AML Multidrug resistance studies

This repository contains the analysis and processing for multiple projects focusing on multidrug resistance for the CPTAC funded OHSU/PNNL PTRC.

All data for this project resides on the Synapse at [http://synapse.org/ptrc2]. To run the code for each project, you will need to navigate to the site nad request access.

Directory structure

The repository is currently laid out as follows, with folders divided roughly according to dataset or experiment that was analyzed

Cell line work

In this project we developed a number of drug resistant cell lines (MOLM14) that were cultured in combination with Gilteritinib, Venetoclax, Decitabine, or some combination there of. These data can be found here.

• ./prelim_analysis: Here we have exploratory work from early projects and data, mainly for historic purposes.
• ./combination_cell_line_proteomics: Here we have data analysis from MOLM14 cells treated with combiantions of venetoclax, gilteritinib and HMA
• ./venetoclax_gilteritinib_resistance: This is analysis of MOLM14 cell lines that are resistant to ven + gilt in combination. Currently going into a manuscript.
• ./NRAS_ASO: This is analysis for a study focusing on the impacs of NRAS ASO on gilteritinib resistance.

Ex vivo cultures

We have also measured proteins expressed in ex vivo culture from patient samples. This analysis can be found below.

• ./drug_treated_samples: analysis of patient samples cultured for months of treatment with single agents or combinations of drugs.

Patient samples

We also measured proteomics measurements of patient samples, all analysis for these is in the following directories.

• ./cd14_cd34_proteomics: This is analysis comparing expression of AML patient samples sorted by CD14+ and CD34+ markers.
• ./aml_outcome_disparities: This analysis focuses on the identification of multiomic mechanisms of outcome disparities in Black AML patients.
• ./ven_hma_samples: Here we have new analysis of data from patient samples before treatemnt with ven+HMA.