Merge pull request #9 from rnabioco/project-3

update proj-3, fix atlas links, update pubs
rnabioco · Aug 13, 2024 · 7106d8d · 7106d8d
2 parents b26cb71 + be7b8f8
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diff --git a/README.md b/README.md
@@ -1,2 +1,32 @@
-# lnsc-cell-browser
-LNSC cell browser
+## lnsc-cell-browser
+
+### Adding a new publication
+
+* Add a new entry to pubs.yml, the only information needed for the entry is
+  the pubmed URL which is added as the "pubmed" field
+* Optional links can also be added under the "links" field,
+  this includes "github", "atlas", and "geo"
+* Run pre-build.R to scrape the remaining information for the publication and
+  to update authors.yml
+* Rebuild site
+
+### Adding a new cell atlas
+
+* Add the atlas link to the associated publication listed in pubs.yml
+* Rebuild site
+
+### Adding a new project
+
+* Add project information to projects.yml
+* Required fields include, "title", "short", "hypothesis", and "abstract"
+* An optional image can also be included
+* Edit authors.yml to add authors to the new project
+* Run pre-build.R to automatically associate publications with the new project
+* Rebuild site
+
+### Building site
+
+* Remove directories from previous build (_site, .quarto)
+* Run pre-build.R and commit changes
+* Render site
+
diff --git a/atlases/2021-carpentier-34618370/index.qmd b/atlases/2021-carpentier-34618370/index.qmd
@@ -2,9 +2,9 @@
 title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination
 
 image: /images/2021-carpentier-34618370.jpg
-subtitle: '[<i class="bi bi-compass"></i> Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
+subtitle: '[<i class="bi bi-compass"></i> Atlas](http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com){.link-box-large}'
 date: 'November 15, 2021'
-categories: [Project-1, Project-2, Core-C, Core-D, 2021]
+categories: [Project-1, Project-2, Project-3, Core-C, 2021]
 about:
   id: about
   template: jolla

diff --git a/atlases/2021-walsh-33843587/index.qmd b/atlases/2021-walsh-33843587/index.qmd
@@ -4,7 +4,7 @@ title: Molecular tracking devices quantify antigen distribution and archiving in
 image: /images/2021-walsh-33843587.jpg
 subtitle: '[<i class="bi bi-compass"></i> Atlas](https://d3898ys7yh3545.cloudfront.net/){.link-box-large}'
 date: 'April 12, 2021'
-categories: [Project-2, Core-C, Core-D, 2021]
+categories: [Project-2, Project-3, Core-C, 2021]
 about:
   id: about
   template: jolla

diff --git a/atlases/2024-lucas-38194268/index.qmd b/atlases/2024-lucas-38194268/index.qmd
@@ -2,9 +2,9 @@
 title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
 
 image: /images/2024-lucas-38194268.jpg
-subtitle: '[<i class="bi bi-compass"></i> Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
+subtitle: '[<i class="bi bi-compass"></i> Atlas](http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com){.link-box-large}'
 date: 'January 09, 2024'
-categories: [Project-1, Project-2, Core-C, Core-D, 2024]
+categories: [Project-1, Project-2, Project-3, Core-C, 2024]
 about:
   id: about
   template: jolla

