Eric Kong

IM-6/11AP

Annotated Source List

Antonarakis, E. S., Lu, C., Wang, H., Luber, B., Nakazawa, M., Roeser, J. C., . . . Luo, J. (2014).
AR-V7 and Resistance to Enzalutamide and Abiraterone in Prostate Cancer. ​New
England Journal of Medicine,371​(11), 1028-1038. doi:10.1056/nejmoa1315815

This article refers to a specific problem that researchers are currently investigating. In
previous studies, researchers found that an androgen-receptor called AR-47 lacked the ability to
bind ligands to larger molecules, and yet the cells could still function and complete transcription.
The two inhibitors- Enzalutamide and Abiraterone- target the ligand binding in order to disrupt
cancer cells’ transcription process. However, it seems that certain cells have adapted and
researchers hypothesize that patients with resistance to Enzalutamide and Abiraterone likely
have the AR-47 isomer which allows the cancer cells to transcribe even without the ligands.
This study is valuable to the researcher because some research deals with the
identification of different substances as AR-47 inhibitors. The article provides essential
background information on AR-47 and also contains knowledge about how certain cancer cells
begin to develop resistance. In addition, it poses a series of questions (E.g Why do AR-47 cells
still function without the ligand binding ability) that helps inspire one’s research.

Bono, Johann S. de, et al. “Circulating Tumor Cells Predict Survival Benefit from Treatment in
Metastatic Castration-Resistant Prostate Cancer.” Clinical Cancer Research, American
Association for Cancer Research, 1 Oct. 2008,
clincancerres.aacrjournals.org/content/14/19/6302.

This informational article is discussing a new method for the detection of prostate cancer
in males. ​The new method for detection is by locating enumerating circulating tumor cells
(CTC). Enumerating circulating tumor cells is a new technology that has just been regulated and
approved. ​Circulating tumor cells are cells that have shed into the vasculature or lymphatics from
a primary tumor and are carried around the body in the blood circulation. The primary objective
of the prospective study discussed in the text was to establish the relationship between
posttreatment CTC count and overall survival in castration-resistant prostate cancer. The purpose
of this relationship was to discover whether or not CTC truly has a positive effect on treatment.
Secondary objectives included determining the prognostic utility of CTC measurement before
initiating therapy, and the relationship of CTC to prostate-specific antigen (PSA) changes and
overall survival over time. at these and other time points.
This article is beneficial to the researcher because it discusses the potential for a new
method for detecting cancer. This is also beneficial to other research because it may cause
prevention to be more likely and aid in the research of management of cancer.
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Chomczynski P, Mackey K. (1995) Short technical report. Modification of the TRIZOL reagent
procedure for isolation of RNA from Polysaccharide-and proteoglycan-rich sources.
Biotechniques 19(6): 942-5.

This scholarly journal publication details a newfound discovery of the TRIZOL reagent
that is commonly used in RNA extraction. The discovery entails a more efficient and sustainable
method to initiate the procedure which is typically expensive. The modified procedure they
describe is to first utilize the reagent to separate the particles including RNA and different
polysaccharides and other contaminants. These are not necessary for the sample because we only
need the RNA. However, with the modified reagent, the RNA immediately forms a pellet as it
has become a precipitate. Normal procedure would entail that the RNA first be separated and
then mixed with the centrifugation to isolate the different density solutes. Then you can aspirate
the medium which contains the contaminants.
This resource is extremely helpful because it summarizes the modified procedure that the
Triptolide treated cells had undergone. It effectively incorporates and explains each step of the
new procedure which is important so that the experiment can be replicated in the future for more
trials.

Edwards, Paul N. "How to Read a Book." How to Read a Book, PDF ed., vol. 5, U of
Michigan, pp. 1-10.

This educational article discusses valuable skills and techniques beginning researchers
can utilize in their investigation. The author mainly discusses techniques for reading non-fiction
professional articles efficiently. Non-fiction educational manuscripts aim to educate and provide
knowledge as opposed to fictional novels-which entertain. Edwards acknowledges this and
provides techniques specifically directed to rapidly gain information such as reading the main
points of the whole manuscript, managing the time spent on each section, skimming and then
focusing on each section, and diverting more attention to paragraphs with more content.
The advice the scholar gives is beneficial because he gives a personal insight into
research and summarizes the skills he has acquired over many years of reading.

Ghanemi A. Cell cultures in drug development: Applications, challenges and limitations. Saudi
Pharm J. 2015;23(4):453-4.

