Cho, Liu 1

The Detection of Differences Between Normal and Cancerous Stem Cells Through
Analysis of Morphology, Gene Expression, and Effects of Dichloroacetate
Hyunjii Cho and Jimmy Liu, advisers: Marie Olzewski, and Dr. Morris Kletzel at the
Children’s Memorial Hospital Stem Cell Laboratory

Abstract
Developments in oncology research point to stem cells as a promising, new means
through which to cure cancer. We observed the morphology, gene expression, and
response to dichloroacetate (DCA) of normal and cancerous stem cells. Mononuclear
cells isolated from human blood were cultured for experimentation. We tested several
different DCA concentrations to determine if cancer cells and normal cells die in DCA.
To determine which stem cell markers exist on the cells, we performed flow-cytometry, a
technique used to analyze physical and chemical characteristics of single cells flowing
through an electronic detection apparatus. We also used RT-PCR to determine the genes
expressed. When DCA was applied to the experimental group, the concentration of cells
was successfully suppressed, implying that DCA has the effect of prohibiting cell
proliferation. This implies the restoration of apoptosis in cancerous cells and the
preservation of normal cells. DCA could be pursued as a cancer therapy because of its
preferential effect on cancerous cells, and consequently, we plan to further test its
potential. In particular, we plan to test DCA on cell cultures with both normal and
cancerous cells combined; current tests have only tested DCA on normal and cancerous
cells individually.

Focusing Question
What are the effects of dichloroacetate on normal and cancerous stem cells with respect
to cell concentration and gene expression?
Introduction
We decided to research oncology because of its significance in today’s society. 

More specifically, we focused on the elucidation of the differences between cancerous 

and normal adult stem cells by analyzing key characteristics such as morphology with 
 Cho, Liu 2

stem cell markers and gene expression, because we firmly believe that it will be essential 

in discovering the mechanisms through which cancer progresses. Another goal of our 

experimentation was to test the efficacy of dichloroacetate (DCA) as a targeted cancer 

therapy. DCA is a promising compound in cancer research because of its non­toxicity and 

versatility. The mechanism through which it acts is unique: it exploits the dysfunctional 

mitochondria, a characteristic unique to cancer cells. Because of this, as well as its small 

size, it is able to treat various types of cancer, including brain, lung and breast cancers. 

DCA restores apoptosis in cancer cells while leaving normal cells unaffected. The 

applications of dichloroacetate as a novel cancer therapy are limitless, because DCA has 

been previously used to treat rare metabolic disorders; it is known to be relatively safe and 

non toxic. Our study further tests the compound in the context of the immortalized human 

myeloid leukemia cell line K562. Previous research has been conducted with DCA testing 

its effectiveness on normal and cancerous cells, but our experimentation adopts a novel 

approach through analyzing the effects of DCA on normal and cancerous stem cells 

(Bonnet, Archer, Allalunis-Turner, & Haromy, 2007).

Hematopoietic stem cells are isolated from the peripheral blood or bone marrow 

and are capable of self­renewal and differentiation into specialized cells. Apoptosis, 

programmed cell death, is necessary in order to prevent an excessive number of cells. 

Normal apoptotic functions are not present in cancerous stem cells, allowing unlimited 

cell regeneration. In healthy stem cell division, the cell regenerates itself and also creates 

a progenitor cell. Although the progenitor cell cannot regenerate itself, it is capable of 

dividing indefinitely into mature specialized cells (Lee & Herlyn, 2007). The progenitor 

cell then matures and become a specialized cell. 

Stem cells are characterized by both “self­renewal and their ability to produce 

cells that differentiate” (Morrison & Kimble, 2006), called progenitor cells.  Stem cells 

divide using two strategies: asymmetric and symmetric stem­cell divisions. In 
 Cho, Liu 3

asymmetric stem­cell division, stem cells divide to produce one identical daughter of 

itself, and one daughter that is capable of differentiating. Through this process, stem cells 

are unable to expand in number and thereby unable to produce stem­cell pools that are 

needed for development and for cell regeneration after injury. Therefore, there must be 

another method that stem cells utilize to maintain control of their numbers. “Symmetric 

divisions are defined as the generation of daughter cells that are destined to acquire the 

same fate.” (Morrison et al., 2006). Through symmetric division, stem cells are able to 

divide into two stem cell daughter cells or two progenitor cells. Most stem cells are able 

to divide both asymmetrically and symmetrically, and these two modes are controlled by 

developmental and environmental signals. However, this balance is sometimes disrupted 

and defective in disease states.

