EPIC package

Description

Package implementing EPIC method to estimate the proportion of immune,
stromal, endothelial and cancer or other cells from bulk gene expression
data. It is based on reference gene expression profiles for the main
non-malignant cell types and it predicts the proportion of these cells
and of the remaining “other cells” (that are mostly cancer cells) for
which no reference profile is given.

This method is described in the publication from Racle et al., 2017
available at https://elifesciences.org/articles/26476.

EPIC is also available as a web application:
http://epic.gfellerlab.org.

Usage

The main function in this package is EPIC. It needs as input a matrix
of the TPM (or RPKM) gene expression from the samples for which to
estimate cell proportions. One can also define the reference cells to
use

# library(EPIC) ## If the package isn't loaded (or use EPIC::EPIC and so on).
out <- EPIC(bulk = bulkSamplesMatrix)
out <- EPIC(bulk = bulkSamplesMatrix, reference = referenceCellsList)

out is a list containing the various mRNA and cell fractions in each
sample as well as some data.frame of the goodness of fit.

Values of mRNA per cell and signature genes to use can also be changed:

out <- EPIC(bulk = bulkSamplesMatrix, reference = referenceCellsList, mRNA_cell = mRNA_cell_vector, sigGenes = sigGenes_vector)
out <- EPIC(bulk = bulkSamplesMatrix, reference = referenceCellsList, mRNA_cell_sub = mRNA_cell_sub_vector)

Various other options are available and are well documented in the help
pages from EPIC:

?EPIC::EPIC
?EPIC::EPIC.package

Installation

install.packages("devtools")
devtools::install_github("GfellerLab/EPIC", build_vignettes=TRUE)

Web application

EPIC is also available as a web application:
http://epic.gfellerlab.org.

Python wrapper

A pyhton wrapper has been written by Stephen C. Van Nostrand from MIT
and is available at https://github.com/scvannost/epicpy.

License

EPIC can be used freely by academic groups for non-commercial purposes.
The product is provided free of charge, and, therefore, on an “as is”
basis, without warranty of any kind. Please read the file “LICENSE”
for details.

If you plan to use EPIC (version 1.1) in any for-profit application, you
are required to obtain a separate license. To do so, please contact
Nadette Bulgin (nbulgin@lcr.org) at the Ludwig Institute for Cancer
Research Ltd.

Contact information

Julien Racle (julien.racle@unil.ch), and David Gfeller
(david.gfeller@unil.ch).

FAQ

Which proportions returned by EPIC should I use?

EPIC is returning two proportion values: mRNAProportions and
cellFractions, where the 2nd represents the true proportion of cells
coming from the different cell types when considering differences in
mRNA expression between cell types. So in principle, it is best to
consider these cellFractions.

However, please note, that when the goal is to benchmark EPIC
predictions, if the ‘bulk samples’ correspond in fact to in silico
samples reconstructed for example from single-cell RNA-seq data, then
it is usually better to compare the ‘true’ proportions against the
mRNAProportions from EPIC. Indeed, when building such in silico
samples, the fact that different cell types express different amount
of mRNA is usually not taken into account. On the other side, if
working with true bulk samples, then you should compare the true cell
proportions (measured e.g., by FACS) against the cellFractions.

What do the “other cells” represent?

EPIC predicts the proportions of the various cell types for which we
have gene expression reference profiles (and corresponding gene
signatures). But, depending on the bulk sample, it is possible that
some other cell types are present for which we don’t have any
reference profile. EPIC returns the proportion of these remaining
cells under the name “other cells”. In the case of tumor samples,
most of these other cells would certainly correspond to the cancer
cells, but it could be that there are also some stromal cells or
epithelial cells for example.

I receive an error message “attempt to set ‘colnames’ on an object with less than two dimensions”. What can I do?

This is certainly that some of your data is a vector instead of a
matrix. Please make sure that your bulk data is in the form of a
matrix (and also your reference gene expression profiles if using
custom ones).

Is there some caution to consider about the cellFractions and mRNA_cell values?

As described in our manuscript, EPIC first estimates the proportion of
mRNA per cell type in the bulk and then it uses the fact that some
cell types have more mRNA copies per cell than other to normalize this
and obtain an estimate of the proportion of cells instead of mRNA
(EPIC function returns both information if you need the one or the
other). For this normalization we had either measured the amount of
mRNA per cell or found it in the literature (fig. 1 – fig. supplement
2 of our paper). However we don’t currently have such values for the
endothelial cells and CAFs. Therefore for these two cell types, we use
an average value, which might not reflect their true value and this
could bias a bit the predictions, especially for these cell types. If
you have some values for these mRNA/cell abundances, you can also add
them into EPIC, with help of the parameter “mRNA_cell” or
“mRNA_cell_sub” (and that would be great to share these values).

If the mRNA proportions of these cell types are low, then even if you
don’t correct the results with their true mRNA/cell abundances, it
would not really have a big impact on the results. On the other side,
if there are many of these cells in your bulk sample, the results
might be a little bit biased, but the effect should be similar for all
samples and thus not have a too big importance (maybe you wouldn’t be
fully able to tell if there are more CAFs than Tcells for example, but
you should still have a good estimate of which sample has more CAFs
(or Tcells) than which other sample for example).

I receive a warning message that “the optimization didn’t fully converge for some samples”. What does it mean?

When estimating the cell proportions EPIC performs a least square
regression between the observed expression of the signature genes and
the expression of these genes predicted based on the estimated
proportions and gene expression reference profiles of the various cell
types.

When such a warning message appears, it means that the optimization
didn’t manage to fully converge for this regression, for some of the
samples. You can then check the “fit.gof$convergeCode” (and
possibly also “fit.gof$convergeMessage”) that is outputted by EPIC
alongside the cell proportions. This will tell you which samples had
issue with the convergence (a value of 0 means it converged ok, while
other values are errors/warnings, their meaning can be found in the
help of “optim” (or “constrOptim”) function from R (from “stats”
package) which is used during the optimization and we simply forward
the message it returns).

The error code that usually comes is a “1” which means that the
maximum number of iterations has been reached in the optimization.
This could mean there is an issue with the bulk gene expression data
that maybe don’t completely follow the assumption of equation (1) from
our manuscript. From our experience, it seems in practice that even
when there was such a warning message the proportions were predicted
well, it is maybe that the optimization just wants to be too
precise, or maybe few of the signature genes didn’t match well but
the rest of signature genes could be used to have a good estimate of
the proportions.

If you have some samples that seem to have strange results, it could
however be useful to check that the issue is not that these samples
didn’t converge well. To be more conservative you could also remove
all the samples that didn’t converge well as these are maybe outliers,
if it is only a small fraction from your original samples. Another
possibility would be to change the parameters of the optim/constrOptim
function to allow for more iterations or maybe a weaker tolerance for
the convergence, but for this you would need to tweak it directly in
the code of EPIC, I didn’t implement such option for EPIC.

Who should I contact in case of a technical or other issue?

Julien Racle (julien.racle@unil.ch). Please provide as much details
as possible and ideally send also an example input file (and/or
reference profiles) that is causing the issue.

GfellerLab/EPIC