diff --git a/authors.yml b/authors.yml
@@ -44,45 +44,15 @@ Beth Tamburini:
     to be well suited for the training and success of the graduate students and post-docs
     in my laboratory.
   image: /images/beth-tamburini.jpg
-Jenna Guthmiller:
-  suffix: PhD
-  links:
-    publications: https://scholar.google.com/citations?user=4arwbfMAAAAJ&hl=en&oi=ao
-    website: https://guthmillerlab.weebly.com/
-    email: mailto:jenna.guthmiller@cuanschutz.edu
-  project: project-3
-  bio: My long-term scientific goals are to understand the complex interactions between
-    pathogens and the immune response mounted against them, with the objective of
-    identifying and developing interventions to limit global infectious disease burdens.
-    Fitting within these goals, my independent laboratory studies how preexisting
-    immunity influences future immune responses against rapidly evolving viruses.
-    My major contributions to science are understanding how protective humoral immunity
-    is generated following infection and vaccination and how vaccination can harness
-    broadly protective humoral immunity. During my postdoctoral studies, I investigated
-    how preexisting immunity against influenza viruses shapes the recall of memory
-    B cells in humans. I found that in the absence of preexisting immunity against
-    the variable epitopes of the hemagglutinin (HA) head domain, humans could recall
-    memory B cells against broadly protective epitopes of HA. These studies identified
-    several novel classes of broadly neutralizing antibodies and a new highly conserved
-    epitope where HA 'anchors' itself into the viral membrane. My research also identified
-    that the first in-human universal influenza vaccine, which is intended to circumvent
-    preexisting antibodies, robustly induced antibodies against broadly protective
-    epitopes, including the anchor epitope. Lastly, I identified influenza vaccination
-    and infection in humans differentially recalled discrete memory B cell specificities,
-    with infection recalling memory B cells primed during childhood against highly
-    conserved, albeit non-protective antigens. Together, these studies highlight the
-    importance of understanding how preexisting antibodies influence the generation
-    of broadly protective immunity.
-  image: /images/jenna-guthmiller.jpeg
 Jay Hesselberth:
   suffix: PhD
   links:
     publications: https://scholar.google.com/citations?user=EnOmNEYAAAAJ
     website: https://hesselberthlab.org/
     email: mailto:jay.hesselberth@cuanschutz.edu
   project:
+  - project-3
   - core-c
-  - core-d
   bio: I am an RNA biochemist and computational biologist with extensive experience
     in developing new high- throughput methods and associated bioinformatic analysis
     software. My RNA biology program spans classical and modern approaches to address
@@ -102,7 +72,7 @@ Ryan Sheridan:
     publications: https://orcid.org/0000-0003-4012-3147
     website: https://github.com/sheridar
     email: mailto:ryan.sheridan@cuanschutz.edu
-  project: core-d
+  project: core-c
 Jennifer Matsuda:
   suffix: PhD
   links:

diff --git a/docs/2024-sheridan-38617225.pdf b/docs/2024-sheridan-38617225.pdf
diff --git a/images/2024-sheridan-38617225.jpg b/images/2024-sheridan-38617225.jpg
diff --git a/images/jenna-guthmiller.jpeg b/images/jenna-guthmiller.jpeg
diff --git a/projects.qmd b/projects.qmd
@@ -31,7 +31,7 @@ proj_yml <- proj_yml %>%
 # Create page text
 text <- proj_yml %>%
   imap(~ {
-    ttl <- str_c("# ", .y, "\n\n")
+    ttl <- str_c("\n\n# ", .y, "\n\n")
     
     .x %>%
       imap(~ {

diff --git a/projects.yml b/projects.yml
@@ -43,26 +43,11 @@ project-2:
     infection of LNSCs to vaccine immunity."
 
 project-3:
-  title: Investigate the role of immune complexes in antigen acquisition and
-    retention by LNSCs to modulate cellular and humoral immunity
-  short: "Project 3 will use stabilized DNA conjugates to track antibody:antigen
-    complexes to determine the spatial and cellular localization of immune
-    complexes"
-  hypothesis: We hypothesize that antibody isotype in an IC regulates protective
-    immunity by determining which LNSC populations acquire and retain antigen
-    via isotype-specific interactions with complement and Fc receptors (FcRs)
-  image: /images/project-3.png
-  abstract: "Project 3 will engineer monoclonal antibodies (mAbs) with fixed
-    antigen specificity on discrete antibody isotypes and subclasses. Using
-    stabilized DNA conjugates, Projects 2 and 3 will track antibody:antigen
-    complexes to determine the spatial and cellular localization of ICs in
-    comparison with free antigen. Project 3 also investigates how FcR expression
-    by LNSCs impacts IC acquisition and will work with Project 1 to determine
-    viral antigen retention and define consequences to protective humoral and
-    cellular immunity. This project will use mouse models engineered to
-    manipulate complement receptor and FcR expression by discrete LNSC
-    populations and will define how different LNSC populations use antibody to
-    determine antigen uptake and localization."
+  title: TBD
+  short: "Project 3 will..."
+  hypothesis: We hypothesize...
+  image:
+  abstract: "Project 3 will..."
 
