Merge pull request #32 from arenasg/main

add kader-lin-hug-2024 publication
gf-dcc · Dec 28, 2024 · d58f58b · d58f58b
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diff --git a/_atlas-datasets/investigating-the-origins-and-early-diagnosis-of-ovarian-cancer.md b/_atlas-datasets/investigating-the-origins-and-early-diagnosis-of-ovarian-cancer.md
@@ -8,7 +8,7 @@ data:
     title: Investigating the origins and early diagnosis of ovarian cancer  
     description: "Ovarian cancer presents a more formidable challenge per case than breast cancer, yet it has seen fewer advancements in treatment and diagnosis. In the United States, we observe approximately 20,000 new ovarian cancer diagnoses annually, which lead to 14,000 tragic deaths. This rate contrasts with breast cancer, which records around 240,000 new cases and 42,000 fatalities. Like breast cancer, ovarian cancer is more prevalent in individuals carrying mutations in the BRCA1 or BRCA2 genes (approximately 1.2% without vs. 40% with mutation). Consequently, people with a BRCA1/2 mutation face the agonizing decision of either living with an elevated ovarian cancer risk or undergoing surgery to remove their healthy ovaries and fallopian tubes, a procedure known as risk-reducing salpingo-oophorectomy.
 
-    
+
     The decision to undergo risk reduction surgery is complicated by the fact that ovarian cancer is often diagnosed at late stages, and we have a limited understanding of its origins. However, recent insights have revealed that certain epithelial ovarian cancers may start in the fallopian tube from a pre-cancerous condition known as serous tubal intraepithelial carcinoma (STIC). Our project aims to characterize the biology of STICs, elucidate their clinical significance, and establish precise diagnostic criteria for identifying STICs in surgical samples."
 
 ---
@@ -23,12 +23,15 @@ data:
 
 ### Contents
 * [Project Overview](#project-overview)
+* [Publications](#publications)
 * [Data Stories](#data-stories)
 * [Explore Tissue Images](#explore-tissue-images)
 
 ## Project Overview
-<div class="col-md-6 mb-4">
-  {% include vimeo-card.html id="866120650" title="Ovarian Cancer Atlas with Dr. Ronny Drapkin and Dr. Tanjina Kader" %}
+<div class="row mb-4">
+  <div class="col-md-6 mb-4">
+    {% include vimeo-card.html id="866120650" title="Ovarian Cancer Atlas with Dr. Ronny Drapkin and Dr. Tanjina Kader" %}
+    </div>
 </div>
 
 ### Uncovering the origins of ovarian cancer
@@ -56,6 +59,15 @@ Preliminary data from our cohort suggest that immune surveillance may break down
 <br>
 Our long-term goal for this project is to extend the characterization of incidental precancers on a larger scale, offering a deeper understanding of the biology of STICs in surgical samples. Given that STICs are a well-known precursor to eventual peritoneal cancer, we intend to stratify the risk associated with STIC lesions for clinical decision-making. Additionally, our analysis of a substantial patient cohort has the potential to open avenues for preventive measures for high-risk patients in the future.
 </details>
+---
+## Publications
+{% comment %}
+  'publicationList' should be a comma-delineated string of publication file names
+{% endcomment %}
+{% assign publicationList = 'multimodal-spatial-profiling-reveals-immune-suppression-and-microenvironment-remodeling-fallopian-tube-precursors-high-grade-serous-ovarian-carcinoma.md' %}
+
+{% include pub-list.html list=publicationList %}
+---
 
 ## Data Stories
 Data Stories are narrated Minerva stories that guide readers through the complexities of a large image dataset via a series of progressive narrated waypoints.
@@ -64,7 +76,7 @@ Data Stories are narrated Minerva stories that guide readers through the complex
     assign overviews = site.data-cards
     | where_exp: "item", "item.url contains 'kader-drapkin-ovarian-pilot/'"
     | where_exp: "item", "item.hide != true"
-    | where_exp: "item", "item.tags contains 'exploration'"
+    | where_exp: "item", "item.tags contains 'narrated'"
 %}
 