Division of a Stem Cell

Source: 
University of 
Medicine and 
Dentistry at 
New Jersey 
(2007).
Figure 1. 
Division of 
stem cells 
displaying 
self­renewal 
and the progenitor cell. Stem cell matures into a progenitor cell, and differentiates into 
various other cells.
 Cho, Liu 4

The K562 human leukemia cell line is strikingly similar to stem cells. According 

to Young and Hwang­chen, K562 has characteristics of self­renewal and pluripotency 

similar to those of stem cells (1981, p.7073). Comparable to leukemic stem cells, K562 

also expresses the WT1 gene (Hidehiko, Masato, & Etsuko, 2006). According to Kanato, 

Hosen, and Yanagihara, WT1 expression is restricted to hematopoietic stem cells or 

progenitor cells. The Wilm’s Tumor 1 gene (WT1) is over­expressed in leukemia, thus 

explaining the proliferation of blood cells causing leukemia (2005). In normal subjects, 

there is low or undetectable expression of the WT1 gene; however, this gene is widely 

expressed in leukemic cell lines, as well as in the majority of lymphoid and myeloid 

leukemias of childhood and adulthood (Hernandez­Caballero, Mayani, & Montesinos, 

2007). 

The rationale for testing the efficacy of DCA on stem cells is the methods of 

current chemotherapy and its success rate. Recent research in oncology points to stem 

cells as a novel method through which to study cancer. When a tumor is targeted, often 

there is a stem cell that differentiates into progenitors. The tumor is essentially composed 

of cancerous cells surrounding a few cancerous stem cells. The reason that many patients 

come out of remission is that although the cancer cells are eradicated, the cancerous stem 

cells remain viable (Lee & Herlyn, 2007). This poses a problem, as cancerous stem cells 

have unlimited potential to differentiate, thus causing cancer to relapse (Lee & Herlyn, 

2007).  

A secondary method used to measure the efficacy of DCA is the analysis of the 

expression of the Wilm’s Tumor gene (WT1). The presence of this gene indicates tumor 

progression, which requires excessive cell proliferation (Kanato, Hosen, Yanagihara,

Nakagata, Shirakata, & Nakasawa, 2005). If WT1 expression is not detected, then the 

culture of cells will not proliferate rapidly and is not cancerous. 
 Cho, Liu 5

In a previous study at the University of Alberta, it was discovered that DCA 

normalizes a dysfunctional mitochondria, thus restoring apoptotic function (Bonnet et al., 

2007). More specifically, cancer is unique in that it has a high membrane potential, 

downregulated K+ channels, and metabolizes through glycolysis. Membrane potential is 

the difference in electrical voltage between the inside and outside of the cell membrane 

(Alberts, 2002). Regular membrane potential allows for a stable cell environment; DCA 

was recently discovered to decrease the high mitochondria membrane potential. In 

addition, DCA up­regulates the K+ channels and shifts metabolic activity from the 

cytoplasm­based glycolysis to the mitochondria­based glucose oxidation (Bonnet et al., 

2007).

By testing the efficacy of DCA on stem cells, we hope to further confirm the 

efficacy of DCA. We hypothesized that DCA would have a positive effect in restoring 

normal apoptosis, or programmed cell death, in cancer stem cells, and effectively inhibit 

cell proliferation. We also hypothesized that DCA would leave normal stem cells 

unaffected. 