 core-b:
   title: Mouse transgenics and tissue characterization
@@ -77,29 +62,16 @@ core-b:
     mouse LNSCs and lymphoid tissues"
 
 core-c:
-  title: Molecular technologies
-  short: "Core C will apply new molecular tools to
-    understand the contributions of lymph node stromal cells to immune responses"
-  abstract: "Core C will apply new molecular tools to
-    understand the contributions of lymph node stromal cells to immune
+  title: Molecular technologies and informatics
+  short: "Core C will develop and apply new molecular tools and bioinformatic
+    approaches to probe LNSC and immune cell biology"
+  abstract: "Core C will apply new molecular tools and bioinformatic approaches
+    to understand the contributions of lymph node stromal cells to immune
     responses, this includes the following tasks.\n\n
-    **Task 1.** Generate validated reagents for and execute single-cell and
-    spatial transcriptomic experiments to probe LNSC biology\n\n
-    **Task 2.** Production of customized lipid nanoparticles with mRNA and siRNA
-    cargo\n\n
-    **Task 3.** Expression and purification of antibodies, antigens, and immune
-    complexes"
-
-core-d:
-  title: Bioinformatics
-  short: "Core D will apply new informatics approaches to
-    understand the contributions of LNSCs to immune responses"
-  abstract: "Core D will apply new informatics approaches to
-    understand the contributions of LNSCs to immune responses, this includes the
-    following tasks.\n\n
-    **Task 1.** Provide a bioinformatics resource for rigorous and reproducible
+    **Task 1.** Generate and supply validated reagents for single-cell and
+    spatial transcriptomic experiments to evaluate LNSC contributions to
+    immunity and infection\n\n
+    **Task 2.** Provide a bioinformatics resource for rigorous and reproducible
     analysis of sequencing experiments\n\n
-    **Task 2.** Develop pipelines for large scale meta-analysis of single-cell
-    and spatial transcriptomic data\n\n
-    **Task 3.** Curate a public-facing LNSC atlas to allow for interactive
-    exploration of published datasets"
+    **Task 3.** Develop pipelines for large scale meta-analysis of single-cell
+    and spatial transcriptomic data"
diff --git a/pubs.yml b/pubs.yml
@@ -1,12 +1,51 @@
+- pubmed: https://pubmed.ncbi.nlm.nih.gov/38617225/
+  key: 2024-sheridan-38617225
+  title: A specific and portable gene expression program underlies antigen archiving
+    by lymphatic endothelial cells
+  pmid: PMID 38617225
+  date: April 02, 2024
+  year: '2024'
+  authors:
+  - Ryan Sheridan
+  - Thu Doan
+  - Cormac Lucas
+  - Tadg Forward
+  - Aspen Uecker-Martin
+  - Thomas Morrison
+  - Jay Hesselberth
+  - Beth Tamburini
+  abstract: Antigens from protein subunit vaccination traffic from the tissue to the
+    draining lymph node, either passively via the lymph or carried by dendritic cells
+    at the local injection site. Lymph node (LN) lymphatic endothelial cells (LEC)
+    actively acquire and archive foreign antigens, and archived antigen can be released
+    during subsequent inflammatory stimulus to improve immune responses. Here, we
+    answer questions about how LECs achieve durable antigen archiving and whether
+    there are transcriptional signatures associated with LECs containing high levels
+    of antigen. We used single cell sequencing in dissociated LN tissue to quantify
+    antigen levels in LEC and dendritic cell populations at multiple timepoints after
+    immunization, and used machine learning to define a unique transcriptional program
+    within archiving LECs that can predict LEC archiving capacity in independent data
+    sets. Finally, we validated this modeling, showing we could predict antigen archiving
+    from a transcriptional dataset of CHIKV infected mice and demonstrated in vivo
+    the accuracy of our prediction. Collectively, our findings establish a unique
+    transcriptional program in LECs that promotes antigen archiving that can be translated
+    to other systems.
+  pdf: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11014631/pdf/nihpp-2024.04.01.587647v1.pdf
+  image: /images/2024-sheridan-38617225.jpg
+  project:
+  - project-1
+  - project-2
+  - project-3
+  - core-c
 - pubmed: https://pubmed.ncbi.nlm.nih.gov/33843587/
   links:
     github: https://github.com/rnabioco/antigen-tracking
     atlas: https://d3898ys7yh3545.cloudfront.net/
     geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150719
   project:
   - project-2
+  - project-3
   - core-c
-  - core-d
   fig_number: 7
   key: 2021-walsh-33843587
   title: Molecular tracking devices quantify antigen distribution and archiving in
@@ -75,13 +114,13 @@
   links:
     github: https://github.com/rnabioco/morrison-chikv
     geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174667
-    atlas: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+    atlas: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
   fig_number: 11
   project:
   - project-1
   - project-2
+  - project-3
   - core-c
-  - core-d
   key: 2021-carpentier-34618370
   title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to
     limit viremia and viral dissemination
@@ -153,12 +192,12 @@
   links:
     github: https://github.com/rnabioco/morrison-lnsc
     geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243638
-    atlas: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+    atlas: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
   project:
   - project-1
   - project-2
+  - project-3
   - core-c
-  - core-d
   key: 2024-lucas-38194268
   title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell
     composition and function via MARCO
@@ -269,8 +308,8 @@
 - pubmed: https://pubmed.ncbi.nlm.nih.gov/31156626/
   project:
   - project-2
+  - project-3
   - core-c
-  - core-d
   links:
     geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129933
   key: 2019-tamburini-31156626
@@ -347,8 +386,8 @@
   project:
   - project-1
   - project-2
+  - project-3
   - core-c
-  - core-d
   key: 2023-tamburini-37841845
   title: Vaccine-induced antigen archiving enhances local memory CD8+ T cell responses
     following an unrelated viral infection