This information paper explains the very essence of cell culturing in pharmacological
studies. It does so by explaining the uses of the technique and when and where to implement
them. It specifies certain cases that would be appropriate and inappropriate for its use and
explains why the technique should be implemented. It also lists the procedures and steps
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normally pursued which can be referenced in the future. Cell culturing enables the researcher to
evaluate the presence of the drug on various cell-lines and cell variants.
This article is beneficial and valuable to the researcher because it details why Triptolide
had undergone different cell cultures. The article listed the applications which include the use of
cell culturing in pharmacological studies of compounds and explains different techniques that
can be used. This advice can be implemented in the future and can be referenced by the
researcher to explain why the technique was used in the respective study.

Hamdy, Freddie C., et al. “10-Year Outcomes after Monitoring, Surgery, or Radiotherapy for
Localized Prostate Cancer.” ​New England Journal of Medicine​, vol. 375, no. 15, 2016,
pp. 1415–1424., doi:10.1056/nejmoa1606220.

This source discusses the 10-year analysis of the effectiveness of several major prostate
cancer treatments. It focuses on evaluating three main therapies: Active monitoring, radical
prostatectomy, and external-beam radiotherapy. Throughout the 10 years, researchers mainly
analyzed the effects of each treatment and found that even clinically localized cancer resulted in
metastases and mortality. The study contained several checkpoints for follow-ups but while it
evaluated the effectiveness of the common treatments, it didn’t compare them. The study only
compared the effectiveness of active monitoring and proactive treatment.
This source is helpful because it introduces methods for prostate cancer therapy and
generally introduces the research process scientists undergo while looking for treatments. The
article also includes a discussion section containing the opinions of several qualified researchers
on the study and emphasizes their thoughts pertaining to the information found in the study.
While the article mentions that it does not focus on comparing the effectiveness of treatments,
the graphs show a clear trend in individual treatment success.

He Q-L, Titov DV, Li J, et al. Covalent Modification of a Cysteine Residue in the XPB Subunit
of the General Transcription Factor TFIIH Through Single Epoxide Cleavage of the
Transcription Inhibitor Triptolide. Angewandte Chemie (International ed in English).
2015;54(6):1859-1863. doi:10.1002/anie.201408817.

This medically published article discusses the implications of a study made about a
traditional Chinese root used for medicinal purposes. The root, known as the “Thunder God
Vine,” has long been known to have immunosuppressive abilities, particularly in combating
cancer. In the research journal, several researchers conducted a study in which they analyzed
specific molecules and sections of cells that are acted upon by the chemical triptolide, which was
found to be the source of the roots medicinal properties. The study had found that a
residue-Cys342 of XPB- underwent a covalent change. This residue is involved in the cell’s
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transcription process, and once it mutated, the cell became immune to the triptolide. Thus, the
study revealed that the XPB subunit may hold valuable implications for future treatments.
Overall, the study is valuable to the researcher because it provides background research
and introduces the molecular theory behind triptolide, the main topic. It serves as a molecular
explanation for the interaction between XPB and triptolide on a biochemical basis. The graphical
depictions of the data served to prove that XPB was, in fact, the residue interacting with the
chemicals which may prove useful in the future.

He, Q., Minn, I., Wang, Q., Xu, P., Head, S. A., Datan, E., . . . Liu, J. O. (2016). Targeted
Delivery and Sustained Antitumor Activity of Triptolide through Glucose Conjugation.
Angewandte Chemie International Edition,55(​ 39), 12035-12039.
doi:10.1002/anie.201606121

A major problem in using natural toxins derived from chemicals such as Triptolide in
cancer treatment is that it may prove toxic and deal more harm than good. However, this
peer-reviewed scientific article investigates the possibility of another form of triptolide that can
be delivered and utilized more effectively for treatment. The scholarly article summarizes the
results from the study and explains the concept behind the method. Specifically, the method
proposes a way to utilize a natural toxin called Triptolide. After utilizing glucose transporters in
combination with triptolide carriers, it became feasible to target only cells that were
overexpressing glucose transporters.
This article is beneficial in that it introduces an aspect of triptolide research that is
currently being investigated upon. It opens up a potential field that is full of prospect.
Furthermore, it reveals a promising lead for future cancer treatment research that can be used for
various other methods. The article is also helpful because it describes the process in which they
pursued the experiment and created the glutriptolide which can be utilized for other mechanistic
drug systems.

Hu R, Dunn TA, Wei S, et al. Ligand-independent Androgen Receptor Variants Derived from
Splicing of Cryptic Exons Signify Hormone Refractory Prostate Cancer. ​Cancer
research​. 2009;69(1):16-22. doi:10.1158/0008-5472.CAN-08-2764.