Materials and Methods:

In order to proceed with the experiment, blood samples that were ready to be
discarded from the Children’s Memorial Hospital were obtained. K562 cells were used in
place of cancer stem cells due to their similarities: K562 cells, like cancer stem cells, are
able to self-renew and proliferate, as well as express the Wilm’s Tumor 1 (WT1) gene,
which is exhibited in stem cells. Mononuclear cells, or stem cells were isolated by
creating a density gradient. Before diluting the blood, an initial cell count was taken with
the Cell Dyn 1700 machine. We then created a density gradient with the use of Ficoll-
Paque, underlayering blood with Ficoll-Paque. To keep the sample sterile, we avoided
contact between the Ficoll-Paque bottle and the test tube when adding the Ficoll-Paque.
Blood diluted with phosphate buffered saline (PBS) in a ratio of 1:1 and was added to this
test tube. The test tube was balanced in a centrifuge and spun at 3000 rpm for 10 minutes
 Cho, Liu 6

without a brake. Mononuclear cells were removed from the resulting contents, as shown
in Figure 2.

Figure 2. Density gradient using Ficoll-paque.

These cells were then collected and washed with PBS and spun in the centrifuge
for 5 minutes at 3000 rpm. Afterwards, the PBS and plasma were poured out and the
compacted cell pellet remained at the bottom (Figure 3).
 Cho, Liu 7

Figure 3. Pellet at the bottom of a test tube formed from the accumulation of
mononuclear cells.

Approximately 2 mL of RPMI tissue culture was added in preparation of culturing

the cells. The cell pellet was resuspended and mixed well. A final cell count was taken
with the Cell Dyn 1700 in order to calculate the amount of cells per well would be
needed. In our experiment, we used about 1.0x106-2.0x106 cells per well for normal bone
marrow stem cells, while we used about 0.1 x 106 cells for K562, since this human
immortalized myelogenous leukemia cell line proliferates rapidly. In order to culture
these cells, 1mL of RPMI was added to each well and the plate was placed in the
incubator. The RPMI was changed roughly every week for normal bone marrow stem
cells, and about every 3 days for the K562 cell cultures.

Cell viability was tested with Trypan Blue. 10 µL of the cell sample was mixed
with 20 µL of Trypan Blue. Then this mixture was inserted into a sterilized
hemacytometer; the hemacytometer was sterilized to remove any residue before
examining the sample of cells and to avoid contamination. The cells were viewed under a
microscope and viable and dead cells were counted. This method works because when a
cell is not viable, the function of its semi-permeable membrane is compromised. This
allows the penetration of Trypan Blue into the cell; unviable cells are permeated with
 Cho, Liu 8

Trypan Blue, while the semi-permeable membrane of living cells prevents the penetration
of Trypan Blue; the cell is not blue.

For our DCA experiment, we made 5, 10, 20, and 40 mM concentrations of DCA
in RPMI solution. To the 1 mL solution of cell culture we added 1 mL of the DCA
solution. Mixing the DCA solution to another 1 mL solution diluted the concentration of
DCA by half. Thus actual 5, 10, 20, and 40 mM concentrations of DCA became 2.5, 5,
10, and 20 mM concentrations, respectively. DCA was added to the cells after a few days
of culturing them. Cell concentrations of the cells in DCA were measured after 48 hours
for normal stem cells, and 96 and 168 hrs for K562 cells.

We also used reverse transcriptase-PCR to analyze the effect of DCA on the

K562. Total RNA was extracted using QIAamp RNA Blood mini-kit (QIAGEN, Inc.,
Valencia, CA, USA). A 2-step reverse transcriptase (RT)-PCR in a 20-uL reaction volume
with 1 microgram (ug) of total RNA from each sample was conducted. The reaction
buffer included 4 uL of 25 nM MgCl2, 8 uL of dNTPs, 1 uL of Oligo d(T)16, 2 uL of
10xPCR buffer II, 1 uL of RNase inhibitor, and 1 uL of Moloney Murine Leukemia Virus
RT (Applie Biosystem, Foster City, CA, USA). We used primer pairs that were designed
to locate particular nucleotide fragments for mRNA of the WT1 gene. Reverse
transcription was incubated at 42 degrees Celsius in a water bath for 60 minutes. The it
was denatured at 96 degrees Celsius in a thermal cycler for 10 minutes. 10 microliters of
the complementary DNA was amplified during the 1st round of PCR. There was an initial
30 cycles of denaturation for 5 minutes, 5 seconds at 95 degrees Celsius amplification,
annealing at 55 degrees Celsius fir 5 seconds, and extension at 72 degrees Celsius for 10
seconds. A second round was performed by taking 1 uL of the 1st round of amplified
product and reamplifying with inner primers utilizing the LightCycler System with
SYBR-Green 1 RNA master mix reagent (Roche Diagnostics, Biochemica, Indianapolis,
IN, USA). Once PCR was complete, the LightCycler Software calculated the
concentration of target molecules. Using a 10-fold serial dilution of K562 leukemia cell
line and the Bone Marrow 2 (BM2) sample, a standard curve was generated for each
sample. Values of 1x 100ng/uL and higher were considered WT1 positive. PCR products
 Cho, Liu 9