diff --git a/pubs/2019-tamburini-31156626/index.qmd b/pubs/2019-tamburini-31156626/index.qmd
@@ -4,7 +4,7 @@ title: Chronic Liver Disease in Humans Causes Expansion and Differentiation of L
 image: /images/2019-tamburini-31156626.jpg
 subtitle: 'PMID 31156626'
 date: 'May 15, 2019'
-categories: [Project-2, Core-C, Core-D, 2019]
+categories: [Project-2, Project-3, Core-C, 2019]
 about:
   id: about
   template: jolla

diff --git a/pubs/2021-carpentier-34618370/index.qmd b/pubs/2021-carpentier-34618370/index.qmd
@@ -4,7 +4,7 @@ title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses t
 image: /images/2021-carpentier-34618370.jpg
 subtitle: 'PMID 34618370'
 date: 'November 15, 2021'
-categories: [Project-1, Project-2, Core-C, Core-D, 2021]
+categories: [Project-1, Project-2, Project-3, Core-C, 2021]
 about:
   id: about
   template: jolla
@@ -22,7 +22,7 @@ about:
     href: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174667
   - text: Atlas
     icon: compass
-    href: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+    href: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
 ---
 
 Kathryn Carpentier, [Ryan Sheridan](https://orcid.org/0000-0003-4012-3147), Cormac Lucas, Bennett Davenport, [Frances Li](https://orcid.org/0000-0001-8798-8290), [Erin Lucas](http://orcid.org/0000-0001-7705-2069), Mary McCarthy, Glennys Reynoso, Nicholas May, [Beth Tamburini](https://orcid.org/0000-0003-1991-231X), [Jay Hesselberth](https://scholar.google.com/citations?user=EnOmNEYAAAAJ), Heather Hickman, [Thomas Morrison](https://scholar.google.com/citations?user=ljkm0eMAAAAJ&hl=en&oi=ao)

diff --git a/pubs/2021-walsh-33843587/index.qmd b/pubs/2021-walsh-33843587/index.qmd
@@ -4,7 +4,7 @@ title: Molecular tracking devices quantify antigen distribution and archiving in
 image: /images/2021-walsh-33843587.jpg
 subtitle: 'PMID 33843587'
 date: 'April 12, 2021'
-categories: [Project-2, Core-C, Core-D, 2021]
+categories: [Project-2, Project-3, Core-C, 2021]
 about:
   id: about
   template: jolla