 {% if overviews.size > 0 %}
@@ -76,9 +88,9 @@ Access the minimally processed, unannotated Minerva stores of additional tissue
 
 {%
     assign overviews = site.data-cards
-    | where_exp: "item", "item.url contains 'kader-drapkin-ovarian-pilot/'"
+    | where_exp: "item", "item.url contains 'kader-lin-hug-2024/'"
     | where_exp: "item", "item.hide != true"
-    | where_exp: "item", "item.tags contains 'overview'"
+    | where_exp: "item", "item.tags contains 'curated'"
 %}
 
 {% if overviews.size > 0 %}

diff --git a/_atlas-datasets/kader-lin-hug-2024.md b/_atlas-datasets/kader-lin-hug-2024.md
@@ -7,10 +7,7 @@ data:
   publication:
     title: 'Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma'
     authors: 'Tanjina Kader, Jia-Ren Lin, Clemens Hug, Shannon Coy, Yu-An Chen, Ino de Bruijn, Natalie Shih, Euihye Jung, Roxanne J. Pelletier, Mariana Lopez Leon, Gabriel Mingo, Dalia Khaled Omran, Jong Suk Lee, Clarence Yapp, Baby Anusha Satravada, Ritika Kundra, Yilin Xu, Sabrina Chan, Juliann B. Tefft, Jeremy Muhlich, Sarah Kim, Stefan M. Gysler, Judith Agudo, James R. Heath, Nikolaus Schultz, Charles Drescher, Peter K Sorger, Ronny Drapkin, Sandro Santagata'
-    journal: 'TBD'
-    description: 'High-Grade Serous Ovarian Cancer (HGSOC) originates from fallopian tube (FT) precursors. However, the molecular changes that occur as precancerous lesions progress to HGSOC are not well understood. To address this, we integrated high-plex imaging and spatial transcriptomics to analyze human tissue samples at different stages of HGSOC development, including p53 signatures, serous tubal intraepithelial carcinomas (STIC), and invasive HGSOC. Our findings reveal immune modulating mechanisms within precursor epithelium, characterized by chromosomal instability, persistent interferon (IFN) signaling, and dysregulated innate and adaptive immunity. FT precursors display elevated expression of MHC-class I, including HLA-E, and IFN-stimulated genes, typically linked to later-stage tumorigenesis. These molecular alterations coincide with progressive shifts in the tumor microenvironment, transitioning from immune surveillance in early STICs to immune suppression in advanced STICs and cancer. These insights identify potential biomarkers and therapeutic targets for HGSOC interception and clarify the molecular transitions from precancer to cancer.'
-    links:
-        Preprint: https://doi.org/10.1101/2024.09.25.615007
+    journal: 'Cancer Discovery (2024)'
 ---
 
 {% assign urlParts = page.url | split: '/' %}
@@ -21,3 +18,48 @@ data:
     pubData=page.data
     thumbnailDir=sectionId %}
 