were then run through a 1.5% agarose gel electrophoresis. Finally the data was analyzed
in the form of graphs.

Results
Figure 4 displays the increase in K562 cell concentration as time increases, thus
confirming the indefinite proliferation of K562. The initial cell concentrations of K562 at
Day 0 were 0.1 thousand per microliter (K/uL).
K562 Control (Jan. 16.08- Jan. 30. 08)

3.5

1.0877x
3 y = 0.0385e
2
R = 0.9541

2.5
Concentration (K/uL)

1.5

0.5

0
D0 D3 D10 D14
Time (days)

Figure 4. Bar graph of the cell concentration as time increases. K562 was cultured and
the cell concentration of the controls (without DCA) were recorded at various times in a
14 day period.

The graph in figure 5 displays a decrease in cell concentration of K562 as the DCA
concentration increases.
 Cho, Liu 10

Figure 5. Protocol a: The effects of increasing DCA concentration on the cell

concentration of K562. Cell concentration (K/uL) of K562 cell cultures with no DCA and
cultures with 2.5 mM, 5mM, 10mM, and 20mM were observed after 168 hours after the
addition of DCA.

The highest concetrations of DCA from protocol a were tested again in another set
of experiments, protocol b. The resulting K562 cell concentrations in 10 mM and 20mM
DCA after 96 hours of the addition of DCA shows to be far less than that of the control
measured at the same time.
 Cho, Liu 11

Figure 6. Protocol b: K562 cell concentrations on day 14 of the culture and 96 hours after
adding DCA to certain cultures. 10mM and 20mM DCA concentrations were tested and
compared to the day 14 control culture.

Protocol c consisted of Bone Marrow Sample #2 (BM2) normal bone marrow

stem cell cultures at different concentrations. The effects of the various DCA
concentrations on BM2 were relatively similar. At day 0 of the culture, the initial cell
concentration was 2.0K/uL. At day 16 of the culture and 48 hours after the addition of
DCA to some of the wells of the culture, the sample was observed. The concentrations
were relatively around 1.7K/uL. There were no significant differences between the BM2
cell concentration of the control and the DCA-treated cultures.
Protocol c: BM2 March 7 Day 16 (48Hrs in DCA)

1.8

1.72 1.72 1.7333333

1.6 1.7

1.4
Cell Concentration (K/uL)

1.2

0.8

0.6

0.4

0.2

0
Control 5mM 10mM 20mM
DCA Concentration (mM)

Figure 7. Protocol c: BM2, a normal stem cell sample, was treated with various
concentrations of DCA. The resulting cell concentrations after 48 hrs of immersion in
DCA were compared to the control, which had been cultured for a total of 14 days.

A secondary result of experimentation is the analysis of gene expression. Again,

the most significant difference can be evidenced through a comparison of non-DCA
treated cultures and DCA-treated cultures. As shown in Figure 8 and Figure 9, when a
pristine culture of K562 cells is used as the baseline, the two cultures treated with 20 mM
of DCA from both protocol a and b have low expressions of WT1, the cell proliferation
gene. BM2, the normal stem cell sample, also has a very low, almost undetectable,
expression of WT1. The control K562 samples and the 10mM DCA concentration K562
 Cho, Liu 12

samples all express the WT1 relatively higher than the 20mM DCA treated K562
samples.