This medically published article summarizes the findings of a study involving

Ligand-independent Androgen receptors. Therapeutic failure and progression to
hormone-refractory PCa (HRPC) are often accompanied by molecular alterations involving the
androgen receptor (AR). In the study presented, the researchers reported novel forms of AR
alteration that was prevalent in hormone-refractory prostate cancer (HRPC). Through ​in silico
sequence analysis and subsequent experimental validation studies, the researchers uncovered
seven AR variant transcripts lacking the reading frames for the ligand-binding domain. This
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meant that these ARs were ligand-independent. The study focused on the two most abundantly
expressed variants, AR-V1 and AR-V7, for more detailed analysis.
These studies are valuable to the research because they identify the most significant and
common ligand-independent Androgen receptors which are pertinent to the research of triptolide.
In order to evaluate the effectiveness of triptolide, one must know what to test it on.
Furthermore, these novel AR variants may be explored as potential biomarkers and therapeutic
targets for advanced Prostate Cancer.

Hu, R., Lu, C., Mostaghel, E. A., Yegnasubramanian, S., Gurel, M., Tannahill, C., . . . Luo, J.
(2012). Distinct Transcriptional Programs Mediated by the Ligand-Dependent
Full-Length Androgen Receptor and Its Splice Variants in Castration-Resistant Prostate
Cancer. ​Cancer Research,72(​ 14), 3457-3462. doi:10.1158/0008-5472.can-11-3892

This peer-reviewed medical article analyzes the development of ligand-independent

Androgen Receptors in Castration-resistant prostate cancer. Continued androgen receptor
signaling is an established mechanism underlying castration-resistant prostate cancer, and
suppression of androgen receptor signaling remains a therapeutic goal. However, there are
certain receptors that lack the androgen receptor ligand-binding domain (AR-LBD), the intended
target of androgen deprivation therapies including CRPC therapies such as abiraterone and
MDV3100. Even though targeting the ligand binding sites is a valid therapeutic technique,
several researchers found that treatment may actually cause an increase in ligand-independent
AR’s. Their findings support an adaptive shift toward AR-V–mediated signaling in a subset of
CRPC tumors as the AR-LBD is rendered inactive, suggesting an important mechanism
contributing to drug resistance to CRPC therapy.
This article is important because it identifies the mechanism that creates drug resistance.
This knowledge is valuable as the research deals with inhibiting such receptors. By identifying
the source of these receptors, the researcher obtains knowledge regarding the main factors that
can create a cure. Furthermore, the article is beneficial because it summarizes a complex finding
through graphs.

Mazhar, D, and J Waxman. “Prostate Cancer.” Postgraduate Medical Journal, The Fellowship of
Postgraduate Medicine, 1 Oct. 2002, pmj.bmj.com/content/78/924/590.

This scholarly article focuses on the natural history and management of prostate cancer.
The management of prostate cancer is also known as the treatment of prostate cancer, including
idle surveillance and monitoring, radical prostatectomy or castration, and radiotherapy. While the
article aims to educate researchers and provide a general introduction to the pathology of prostate
cancer, it also evaluates the effectiveness of early detection with treatment. One main focus of
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this article is also to analyze hormonal therapy, a form of chemotherapy used to block androgens,
the hormones found in the reproductive system that foster cell growth. This article summarizes
multiple treatments and introduces screening techniques to provide an introduction for new
prostate cancer researchers.
This article is beneficial to a researcher because it serves as a general source of
information. It summarizes the intricacies of prostate cancer development and treatment, which
can help new researchers. However, this is also a flaw because it is simple information for an
experienced and knowledgeable researcher.

Rio DC, Ares M, Hannon GJ, Nilsen TW. Purification of RNA using TRIzol (TRI reagent). Cold
Spring Harb Protoc. 2010;2010(6):pdb.prot5439.

This informative article details the procedure for RNA isolation and extraction using
TRIzol, a modern revised TRI reagent. The procedure also includes the use of chloroform.
TRIzol RNA extraction is a relatively recently developed method for deproteinizing RNA but it
is becoming widespread. This method is particularly beneficial when the separation of proteins
and RNA are impossible by other means. TRIzol (or TRI Reagent) is a monophasic solution of
phenol and guanidinium isothiocyanate that simultaneously solubilizes biological material and
denatures the protein. The protein is unnecessary and is considered a contaminant which makes
TRIzol extraction a superior option. After solubilization, the addition of chloroform causes phase
separation, where a protein is extracted to the organic phase, DNA resolves at the interface, and
RNA remains in the aqueous phase. They are all at different densities so by aspirating the
aqueous portion, the RNA can be extracted. However, TRIzol is expensive and RNA pellets can
be difficult to resuspend for further use.
This article is beneficial because it contains each step of the procedure that was used in
analyzing the efficacy of Triptolide. The researcher isolated the RNA of the cell knockout lines
using this operation so this article is essential because further replications of the experiment can
be made in the future.

