GlyGen Monthly Talks

On 1st Tuesday of every Month at 11 AM EST, GlyGen team will meet and make monthly progress report. Invited speakers will give a talk for possible collaboration with GlyGen. New technological breakthroughs, new discoveries, possible improvement and proposals that may promote the development of Glygen will be discussed and shared.

October 10/06/2020

Attendees: Jeet, Nathan, Nhat Duong, Rahi, Raja, Akul, Frederique, Lihua, Preethi, Mike, Rene, Sujeet, Rupali, Ten, Vijay, Will, Tatiana,

Agenda:

• Monthly Progress Report
• Talk by - Nhat Duong and Nathan Edwards - Title: “Glycan Structure Extraction from Scientific Literature”

https://edwardslab.bmcb.georgetown.edu/glyimgdemo/

Abstract:

The extraction and representation of accepted glycobiology knowledge is challenging due to the widespread use of images to represent glycans in published literature. In the absence of an explicit computer-readable glycan sequence or accession number, human curation is required to extract published glycosylation knowledge for our glycomics data-resources. Glycan structure images in published literature are highly stylized but poorly standardized, despite efforts by the Standardized Nomenclature for Glycans (SNFG) group to make them more consistent. Automated extraction of glycan structures from figures in published manuscripts will ease the curation effort.

We use a combination of open-source Python modules for parsing and manipulating PDF files; neural network-based object classification to locate glycans in manuscripts’ figures; and OpenCV-based image analysis to extract glycan structure details. Figures from GlyGen and UniCarbKB manuscript annotations were curated to construct a training set of figures with glycan bounding-box locations.This object classification approach successfully identifies glycan structures in manuscript figures for subsequent detailed glycan image analysis and highlights the glycan structures in the manuscript.

Glycan structure details are extracted using the open-source OpenCV library. Using color masks, monosaccharides' distinctive colors and shapes are recognized, establishing the monosaccharide composition of the glycan. Monosaccharide linkage is then determined, where possible. The glycan structure’s orientation and the reducing-end monosaccharide is then established by identifying common glycan cores. Together, this information is sufficient to construct a GlycoCT format sequence for the

structure’s topology and to then search for a matching glycan in GlyTouCan. Once matched, the GlyTouCan accession is used to embed a targeted, clickable link to the GNOme Structure Browser on top of the glycan structure in the original PDF file.

This infrastructure provides a surprisingly effective tool for extracting glycan structures from the figures of published glycobiology manuscripts. The method successfully identifies glycans' positions on all pages, extracts their topological structure in GlycoCT format, and annotates them in-place with deep-links to  GNOme so the curator can verify or refine the specific details of the structure. This prototype demonstrates the potential utility of automated extraction of glycan structures from published manuscript figures, significantly lowering the curation burden for the representation of glycosylation knowledge in

glycomics resources.

Minutes:

• Monthly Progress Report
• Link to the tool - https://edwardslab.bmcb.georgetown.edu/glyimgdemo/
• Slides: Nhat Duong - Glycan Structure Extraction from Scientific Literature -Oct 2020
• Recording: Nhat Duong - Glycan Structure Extraction from Scientific Literature -Oct 2020

September 09/01/2020

Attendees:

Agenda:

• Monthly Progress Report
• Talk by - Gareth Owen - Title "Integration of GlyGen/GlyTouCan glycans in ChEBI"

Abstract - The importance of glycans and glycoproteins in molecular biology has grown rapidly in recent years. In this talk, the development of procedures to enhance the flexibility of glycan registration in ChEBI through a collaboration between ChEBI and GlyGen is described.

Minutes:

• Monthly Progress Report
• Slides: Gareth Owen - Integration of GlyGen GlyTouCan Glycans in ChEBI 23_09_2020
• Recording: Gareth Owen - Integration of GlyGen GlyTouCan Glycans in ChEBI 23_09_2020

July 07/05/2020

Attendees: Jeet, Lance Wells, Doug, Ganka, Maria Martin, Michael Pierce, MikeT, Oliver Grant, Preethi Vasudev, Rado, Rahi, Raja, Rene, Rob, Rupali, Sena, Simon Kimuda, Sujeet, Tatiana, Ten, Vijay, Will, Xiying Ding, Yan Liu, Yukie Akune, Amanda Mellilo

Agenda:

• Monthly Progress Report
• Talk by Dr. Lance Wells

Talk by Dr.Lance Wells - “Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor”

Summary - The current COVID-19 pandemic is caused by the SARS-CoV-2 betacoronavirus, which utilizes its highly glycosylated trimeric Spike protein to bind to the cell surface receptor ACE2 glycoprotein and facilitate host cell entry. We utilized glycomics-informed glycoproteomics to characterize site-specific microheterogeneity of glycosylation for a recombinant trimer spike mimetic immunogen and for a soluble version of human ACE2. We combined this information with bioinformatic analyses of natural variants and with existing 3D-structures of both glycoproteins to generate molecular dynamic simulations of each glycoprotein alone and interacting with one another. Our results highlight roles for glycans in sterically masking polypeptide epitopes and directly modulating Spike-ACE2 interactions. Furthermore, our results illustrate the impact of viral evolution and divergence on Spike glycosylation, as well as the influence of natural variants on ACE2 receptor glycosylation that, taken together, can facilitate immunogen design to achieve antibody neutralization and inform therapeutic strategies to inhibit viral infection.