Figure 8. WT1 expression in K562 controls, 10mM and 20mM DCA treated K562
samples, and BM2. The resulting data was examined through the LightCycler Data
Analysis.

Figure 9. WT1 expression show in bar graphs for K562 controls, 10mM and 20mM DCA
treated K562 samples, and BM2.

Conclusion
 Cho, Liu 13

In the first set of experiments (protocol A), various concentrations of DCA were
tested on cultures of 2x106 cells per well: K562 control group (n=2), K562 group with
2.5mM (n=2), 5mM DCA (n=2), K562 group with 10mM DCA (n=2). The control group,
which was not treated with DCA, continued normal cell proliferation. The DCA-treated
groups exhibited a decreased concentration of cells, indicating decreased cell
proliferation. Using regression analysis, we determined that the concentration of cells
decreased exponentially as the concentration of DCA increased. The second set of
experiments (protocol B) consisted of testing 10mM and 20mM DCA concentrations on
K562.

10mM and 20mM DCA concentrations were chosen for the second set of
experiments (protocol B) on K562 because they exhibited almost no increase in cell
concentration. The initial cell concentration was 0.1 K/uL, while the cell concentrations
of K562 cells in 10mM and 20mM DCA for 168 hrs only had 0.2 K/uL cell
concentrations. This is not a significant increase and can be accounted for by few trials,
and human and machine (Cell Dyn 1700) error. Protocol B confirmed that DCA may
inhibit cell proliferation because it also showed that cell concentrations did not increase
significantly from the initial cell concentration of 0.1 K/uL and they also did not
proliferate as much as the control did.

RT-PCR was performed on protocol A and protocol B. The expression of WT1 in

protocol A and B was measured through RT-PCR. In protocol A, the K562 group treated
with 10mM of DCA showed that the cells still expressed the Wilm’s tumor suppressor
gene (WT1), which regulates cell proliferation. However, the cells in protocol A that were
treated with 20mM of DCA did not significantly exhibit the WT1 gene. The test was
repeated for protocol B and similar results were achieved. These results indicate that a
20mM concentration of DCA is more effective than a 10mM concentration because it
successfully inhibits the expression of WT1. They also support the correlation between
increased DCA concentration and decreased cell concentration.

The effects of DCA were also tested on normal, non-cancerous adult stem cells
(Sample BM2). DCA had no significant effect on the cell concentrations of BM2. This
shows that while DCA affects cancerous cells, it does not affect normal stem cells. More
 Cho, Liu 14

tests will need to be performed on normal cells in the future, in order to wholly support
our conclusion. Due to the lack of normal bone marrow stem cells available, we were not
able to perform many tests on normal stem cells.

Our findings in the morphology through analysis of stem cell markers contradict
the discoveries in WT1 expression, and were thus, unexpected. Through flow cytometry,
we found that the percentage of K562 cells that are both CD123 and CD 34 positive
increases as the concentration of DCA increases. This means that the percentage of K562
cells that are capable of proliferating have a positive correlation with DCA
concentrations. The stem cell marker CD123 may be present on cells for more than just
capability of proliferation; therefore, the RT-PCR results would prove to be more reliable.
Gene expression is more specific in determining function than the stem cell markers. In
order to understand why the two assays contradict each other, further research will be
conducted attempting to determine the cause of the presence of CD123 on cells. One
might hypothesize that the CD123 stem cell marker has other functions than indicating
cell proliferation.

The prospect of dichloroacetate as a novel, therapeutic cancer treatment is

realistic because it restores mitochondrial function, one of the fundamental pathways
unique to the progression of cancer. Additionally, as it has been used for many decades in

the treatment of metabolic diseases, it is known to be relatively non-toxic (Bonnet, et al., 

2007). The most significant property of dichloroacetate is that it has no effect on normal

cells (Bonnet, et al., 2007).