Shalem O, Sanjana NE, Hartenian E, et al. Genome-scale CRISPR-Cas9 knockout screening in

human cells. Science. 2014;343(6166):84-87.

This scholarly article details a new method for knocking out different genes to create
different cell-lines. The process still involves CRISPR-Cas9 like the standard procedure but has a
broader use. While the standard CRISPR procedure is implemented for small cell samples
in-vitro, the new procedure can knockout entire genomes. This procedure can be used for large
cell samples and cell-variants in the near future.
This article is helpful but has its downsides. It does explain the molecular reasoning
behind CRISPR-Cas9 but it discusses a different method and procedure. However, the
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explanation is sufficient because all procedures share the same molecular reasoning. The
research utilized CRISPR to knock out certain genes and see which gene the triptolide had the
best transcription inhibitory effect on.

Sweeney, Christopher J., et al. “Chemohormonal Therapy in Metastatic Hormone-Sensitive

Prostate Cancer.” ​New England Journal of Medicine,​ vol. 373, no. 8, 2015, pp. 737–746.,
doi:10.1056/nejmoa1503747.

This featured research article summarizes the effectiveness of a common treatment for
prostate cancer. It also introduces an experiment that analyzes the effectiveness of common
chemotherapy medication with the addition of alternative medications. Chemotherapy is one of
the most effective and regular treatments prescribed to patients because it utilizes chemicals to
target cell growth, the main cause of cancer. Androgen-deprivation therapy has been the
foundational chemotherapeutic element of prostate cancer treatment because it attempts to
dispossess the prostate cells of androgens-the male sex hormones which stimulate growth. The
experiment also evaluated a new medication derived from plant-based ingredients called
“docetaxel,” by comparing the lifespan of those with docetaxel and those without.
This paper is important because it introduces medications that are commonly used in
prostate cancer treatment and analyzes the effectiveness of such medications compared to others.
It also summarizes the chemical processes involved in prostate cancer chemotherapy treatment
and includes information about the reasoning behind chemotherapeutic treatment.

Titov, D. V., Gilman, B., He, Q., Bhat, S., Low, W., Dang, Y., . . . Liu, J. O. (2011). XPB, a
subunit of TFIIH, is a target of the natural product triptolide. ​Nature Chemical
Biology,7​(3), 182-188. doi:10.1038/nchembio.522

Natural products have played an important role in the discovery and development of
drugs. In recent years, they have also become important molecular probes for studying different
cellular processes by virtue of their ability to bind to specific protein targets and interfere with
their cellular functions. This scientific article studies a specific natural inhibitor called triptolide,
which has commonly been used by Chinese medical practitioners to combat autoimmune
diseases. The study they conducted was on the biochemistry and physiology behind the
inhibiting process as it has long been unknown as to how triptolide operated. The study revealed
that triptolide covalently binds to human XPB, a subunit of the transcription factor TFIIH, and
inhibits its DNA-dependent ATPase activity. This leads to the inhibition of RNA polymerase
II-mediated transcription and likely nucleotide excision repair.
This study is important because it reveals the essential part that causes cancer cells’
overexpression of transcription and replication. The identification of XPB as the target of
triptolide accounts for the majority of the known biological activities of triptolide. These findings
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also suggest that triptolide can serve as a new molecular probe for studying transcription and,
potentially, as a new type of anticancer agent through inhibition of the ATPase activity of XPB.
It reveals the process behind natural inhibitors. Furthermore, the article contains quality
depictions of the molecular process in the inhibition. These illustrations simplify the concept and
benefit it.

Tovar CL, Zerón HM. Cell Culture Models and Pharmacological Perspective for the Study of
Breast Cancer Markers. EJIFCC. 2013;24(2):53-60. Published 2013 Jul 16.
doi:10.1371/journal.pone.0012860.

This scholarly article aims to analyze the importance of Cell-culturing in breast cancer
treatment. The author explains its relevance in advancing treatments for Breast cancer, which is
strongly correlated with other types of cancer as well. It also details the relevance of
cell-culturing in detection as well which can result in an accurate diagnosis of patients’
condition. The article also mentions different types and methods of cell-culturing as well as
future implications and obstacles that can be encountered.
Although the article is evaluating Breast Cancer as opposed to Prostate cancer and thus
contains periods of irrelevant information, it is helpful in that it explains the value of
cell-culturing in all types of cancer and pharmacological research. Breast cancer ties in very
closely with other cancers so it explains in a manner that can be easily understood. Furthermore,
it provides valuable evidence for the importance of cell-culturing and exemplifies how it can be
incorporated into studies analyzing compounds such as the one the researcher is currently
undergoing.