The link to the article: https://www.biorxiv.org/content/10.1101/2020.06.25.172403v1

June 06/02/2020

Agenda:

• Monthly Progress Report
• Talk by Dr. Stéphanie Olivier - “The human O-GlcNAcome database”
• GlyGen virtual F2F meeting announcements

Minutes

• Monthly Progress Report
• Slides - Stephanie OVS human O-GlcNAcome database - 06-02-2020
• Recording - Stephanie OVS human O-GlcNAcome database - 06-02-2020

April 04/07/2020

Attendees: Jeet Vora, Tom Gerken, Jon Mohl, Tatiana W, Raja Mazumder, Rahi Navelkar, Earnest James, Nathan Edwards, Vijay Shankar, Will York, Sujeet Kulkarni, Ten Feizi, Rene Ranzinger, Rupali Mahadik, Tyler Stewart, Ming Ying, Rado Goldman, Doug, Amanda Mellilo, MikeT, Earnest James, Gareth Owen, Will York, Ruplai Mahadik

Agenda:The agenda items for the call are

• Monthly Progress Report
• Talk by Dr. Thomas Gerken - Short intro to O-glycosylation and current research in lab
• Talk by Dr. Johnathon Mohl and Dr, Ming-Ying Leung

Title - ISOGlyP: de novo prediction of isoform specific mucin-type O-glycosylation  

Abstract -

Using position-specific enhancement values generated based on GalNAc-T isoform specific amino acid preferences, ISOGlyP predicts the propensity that a site would be glycosylated by a specific transferase. Additionally, ISOGlyP can identify the known effects of long- and short-range prior glycosylation and can generate potential peptide sequences selectively glycosylated by specific isoforms. Isoglyp.utep.edu is an easy to use web-interface that makes these features readily available.

Minutes

Monthly Progress Report

Slides -

1. Tom Gerken’s slides - Orchestration of Mucin Type O-Glycosylation by the Multiple Activities of the GalNAc-T Family of Transferases
2. Jon Mohl and Ming-Ying Leung slides - ISOGlyP: de novo prediction of isoform specific mucin-type O-glycosylation

Meeting Recording

March 03/03/2020

Attendees: Raja, Ten, Vijay, Karen Ross, Rahi Navelkar, Jeet Vora, Amanda Mellilo, Will York, Rene, Tatiana, Sujeet Kulkarni, Rob Woods, Evan Bolton, Nathan Edwards.

Agenda:The agenda items for the call are

• Monthly update on the project
  • GlyGen conference/demos: https://docs.google.com/spreadsheets/d/1CztEZ23Hzx1pGE3UTkw9uvSrf02HmYUTR6KhhqkVx6g/edit#gid=0
  • GlyGen all-hands f2f: June 29th - July 1st (M-W)
  • Vijay Shankar's Talk

Title:

Development of an automatic literature mining pipeline for extracting specific glycosylation information from publications

Abstract:Using the abstracts of UniCarbKB glycoprotein publications in GlyGen, we have identified patterns to detect glycoprotein and sites from the literature. The current tool identifies the glycoprotein and the site from Medline abstracts and has been applied on approximately 10,000 abstracts as proof of concept. The presentation will focus on the current development, future plans, and representation of the generated data in GlyGen.  

Minutes:

• Jeet and Rahi gave a progress update on GlyGen for the month of Feb
• GlyGen F2F 2020 is scheduled from June 29-July 01 in GW, DC. GW will be monitoring the coronavirus situation and provide update if there is a major change. There will be provisions for AV for attending meeting remotely.
• Vijay Shakar gave an excellent talk
  • Slides
  • Recorded Meeting

February 02/04/2020

Attendees: Jeet, Mike, Akul, Amanda, Doug, Gareth, Nathan, Preethi, Nathan, Rahi, Raja, Tyler, Rene, Sena, Sujeet, Tatiana, Ten, Vijay, Will

Agenda:

• Monthly update on the project
• Michael Tiemeyer's Talk
• Discussion on Advocate’s feedback on GlyGen

Talk: Title:  

"The glycomic diversity of homogeneous cell populations derived from pluripotent precursors"

Brief abstract:

"Deciphering tissue and cell-specific glycan expression in humans is complicated by the cellular heterogeneity that characterizes all tissues.  Induced pluripotent stem cells provide opportunities to generate pure cell populations for glycomic and glycobiologic studies.  We have generated glycomic profiles for human ES and iPS cells differentiated into multiple lineages. Each lineage elaborates its own characteristic portfolio of glycans.  Patient-derived iPS cells can now be examined for cell-type-specific glycan expression changes to generate novel biomarkers and understand novel mechanisms related to the glycopathology of human diseases".

Minutes:

• GW team gave an update on work done in Jan

GlyGen Project Update for January 2020

• Michael’s Talk -

Download (https://drive.google.com/open?id=1QQAMOui-ZmATnVmfTazuTVdFTcMafYZr)

Stream (https://gwu.webex.com/gwu/ldr.php?RCID=2b8a73cecced03f0d723ab6b540ecc62)

Slides - (https://drive.google.com/open?id=1P42eIQ-y_uoyb2bTRtGfw2_C7agZa_Qi)

• Advocate Feedback - The feedback will be discussed first in the weekly meeting and then again discussed in the Monthly Meeting