Our results corroborate our hypothesis that dichloroacetate would inhibit cell
proliferation and are highly indicative of the veracity of DCA as a cancer-targeting drug.
The 20mM DCA concentration seemed to be most effective. In protocol A, after 168 hrs
in 20mM DCA, K562 showed little to no proliferation. Protocol B showed similar results.
This, however, does little to show the effects of DCA on normal stem cells. Thus, we
tested 10mM and 20mM concentrations of DCA on normal, noncancerous stem cells
(Sample BM2) and found that the cell concentrations did not significantly change. As
evidenced in Protocol A and Protocol B, these results suggest that DCA decreases cell
proliferation in cancer cells as its concentration increase.
 Cho, Liu 15

In the future, more tests on normal stem cells and cancer stem cells will need to
be performed. Since this is an ongoing project, we will aim to establish a more solid
foundation testing the efficacy of DCA by testing more on normal stem cells and creating
assays that involve normal and cancerous stem cells in a single culture.
Discussion
In our analysis of the differences between cancerous and normal stem cells, we
investigated the gene expression of the Wilm’s Tumor (WT1) gene and its implications in
our experiment. The WT1 gene controls cell proliferation and is often present in the case
of a tumor, because rapid cell proliferation is involved. In our investigation, the K562
treated with 20mM of DCA exhibited a low expression of the WT1 gene—about the same
level of expression as a normal, non-cancerous stem cell sample. In contrast, a sample of
K562 not treated with DCA exhibited a much higher expression of the WT1 gene, as
evidenced in Figure 9. “the Wilms’ tumor gene WT1 plays an important role in cell
proliferation and differentiation” (Kanato et al., 2005). This explains why K562, a
leukemia cell line would have a high expression of this gene. Normal stem cells would
not because, although they self-renew themselves, they do not proliferate constantly like
cancer cells.
The results that we achieved were similar to the experimentation conducted at the
University of Alberta. DCA had the effect of eradicating cancer stem cells and inhibiting
cell proliferation, as well as leaving noncancerous cells unaffected. According to this
article, cancer cells make energy through glycolysis, instead of making use of the
mitochondria for energy. Cancer cells prefer glycolysis, because this process still operates
in the absence or lack of oxygen to the rapidly multiplying cells. The mitochondria
operates apoptosis, thus turning off the mitochondria prevents apoptosis from occurring.
DCA attacks the glycolysis process by inhibiting the use of pyruvate by glycolysis
through activation of oxidative phosphorylation in the mitochondria.
We found that as the concentration of dichloroacetate increases, the cell
concentration of K562 decreases. This shows the effectiveness of DCA on cancer cells. In
order to validate our findings, we tested on normal stem cells with 5, 10, and 20 mM of
DCA and found that the differences in the concentrations of the controls and the
experimental samples were insignificant. This further supports the DCA investigation at
 Cho, Liu 16

the University of Alberta. Scientists researching this compound discovered that DCA
inhibits cancer and does not harm normal cells. In order to mimic what occurs in the
human body, tests of DCA in an environment with cancer and normal stem cells would be
recommended.
The current problem in chemotherapy of targeting cancer cells while leaving
cancer stem cells viable can be solved in the future with more research involving DCA.
Our findings and novel application of DCA on stem cells serve as a foundation on which
to continue research in oncology.

Inquiry Process
Jimmy Liu
Investigation in the field of oncology was both challenging and rewarding for me. 

Although the rigor of IMSA’s advanced science classes prepared me well for our 

experimentation, there is no substitution for real lab­work at an institution such as 

Children’s Memorial Hospital. Working at the Stem Cell Transplant Lab was a unique 

experience that challenged me to stretch the limits of my creative thinking and integrate 

novel methods of solving age­old problems.

Our advisers provided invaluable guidance, but ultimately, because the project was 

our own, it was our duty to determine what tests to conduct and to discover new 

approaches to test our hypothesis. Instead of supplementary worksheets, we conducted all 

of our own background research and used creative problem solving in our calculations. 

This project has taught me that creative thinking is essential, especially in science. 

If our first approach didn’t work, we were forced to analyze and synthesize an 

explanation, and formulate a solution. For example, when we first diluted DCA with 

water, all of the cells died. After thinking back to our biology courses, we realized that 

water would cause the cells to become hypotonic and burst.