Widmark, Anders. "Endocrine treatment, with or without radiotherapy, in locally advanced

prostate cancer (SPCG-7/SFUO-3): an open randomised phase III trial." ​The Lancet,​ vol.
373, no. 9660, 16 Dec. 2008.

This investigative article discusses endocrine treatment of prostate cancer, which is a

variation of androgen-deprivation treatment. While androgen-deprivation therapy primary goal is
to deprive and block the synthesization of hormones, endocrine treatment is broader and can
block, add, or remove chemicals to reduce prostate cancer cell growth and progression.
Furthermore, the source also evaluates the effectiveness of endocrine treatment with radiotherapy
and possibly castration in high-risk cancer, which has long been perceived as the best treatment.
The trial analyzed citizens from Scandinavia, so there were fewer variables and measured the
survival rate to evaluate the effectiveness of the treatment.
Despite the treatment being summarized as much more effective due to halving the
10-year mortality rate, it possessed adverse side effects such as cardiometabolic problems and
osteoporosis that can potentially counteract the benefits of hybrid hormonal therapy.
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Wu BY, Wang HF, Chen JT, Yan XP. Fluorescence resonance energy transfer inhibition assay
for α-fetoprotein excreted during cancer cell growth using functionalized persistent
luminescence nanoparticles. J Am Chem Soc. 2011;133(4):686-8.

This scholarly article explains the positive implications a new form of study can bring
about. Although luminescence of particles has been a widespread technique to analyze cells, the
development of nanoparticles can bring about numerous benefits. The study explains these
benefits by referring to their data collection and study on the fluorescence assay of a specific
protein, the α-fetoprotein. Α-fetoprotein is exocytosed by cancer cells so by measuring their
fluorescence rate and complexity of cancer growth can be evaluated. The α-fetoprotein is binded
to an agent and by doing so releases light that can be measured.
Although the article is focused heavily on explaining the data and reasoning what it
means, they do include explanations behind luminescence use. They tie it into cancer growth, but
the inverse can also be said. Luminescence can also evaluate cell deterioration in drug-treated
cell samples.

Zhe, X., Cher, M. L., & Bonfil, R. D. (2011). Circulating tumor cells: finding the needle in the
haystack. American journal of cancer research, 1(6), 740-51.

This scholarly article published in a renown medical journal explains the presence of
Circulating tumor cells (CTC) and how they can be used in prognosis and treatment. Circulating
tumor cells can be detected in the bloodstream meaning they are easily obtainable and data can
be collected easy. Furthermore, blood collection is an efficient means of extracting cell samples.
While blood sampling is the main procedure, the authors refer to other methods of extraction and
CTC detection. They explain how they collect and evaluate the presence of cancer cells and how
they can use this data to infer the degree of metastasis and severity of cancer. They also connect
it to clinical medicine and what this can mean for future means of prognosis.
This article is valuable because it explains how cancer cells can be obtained and detected.
This detection is imperative for the experiments involved in the researcher’s study on Triptolide
because they can be replicated to visualize cell-decay caused by Triptolide’s inhibitory effect.
Although the researcher typically utilizes standard procedures such as PCR and reverse
transcriptase, the article alludes to future methods that can be utilized later on.

Zhu, Y., Sharp, A., Anderson, C. M., Silberstein, J. L., Taylor, M., Lu, C., . . . Luo, J. (2018).
Novel Junction-specific and Quantifiable In Situ Detection of AR-V7 and its Clinical
Correlates in Metastatic Castration-resistant Prostate Cancer. ​European Urology,73(​ 5),
727-735. doi:10.1016/j.eururo.2017.08.009
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This article refers to the Androgen receptor splice variant 7 (AR-V7), which has been
reasoned as the source of resistance to certain cancer treatment drugs. It has been implicated in
resistance to abiraterone and enzalutamide treatment in men with metastatic castration-resistant
prostate cancer (mCRPC). However, the detection of AR-47 is limited due to the assay’s
capacity in situ detection. The research addressed in the article and carried out by the researchers
aims to address current limitations in the precision measurement of AR-V7 in developing a novel
junction-specific AR-V7 RNA in situ hybridization (RISH) assay compatible with automated
quantification.