and generates graphical output that demonstrates the likelihood of finding biologically significant differences in glycosylation abundance dataset. Investigators can assess dataset quality, holistically differentiate glycosites, and identify which glycopeptides are responsible for glycosylation pattern expression change. Herein RAMZIS approach is validated by theoretical cases and by a proof-of-concept application. RAMZIS enables comparison between datasets too stochastic, small, or sparse for interpolation while acknowledging these issues in its assessment. Using our tool, researchers will be able to rigor-ously define the role of glycosylation and the changes that occur during biological processes.

[Research progress on the treatment of presbyopia]

Presbyopia is a physiological aging situation that the plasticity and elasticity of the lens and the function of the ciliary muscle become weaker, resulting in a decreased accommodation and inability to focus on near objects. Nowadays, there are many clinical strategies to correct presbyopia, each of which has its own advantages and disadvantages, however, there is no true sense of way to restore accommodation function. This article reviews both worldwide and domestic research on presbyopia, and analyzes and summaries the status quo as well as research progress of presbyopia correction modalities, surgical approaches, and drug therapies, hoping to provide a reference for clinical works.

Methods to improve quantitative glycoprotein coverage from bottom-up LC-MS data

Advances in mass spectrometry instrumentation, methods development, and bioinformatics have greatly improved the ease and accuracy of site-specific, quantitative glycoproteomics analysis. Data-dependent acquisition is the most popular method for identification and quantification of glycopeptides; however, complete coverage of glycosylation site glycoforms remains elusive with this method. Targeted acquisition methods improve the precision and accuracy of quantification, but at the cost of throughput and discoverability. Data-independent acquisition (DIA) holds great promise for more complete and highly quantitative site-specific glycoproteomics analysis, while maintaining the ability to discover novel glycopeptides without prior knowledge. We review additional features that can be used to increase selectivity and coverage to the DIA workflow: retention time modeling, which would simplify the interpretation of complex tandem mass spectra, and ion mobility separation, which would maximize the sampling of all precursors at a giving chromatographic retention time. The instrumentation and bioinformatics to incorporate these features into glycoproteomics analysis exist. These improvements in quantitative, site-specific analysis will enable researchers to assess glycosylation similarity in related biological systems, answering new questions about the interplay between glycosylation state and biological function.

Heterogeneity of management practices surrounding operable gallbladder cancer - results of the OMEGA-S international HPB surgical survey

BACKGROUND

Gallbladder cancer (GBC) is an aggressive, uncommon malignancy, with variation in operative approaches adopted across centres and few large-scale studies to guide practice. We aimed to identify the extent of heterogeneity in GBC internationally to better inform the need for future multicentre studies.

METHODS

A 34-question online survey was disseminated to members of the European-African Hepatopancreatobiliary Association (EAHPBA), American Hepatopancreatobiliary Association (AHPBA) and Asia-Pacific Hepatopancreatobiliary Association (A-PHPBA) regarding practices around diagnostic workup, operative approach, utilization of neoadjuvant and adjuvant therapies and surveillance strategies.

RESULTS

Two hundred and three surgeons responded from 51 countries. High liver resection volume units (>50 resections/year) organised HPB multidisciplinary team discussion of GBCs more commonly than those with low volumes (p < 0.0001). Management practices exhibited areas of heterogeneity, particularly around operative extent. Contrary to consensus guidelines, anatomical liver resections were favoured over non-anatomical resections for T3 tumours and above, lymphadenectomy extent was lower than recommended, and a minority of respondents still routinely excised the common bile duct or port sites.

CONCLUSION

Our findings suggest some similarities in the management of GBC internationally, but also specific areas of practice which differed from published guidelines. Transcontinental collaborative studies on GBC are necessary to establish evidence-based practice to minimise variation and optimise outcomes.

[Recent progress of aptasensors for tumor exosome-associated protein detection]

Exosomes are phospholipid bilayer membrane-enclosed vesicles released from cells with diameters of 30-150 nm, exosomes can directly reflect the physiological and functional state of secretory cells, participate in material transport and information communication between cells, which are of great significance as biomarkers for early tumor diagnosis and treatment evaluation. There are many detection methods for exosomes, among which aptasensor technology with the properties of low price and easy operation, fast response, high sensitivity, remarkable specificity helps tumor patients to find, diagnose and treat early, improve the survival rate, and provide important basis for the evaluation of the prognosis. There are seven types of common aptasensors: fluorescent, electrochemical, colorimetric, luminescence, lateral flow strips, surface-enhanced Raman scattering and surface plasmon resonance sensors. Different aptasensors have different characteristics, this article focuses on the research progress of several common aptasensor for tumor exosomes detection.

Improving Statistical Certainty of Glycosylation Similarity between Influenza A Virus Variants Using Data-Independent Acquisition Mass Spectrometry

Amino acid sequences of immunodominant domains of hemagglutinin (HA) on the surface of influenza A virus (IAV) evolve rapidly, producing viral variants. HA mediates receptor recognition, binding and cell entry, and serves as the target for IAV vaccines. Glycosylation, a post-translational modification that places large branched polysaccharide molecules on proteins, can modulate the function of HA and shield antigenic regions allowing for viral evasion from immune responses. Our previous work showed that subtle changes in the HA protein sequence can have a measurable change in glycosylation. Thus, being able to quantitatively measure glycosylation changes in variants is critical for understanding how HA function may change throughout viral evolution. Moreover, understanding quantitatively how the choice of viral expression systems affects glycosylation can help in the process of vaccine design and manufacture. Although IAV vaccines are most commonly expressed in chicken eggs, cell-based vaccines have many advantages, and the adoption of more cell-based vaccines would be an important step in mitigating seasonal influenza and protecting against future pandemics. Here, we have investigated the use of data-independent acquisition (DIA) mass spectrometry for quantitative glycoproteomics. We found that DIA improved the sensitivity of glycopeptide detection for four variants of A/Switzerland/9715293/2013 (H3N2): WT and mutant, each expressed in embryonated chicken eggs and Madin-Darby canine kidney cells. We used the Tanimoto similarity metric to quantify changes in glycosylation between WT and mutant and between egg-expressed and cell-expressed virus. Our DIA site-specific glycosylation similarity comparison of WT and mutant expressed in eggs confirmed our previous analysis while achieving greater depth of coverage. We found that sequence variations and changing viral expression systems affected distinct glycosylation sites of HA. Our methods can be applied to track glycosylation changes in circulating IAV variants to bolster genomic surveillance already being done, for a more complete understanding of IAV evolution.