Luckily, our problem solving, coupled with the advice of our advisers, allowed us to 

achieve our ultimate goal: learning through experimentation. An obvious task we wanted 
 Cho, Liu 17

to accomplish was to discover the effects of dichloroacetate on stem cells; however, we 

also set our mind to learning through our mistakes and experiencing real lab situations. 

Although more research and experimentation will be needed to confirm our findings, we 

succeeded in touching on the effects of DCA. 

Previous to starting our investigation, I had read about cancer stem cells and new 

implications in the cancer field. We started our project on a broad topic of the difference 

between normal and cancer stem cells, because we wanted to be in the forefront of cancer 

research. A couple of weeks into the SIR program, we decided to narrow our path of 

investigation to specifically looking at the effects of DCA on cancer and normal stem 

cells. DCA was found to inhibit cancer growth while leaving normal cells unaffected, so 

in our experiment we wanted to confirm this discovery.  

Idyllically, we wanted to test several samples; however, since we were receiving 

discarded blood samples, we had a difficult time attaining enough samples for stem cells. 

Many times we did not have enough cells to create a lasting sample and many times these 

samples were not fresh. We overcame this by replacing cancer stem cells with the K562 

cell line. However, we did not have replacements for the normal bone marrow stem cells, 

so we used what was available for us. The whole experience was a learning process. At 

the beginning, we did not wash out the Trypsin­EDTA. Due to this, the data we compiled 

were invalid. Even with this fall­back, we advanced in our investigation and learned from 

our inaccuracies.

Justina

Throughout inquiry, I gained many valuable laboratory skills and built relationships

that I never would have without the research opportunity. I discovered that the best way

to learn is through experiences. IMSA’s advanced science classes prepared me for basic

labwork; however, actually being in a lab and conducting high-level research challenged

me to go beyond my limits. I was able to build upon my basic lab skills and accomplish
 Cho, Liu 18

more than I previously expected.

Ms. Marie Olszewski and Wei Huang, the lab technician, helped us a great deal

throughout our project. Marie explained the basic procedures we would most likely be

using, and then allowed us to conduct the experiments ourselves. Since this was an

independent investigation separate from our mentors’, we learned old procedures and

even created our own. The off-campus SIR experience was different than anything I have

done in school, because I did my own background research, solved any problems by

myself (without the help of a teacher), and did not have limits like school assignments. I

felt a lot more independent being able to do my own experiments.

I started the project by myself with little direction to what I wanted to accomplish. 

My current partner joined me in my investigation and brought with him his own 

knowledge of recent cancer research. He suggested testing dichloroacetate as another 

assay to assess stem cells. The general question, “What is the difference between cancer 

and normal stem cells?” evolved into, “What are the effects of dichloroacetate on cancer 

and normal stem cells with respect to cell concentration and gene expression?” 

Our mentor emphasized that experimenting was a learning process, and when we 

made mistakes she did not correct us, because she wanted us to learn by ourselves. In one 

instance we diluted the DCA for our experiment with water and later discovered that the 

cells had all died. We pondered over how the cells had died, and figured out that the cells 

became hypotonic and burst. Thus, we changed our procedure to diluting the DCA with 
 Cho, Liu 19

RPMI tissue culture instead of water.

We also had trouble getting the results we wanted because our blood samples were 

not fresh.  Since we were receiving discard samples, blood samples were not readily 

available. We overcame this by using K562, the human myeloid leukemia cell line, 

instead of cancer stem cells. This was a valid replacement because K562 has many 

similar characteristics to hematopoeitic cancer stem cells. However, we did not have a 

replacement for normal stem cells, so we had to use what was available to us. These 

drawbacks did not hinder our investigation. We pulled through and achieved many great 

results.  

References
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Alberts, B., (2002). Molecular Biology of the Cell. New York: Garland Science.

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Bonnet, S., Archer, S. L., Allalunis-Turner, J., & Haromy, A.(2007). A

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Leukemia and Lymphoma Society. (2007, June). Leukemia Facts and Statistics.

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2007, from http://www.leukemia-lymphoma.org/all_page?item_id=9346&

viewmode=print

Morrison, S. J., & Kimble, J. (2006). Asymmetric and symmetric

stem-cell divisions in development and cancer. Nature, 441, 1068-1074.
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nchs/fastats/deaths.htm

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info/scireport/chapter5.asp

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 Cho, Liu 22

Appendix A.
Flow-cytometry.