diff --git a/pubs/2023-tamburini-37841845/index.qmd b/pubs/2023-tamburini-37841845/index.qmd
@@ -4,7 +4,7 @@ title: Vaccine-induced antigen archiving enhances local memory CD8+ T cell respo
 image: /images/2023-tamburini-37841845.jpg
 subtitle: 'PMID 37841845'
 date: 'September 25, 2023'
-categories: [Project-1, Project-2, Core-C, Core-D, 2023]
+categories: [Project-1, Project-2, Project-3, Core-C, 2023]
 about:
   id: about
   template: jolla

diff --git a/pubs/2024-lucas-38194268/index.qmd b/pubs/2024-lucas-38194268/index.qmd
@@ -4,7 +4,7 @@ title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cel
 image: /images/2024-lucas-38194268.jpg
 subtitle: 'PMID 38194268'
 date: 'January 09, 2024'
-categories: [Project-1, Project-2, Core-C, Core-D, 2024]
+categories: [Project-1, Project-2, Project-3, Core-C, 2024]
 about:
   id: about
   template: jolla
@@ -22,7 +22,7 @@ about:
     href: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243638
   - text: Atlas
     icon: compass
-    href: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+    href: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
 ---
 
 Cormac Lucas, [Ryan Sheridan](https://orcid.org/0000-0003-4012-3147), Glennys Reynoso, Bennett Davenport, Mary McCarthy, Aspen Martin, [Jay Hesselberth](https://scholar.google.com/citations?user=EnOmNEYAAAAJ), Heather Hickman, [Beth Tamburini](https://orcid.org/0000-0003-1991-231X), [Thomas Morrison](https://scholar.google.com/citations?user=ljkm0eMAAAAJ&hl=en&oi=ao)

diff --git a/pubs/2024-sheridan-38617225/index.qmd b/pubs/2024-sheridan-38617225/index.qmd
@@ -0,0 +1,22 @@
+---
+title: A specific and portable gene expression program underlies antigen archiving by lymphatic endothelial cells
+
+image: /images/2024-sheridan-38617225.jpg
+subtitle: 'PMID 38617225'
+date: 'April 02, 2024'
+categories: [Project-1, Project-2, Project-3, Core-C, 2024]
+about:
+  id: about
+  template: jolla
+  links:
+  - text: Pubmed
+    icon: file-earmark
+    href: https://pubmed.ncbi.nlm.nih.gov/38617225/
+  - text: PDF
+    icon: filetype-pdf
+    href: /docs/2024-sheridan-38617225.pdf
+---
+
+[Ryan Sheridan](https://orcid.org/0000-0003-4012-3147), Thu Doan, Cormac Lucas, Tadg Forward, Aspen Uecker-Martin, [Thomas Morrison](https://scholar.google.com/citations?user=ljkm0eMAAAAJ&hl=en&oi=ao), [Jay Hesselberth](https://scholar.google.com/citations?user=EnOmNEYAAAAJ), [Beth Tamburini](https://orcid.org/0000-0003-1991-231X)
+
+Antigens from protein subunit vaccination traffic from the tissue to the draining lymph node, either passively via the lymph or carried by dendritic cells at the local injection site. Lymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens, and archived antigen can be released during subsequent inflammatory stimulus to improve immune responses. Here, we answer questions about how LECs achieve durable antigen archiving and whether there are transcriptional signatures associated with LECs containing high levels of antigen. We used single cell sequencing in dissociated LN tissue to quantify antigen levels in LEC and dendritic cell populations at multiple timepoints after immunization, and used machine learning to define a unique transcriptional program within archiving LECs that can predict LEC archiving capacity in independent data sets. Finally, we validated this modeling, showing we could predict antigen archiving from a transcriptional dataset of CHIKV infected mice and demonstrated in vivo the accuracy of our prediction. Collectively, our findings establish a unique transcriptional program in LECs that promotes antigen archiving that can be translated to other systems.