Task Progress:
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Overall progress and work to date:
In the past year, we have focused efforts on curating and testing banked tissues for processing with spatial and single-cell methods. Specifically, we have focused on the retinal tissues (acquired and tested), liver, brain, femur, heart, and duodenum. We have dissected test samples from donor mice in our laboratory, and processed on Visium, and also we have run one sample through single-nucleus RNA-seq (snRNA-seq) using the 10xGenomics Chromium controller and assay.
So far, we have: 1) Completed sample selection and quality control (QC), including the RNA Integrity Number (RIN) and cell count matrices; 2) Ran two Visium tests and continued data processing optimization; 3) Tested single nucleus RNA sequencing (snRNA-seq) on retina tissues, and finished the sequencing; 4) Tested the new SpaTial Enhanced REsolution Omics sequencing (STEREO-seq) spatial biology tool, to use as an orthogonal method if needed.
Of note, we have also established a collaboration with NanoString Technologies (NanoString) to optimize the processing of samples for the GeoMx Digital Spatial Profiler system, and we have also placed an order to acquire the latest instrument that has the highest resolution for profiling tissues, call the CosMx, which is slated for delivery in Q4 2022 at Weill Cornell Medicine.
We have one paper that used the methods described in our grant for spatial biology profiling in COVID-19 patients:
Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Reports Med. 2022 Feb 15;3(2):100522. https://doi.org/10.1016/j.xcrm.2022.100522
We have two other papers in review about the Spatial Tissue analysis algorithms, which we expect to be published in 2023.
Also, I have been serving on the National Academies of Science (NAS) Decadal Survery Panel on Research in Space for NASA, where many of the tools and methods described in our grant are being added to the NAS report that will be sent to Congress: https://www.nationalacademies.org/our-work/decadal-survey-on-life-and-physical-sciences-research-in-space-2023-2032
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Articles in Peer-reviewed Journals
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Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE. "System-wide transcriptome damage and tissue identity loss in COVID-19 patients." Cell Reports Med. 2022 Feb 15;3(2):100522. https://doi.org/10.1016/j.xcrm.2022.100522 , Feb-2022
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Articles in Peer-reviewed Journals
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Saravia-Butler AM, Schisler JC, Taylor D, Beheshti A, Butler D, Meydan C, Foox J, Hernandez K, Mozsary C, Mason CE, Meller R. "Host transcriptional responses in nasal swabs identifies potential SARS-CoV-2 infection in PCR negative patients.
" iScience. 2022 Oct 7;105310. https://doi.org/10.1016/j.isci.2022.105310 ; PMID: 36246576; PMCID: PMC9540688
, Oct-2022
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Articles in Peer-reviewed Journals
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Cope H, Willis CRG, MacKay MJ, Rutter LA, Toh LS, Williams PM, Herranz R, Borg J, Bezdan D, Giacomello S, Muratani M, Mason CE, Etheridge T, Szewczyk NJ. "Routine omics collection is a golden opportunity for European human research in space and analog environments." Patterns. 2022 Oct 14;3(10):100550. Review. https://doi.org/10.1016/j.patter.2022.100550 ; PMID: 36277820; PMCID: PMC9583032 , Oct-2022
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