Introduction:
Flow-cytometry analysis was used in our experimentation, but ultimately did not support
our conclusions or further our experiments or results. However, it did force us to question
why the results we achieved in the flow-cytometry were not those that we expected. As a
result, the flow-cytometry section of our experimentation caused us to further research
certain stem cell markers and their applicability in our experimentation.
The principles of flow-cytometry are relatively simple; light scattering and
fluorescent tagging are employed in this procedure, and a laser is usually the light source.
When the light from the laser strikes a particle of interest, it is excited to the next energy
level, and a photon is released. Flow-cytometry is unique in that it measures fluorescence
per cell.
Our flow-cytometry results consisted of two-parameter histograms, with different
 Cho, Liu 23

antibodies on the x- and y-axis. Each dot on the histogram represents a cell or particle;
the histogram provides an excellent visual representation of the cells tagged by
fluorescence. The following results were a part of our investigation, but did not add to our
conclusion.
The types of stem cells present in a culture can be determined with cell surface 

markers. The cell markers bind to specialized proteins on the surface of every cell in the 

body called receptors. Fluorescent tags are attached to surface markers (Figure 10) and 

these fluorescent tags are then detected via flow cytometry, a technique which picks up 

fluorescent light and thus identifies the cell surface markers. 

Table 1. The types of cells that are positive for various cell surface markers and the 

sources used for this experiment.

Cell Surface Marker Cell Type
CD34 (Miltenyi Biotec) Hematopoeitic Progenitor cells (stem cells)
CD123 (BD Pharmingen) Multipotential hematopoietic
stem/precursors. Expressed in cells that
proliferate.
CD133 (Miltenyi Biotec) Hematopoeitic stem cells (younger stem 

cell)
CD14 (BD Simultest) Monocyte
CD45 (BD Simultest) Lymphomas, B­cell chronic lymphocytic 

leukemia

White cells, pan­leukocyte

Fluorescent Tagging of Cells
 Cho, Liu 24

Source: Appendix E: Stem Cell Markers (2001).

Figure 10. Identifying Cell Surface Markers Using Fluorescent Tags.

Methods and Materials:

In order to determine the types of cells in our sample, we performed flow

cytometry. Falcon tubes were labeled with the following monoclonals:

• Isotype control (G1/G2a)

• CD14+/CD45+
• CD133+/CD34+
• CD123+/CD34+

Then to each of the test tubes, 10 microliters (uL) of the appropriate monoclonal antibody
and 50 uL of cells were added. The tube is gently vortexed and then incubated for 10-15
minutes at room temperature away from light. We added 2 mL of 1xBD FACS Lyse
working solution and then vortexed and incubated for a maximum of 10 minutes. This
solution was centrifuged at 1800 rpm for 5 minutes. The supernatant was poured out and
2 mL of wash solution was added. After the second wash, we decanted the supernatant
and added 350 uL of 1% Paraformaldehyde. Finally, we put the sample in the vortex and
refrigerated it until it was ready to use.

Through flow cytometry, certain characteristics of the normal and cancer cells
were determined. In protocol a, 23.53% of the K562 control cells were double positive
for CD123 and CD 34. CD123 is a cell surface marker for cells capable of proliferation,
while CD34 is a marker for hematopoietic stem cells. The percentage of cells that are
both positive steadily increases as the concentration increases. Table 2 shows the results
 Cho, Liu 25

of flow cytometry detecting the markers of CD 123 and CD34 on the control K562, K562
treated with 10mM DCA, and K562 treated with 20 mM DCA.

Table 2. The percentage of cells that are both CD123 and CD34. Flow cytometry was
performed to determine the types of cell surface markers on the cells.
Protocol a CD123+ and CD34+
K562 control 28.53%
10mM DCA treated 49.86%
20mM DCA treated 48.95%

Flow cytometry was also performed on normal stem cells and only 1.50% of the cells
were both CD123 and CD34 positive.