Hello!

Created by giuliano scarcelli scarc
Sorry for the delay, everyone. Notes from the meeting at 12PM EDT on 5/26 are posted. Best of luck!!${buttonlink?text=Friday 12PM notes&url=https%3A%2F%2Fdocs%2Egoogle%2Ecom%2Fdocument%2Fd%2F1GOkACS73sZla1p2pIKCcig5CmoWfED0zjcNzsO1NsNk%2Fedit}
Looking forward to the noon discussion. @alexandra.naba: what does spatial mapping constitute? perhaps we could talk more on this at the noon meeting. there are few interesting computational tools i would like to bring to the table in understanding the spatial interactions of a TME. here is a summary: https://www.dropbox.com/s/w7bcu6fmqhyk7sp/TME.pdf?dl=0
For the integration of the imaging / proteomics that we were discussing it would be really interesting to time the proteomics profiling based on relevant timing determined from imaging. Then we could perform analysis of the proteomics data at key time points and associate with the phenotype from imaging. The imaging-based phenotype could be included in the bioinformatics analysis or associated with protein changes post-hoc as we have done previously (http://biorxiv.org/content/early/2017/05/10/136564). This sort of time course data for the progression of metastatic niches would be really exciting!
Hi guys, in preparation of tomorrow's VC with Tony and Julio, it would be great if you could describe what you could contribute to the project (ideas, technologies or datasets). As you know, we propose to conduct a multi-scale analysis of ECM-driven tumor cell phenotypes at metastatic sites. In brief, we will use intravital imaging to monitor DTC phenotype using GTPase sensors and acquire in parallel SHG images to evaluate ECM architecture [Javier], in parallel we will collect data on oxygenation level [Daniele] and mechanical properties [Giuliano] of the niches. We will then use proteomics to profile the ECM composition of the different niches imaged [Alexandra]. And last we propose to integrate the different data collected and devise a model [Aedin, Elana] predicting how the ECM controls DTC phenotype(s) in distinct niches. We have created a wikipage to start gathering datasets and ideas (https://www.synapse.org/#!Synapse:syn9855574), feel free to add to that page or to reply to the thread. Looking forward to chatting with those of you who can make it tomorrow at 12pm Eastern time!
@aedinc @lanilonzo @ejfertig1 @scarc @dgilkes @jjbravo, I have started a wikipage (https://www.synapse.org/#!Synapse:syn9855574) where we can each indicate which preliminary data we have available so that the bioinformaticians/computational biologists/modellers of the team can start thinking about way to integrate the different data sets (cell phenotypes, mechanical properties, oxygenation, ECM composition, etc.). Looking forward to chatting with you all on Friday! Alexandra
Elana.. agree
Very interesting topic! I am in. Keep me posted for the next calls
@aedinc we should coordinate so that our efforts on this project wouldn't overlap.
Hi everyone Sorry I was missing the past week. Wifi went down where I was staying in and it was difficult to stay in contact. I am happy to take on the computational role. Where is the most upto date info Aedin
I had some follow-up questions on experimental design per the conversation yesterday -- needed a night to let it sink in. @alexandra.naba you said the proteomic landscape of the ECM is relatively homogeneous when tumors invade. Do you have a sense of what the scope of the effect size is before / after invasion? Do you know how similar the changes are or have reason to hypothesize they would be different in different organ sites? Both would be critical to the proper design to find remodeling specific signatures vs tissue-specific signatures.
Another good discussion can be found at [this link](https://docs.google.com/document/d/1LYq9eKidrZIGS3F6Odq0H0FTuid1ja5km44dLnfmhgc/edit?usp=sharing). If someone @jjbravo @dgilkes @alexandra.naba wants to send me a slide deck, I will make a folder under the 'Files' tab for you.
Very interested in participating in this discussion, but unfortunately can't join in today. Here is a link to the [Notes](https://docs.google.com/document/d/1lCPABY-E9sPTTJPeELS4HOEpVI4y9iREryEmjB_409I/edit#) (thanks to Shannon) from a call last week that I participated in. Here is some recent work from us: [PMID 27994939](https://www.ncbi.nlm.nih.gov/pubmed/27994939), [PMID 28231035](https://www.ncbi.nlm.nih.gov/pubmed/28231035), [PMID 28328502](https://www.ncbi.nlm.nih.gov/pubmed/28328502).
Here is a [link to the notes](https://docs.google.com/document/d/1LYq9eKidrZIGS3F6Odq0H0FTuid1ja5km44dLnfmhgc/edit?usp=sharing) from the call on this subject today. Spoiler -- recruiting an investigator with computational know-how to aid in data integration and predictive model building. Next call: Tomorrow (3/18) at 4pm.
Happy to bring in my ECM expertise! @jjbravo @scarc @ejfertig1 @dgilkes
Interaction of tumor cells with the extracellular matrix (ECM) regulates the hallmarks of cancer, from primary tumor growth to metastasis. While the mechanisms mediating ECM/tumor-cell interaction in primary tumors have been well studied, our understanding on how the physical and biochemical properties of the ECM dictate in vivo the fate and the motile behavior of tumor cells within disseminated organs remains unknown. We are thinking of addressing questions in this space by looking at (1) Spatiotemporal regulation of tumor cell signaling in metastatic niches; (2) Evolution of ECM composition and architecture within different metastatic niches; and maybe (3) Modeling/in vitro validation of ECM/Tumor cell phenotypes. We welcome anyone interested in joining us and provide complementary expertise to answer these questions!
I am in!

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