+<a href="https://www.cbioportal.org/study/summary?id=ovary_geomx_gray_foundation_2024" class="button">Data</a>
+<a href="https://doi.org/10.1158/2159-8290.CD-24-1366" class="button">Publication</a>
+<a href="https://doi.org/10.1101/2024.09.25.615007" class="button">Preprint</a>
+
+## Contents
+  * [Abstract](#abstract)
+  * [Narrated Minerva Stories](#narrated-minerva-stories)
+  * [Data Overviews](#data-overviews)
+  * [Data Access](#data-access)
+
+### Abstract
+  High-Grade Serous Ovarian Cancer (HGSOC) originates from fallopian tube (FT) precursors. However, the molecular changes that occur as precancerous lesions progress to HGSOC are not well understood. To address this, we integrated high-plex imaging and spatial transcriptomics to analyze human tissue samples at different stages of HGSOC development, including p53 signatures, serous tubal intraepithelial carcinomas (STIC), and invasive HGSOC. Our findings reveal immune modulating mechanisms within precursor epithelium, characterized by chromosomal instability, persistent interferon (IFN) signaling, and dysregulated innate and adaptive immunity. FT precursors display elevated expression of MHC-class I, including HLA-E, and IFN-stimulated genes, typically linked to later-stage tumorigenesis. These molecular alterations coincide with progressive shifts in the tumor microenvironment, transitioning from immune surveillance in early STICs to immune suppression in advanced STICs and cancer. These insights identify potential biomarkers and therapeutic targets for HGSOC interception and clarify the molecular transitions from precancer to cancer.
+
+### Narrated Minerva Stories
+Narrated stories use multi-step narrations and annotations to walk a viewer through key features of the data. Narrated stories distill the multidisciplinary knowledge encompassed by each dataset into a single product that grounds the scientific analyses in the underlying data and metadata. Click the Minerva story icon for an interactive view of the full-resolution images.
+
+{%
+    assign overviews = site.data-cards
+    | where_exp: "item", "item.url contains 'kader-drapkin-ovarian-pilot/'"
+    | where_exp: "item", "item.hide != true"
+    | where_exp: "item", "item.tags contains 'narrated'"
+%}
+
+{% if overviews.size > 0 %}
+  {% include cards.html cards=overviews %}
+{% endif %}
+
+### Curated Minerva Stories
+Curated stories provide access to images that have undergone a quality control step to remove failed markers, ensure appropriate channel intensity settings, and provide metadata about the underlying sample and image. Click the Minerva story icon for an interactive view of the full-resolution images.
+
+{%
+    assign overviews = site.data-cards
+    | where_exp: "item", "item.url contains 'kader-lin-hug-2024/'"
+    | where_exp: "item", "item.hide != true"
+    | where_exp: "item", "item.tags contains 'curated'"
+%}
+
+{% if overviews.size > 0 %}
+  {% include cards.html cards=overviews %}
+{% endif %}
+
+
+## Data Access
+
+Data for this paper is available to explore in [cbioportal](https://www.cbioportal.org/study/summary?id=ovary_geomx_gray_foundation_2024), including access to associated GeoMx microregional transcriptomic data, ROI annotations, clinical data, and  Minerva stories.
diff --git a/_data-cards/kader-drapkin-ovarian-pilot/lsp16696.md b/_data-cards/kader-drapkin-ovarian-pilot/lsp16696.md
@@ -9,7 +9,7 @@ tags:
     - Gray
     - BRCA
     - STIC
-    - Overview
+    - curated
     - CyCIF
 
