Francis Deng*1, Siniša Hrvatin*
1, Philip diIorio
2, Alireza Rezania
3, Douglas Melton
1
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
2Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 3BetaLogics Venture, Janssen Research and Development, LLC, Raritan, NJ
Abstract
High quality RNA isolation and transcriptome profiling of human pancreatic
cells purified by FACS using intracellular markers without reporters
Comparing hESC-derived,
fetal, and adult β-cells
Acknowledgments
We thank Anastasie Kweudjeu and Eliza Scadden for excellent
technical assistance.
Culture products of stem cell differentiation and somatic
cell reprogramming, as well as native tissues, exhibit high cell
type heterogeneity. Specific cell surface markers are often
unknown, hampering molecular analysis of defined
subpopulations. We report a method to obtain high-quality, global
gene expression profiles of primary human and hESC-derived cells
purified by fluorescence-activated cell sorting (FACS) using
intracellular/cytoplasmic markers.
The method enabled, for the first time, the discovery of the
molecular signatures of primary human fetal and adult pancreatic
beta-cells FACS-purified from other pancreatic cell types. These
included novel and known beta-cell factors. For instance, both
fetal and adult beta-cells were enriched for the transcription
factors Pdx1 and Nkx6-1, while only fetal beta-cells were enriched
for the earlier developmental regulators FoxA2 and Pax4, and
adult beta-cells preferentially expressed the maturity markers
MafA and Ucn3.
Subsequently, we compared these beta-cell transcriptomes
to that of insulin-positive cells derived from genetically
unmodified hESCs. Human ESC-derived insulin-positive cells were
more similar to fetal beta-cells than to adult β-cells, but also
lacked critical insulin processing/secretion machinery and
expressed many genes characteristic of other endodermal cell
types, Additionally, insulin-positive cells derived from multiple
pluripotent stem cell lines were highly similar.
We suggest that probing the differences in genes and
pathways between hESC-derived, fetal, and adult beta-cells will
provide heuristics for improving directed differentiation protocols
and generating functionally mature beta-cells that could
ameliorate type 1 diabetes upon transplantation. More generally,
this approach holds broad potential for comparing specifically
defined cell populations from in vitro stem cell-derived cultures
and native human tissues.
Modified intracellular FACS
Background
Overlaps between genes with enriched expression
(compared to non-β pancreatic cells) in human insulin+
cells derived from different sources. Noteworthy genes
and statistically significant gene ontology term
enrichment for each set are shown.
hESC-derived insulin+ cells share more enriched genes
with fetal β-cells than with adult β-cells. hESC-derived
insulin+ cells are missing or expressing low levels of key
β-cell transcriptional regulators, and aberrantly express
genes characteristic of other cell types (e.g. liver,
enteroendocrine, α-cells).
Hierarchical clustering of samples using probes that
are significantly differentially expressed between any
two cell types.
hESC-derived insulin+ cells cluster more closely with
fetal β-cells than with adult β-cells.
1. Modified intracellular FACS is a highly versatile approach that
permits isolating high-quality RNA from defined cell
populations without resorting to genomic modification
(reporters) or surrogate markers (surface antigens)
2. Insulin+ cells differentiated under similar conditions from two
hESC lines, H1 and HUES 8, are virtually indistinguishable.
3. On a global transcriptional level, hESC-derived insulin+ cells
resemble fetal β-cells more than mature β-cells.
Conclusions
In group-wise comparisons between H1- and HUES 8-
derived stage 6 insulin+ cells, only 328 probes (0.7%)
were significantly differentially expressed. No gene
ontology terms were significantly enriched in this set.
Insulin+ cells derived from
different hESC lines
Based on all detectably expressed genes, H1- and HUES
8-derived insulin+ cell samples cluster closely, often
closer than do cadaveric β-cells from separate donors.
Glucose stimulated insulin secretion
hESC-derived islet0
1
2
3
4
5
6 Low glucose
High glucose
KCl
***
******
pg
in
su
lin
secre
ted
per
cell
INS/
GC
G/D
NA
hESC-derived stage 6 differentiation
Intact adult human islet
Though directed
differentiation mimics
stages of
development, end-
stage in vitro cultures
are dysfunctional and
highly heterogeneous.
• To elucidate the basis of functional impairment and identify
targets for improving directed differentiation, it is important to
compare the transcriptomic profiles hESC-derived cells and
human in vivo-derived β-cells.
• Due to tissue/culture heterogeneity that can obscure salient
signals in one uncommon cell type, one must somehow
purify/isolate the insulin+ cells of interest.
• Cell surface markers and reporter lines face major technical
challenges for this purpose.
stage 6 culture
Fixed, permeabilized, stained Average signal; n=3
Illumina microarray on hESC-derived S6 cells
Fre
sh
Ave
rage
sig
nal
; n
=3
r2 = 0.9882 Best-fit: Y=0.01+1.0X
Standard staining protocol
A
B
Fres
h
Fixe
d/
Perm
’d
Stai
ned
RIN: 7.7
RIN: 5.9
RIN: 2.2
RIN: 5.4
RIN: 4.7
+RNasin Plus
RIN: 3.9 RIN: 8.4
C
FAC
S so
rted
Standard RNA isolation protocol
Protease digestion for 3 h at 50°C
5.6 ng/μl 6.0 ng/μl
Yield Quality0
5
10
15
20
25
0
2
4
6
8
10
pg
to
tal R
NA
per
cell
RN
A In
teg
rity N
um
ber
Optimized FACS
protocol preserves
RNA quality:
All initial steps at 4°C, with
concentrated RNasin Plus (RNase
inhibitor). Decontaminated and
DEPC-PBS-filled FACS sorter. No
high temp during RNA isolation.
Strategy
mRNA detection is unaffected by
the optimized protocol for
fixation/permeabilization,
intracytoplasmic staining, and
RNA isolation
insu
lin
glucagon
Human adult islets
hESC-derived stage 6 cells
glucagon and somatostatin
RNA integrity
assessed by
Bioanalyzer
Human fetal pancreas
empty
The modified FACS method can
distinguish populations defined
by intracellular hormones:
Separation/enrichment for cells
of interest was confirmed by
qRT-PCR for the hormone
genes insulin and glucagon.