 ---
diff --git a/_data-cards/kader-drapkin-ovarian-pilot/lsp16697.md b/_data-cards/kader-drapkin-ovarian-pilot/lsp16697.md
@@ -9,6 +9,6 @@ tags:
     - Gray
     - BRCA
     - STIC
-    - Overview
     - CyCIF
+    - curated
 ---
diff --git a/_data-cards/kader-drapkin-ovarian-pilot/lsp16698.md b/_data-cards/kader-drapkin-ovarian-pilot/lsp16698.md
@@ -9,6 +9,6 @@ tags:
     - Gray
     - BRCA
     - STIC
-    - Overview
     - CyCIF
+    - curated
 ---
diff --git a/_data-cards/kader-drapkin-ovarian-pilot/lsp16699.md b/_data-cards/kader-drapkin-ovarian-pilot/lsp16699.md
@@ -11,4 +11,5 @@ tags:
     - STIC
     - Overview
     - CyCIF
+    - curated
 ---
diff --git a/_data-cards/kader-drapkin-ovarian-pilot/lsp16814.md b/_data-cards/kader-drapkin-ovarian-pilot/lsp16814.md
@@ -9,6 +9,6 @@ tags:
     - Gray
     - BRCA
     - STIC
-    - Overview
+    - curated
     - CyCIF
 ---
diff --git a/_data-cards/kader-drapkin-ovarian-pilot/ovarian-cancer-with-annotation-lsp15327.md b/_data-cards/kader-drapkin-ovarian-pilot/ovarian-cancer-with-annotation-lsp15327.md
@@ -10,6 +10,6 @@ tags:
     - Gray
     - BRCA
     - STIC
-    - exploration
+    - narrated
     - CyCIF
 ---
diff --git a/_data-cards/kader-drapkin-ovarian-pilot/ovarian-cancer-with-annotation-lsp15343.md b/_data-cards/kader-drapkin-ovarian-pilot/ovarian-cancer-with-annotation-lsp15343.md
@@ -10,6 +10,6 @@ tags:
     - Gray
     - BRCA
     - STIC
-    - exploration
+    - narrated
     - CyCIF
 ---
diff --git a/_data-cards/kader-lin-hug-2024/LSP11060.md b/_data-cards/kader-lin-hug-2024/LSP11060.md
@@ -0,0 +1,15 @@
+---
+title: LSP16696
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11060/LSP11060.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11060/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP11064.md b/_data-cards/kader-lin-hug-2024/LSP11064.md
@@ -0,0 +1,15 @@
+---
+title: LSP11064
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11064/LSP11064.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11064/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP11068.md b/_data-cards/kader-lin-hug-2024/LSP11068.md
@@ -0,0 +1,15 @@
+---
+title: LSP11068
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11068/LSP11068.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11068/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP11072.md b/_data-cards/kader-lin-hug-2024/LSP11072.md
@@ -0,0 +1,15 @@
+---
+title: LSP11072
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11072/LSP11072.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11072/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP11076.md b/_data-cards/kader-lin-hug-2024/LSP11076.md
@@ -0,0 +1,15 @@
+---
+title: LSP11076
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11076/LSP11076.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11076/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP11088.md b/_data-cards/kader-lin-hug-2024/LSP11088.md
@@ -0,0 +1,15 @@
+---
+title: LSP11088
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11088/LSP11088.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP11088/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP15327.md b/_data-cards/kader-lin-hug-2024/LSP15327.md
@@ -0,0 +1,15 @@
+---
+title: LSP15327
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15327/LSP15327.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15327/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP15331.md b/_data-cards/kader-lin-hug-2024/LSP15331.md
@@ -0,0 +1,16 @@
+---
+title: LSP15331
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15331/LSP15331.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15331/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - GeoMx
+    - cbioportal
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP15335.md b/_data-cards/kader-lin-hug-2024/LSP15335.md
@@ -0,0 +1,15 @@
+---
+title: LSP15335
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15335/LSP15335.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15335/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP15339.md b/_data-cards/kader-lin-hug-2024/LSP15339.md
@@ -0,0 +1,15 @@
+---
+title: LSP15339
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15339/LSP15339.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15339/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP15343.md b/_data-cards/kader-lin-hug-2024/LSP15343.md
@@ -0,0 +1,15 @@
+---
+title: LSP15343
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15343/LSP15343.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15343/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP15347.md b/_data-cards/kader-lin-hug-2024/LSP15347.md
@@ -0,0 +1,15 @@
+---
+title: LSP15347
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15347/LSP15347.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15347/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
diff --git a/_data-cards/kader-lin-hug-2024/LSP15355.md b/_data-cards/kader-lin-hug-2024/LSP15355.md
@@ -0,0 +1,15 @@
+---
+title: LSP15355
+image: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15355/LSP15355.png
+date: 2024-12-10
+minerva_link: https://s3.amazonaws.com/www.cycif.org/110-BRCA-Mutant-Ovarian-Precursors/LSP15355/index.html
+info_link: null
+show_page_link: false
+tags:
+    - Gray
+    - BRCA
+    - STIC
+    - CyCIF
+    - curated
+
+---
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,7 @@ tags: @@
         - Gray
         - BRCA
         - STIC
-        - Overview
+        - curated
         - CyCIF
     ---