Rewriting the Book on Chemo-Resistant Cancers with a DNA Library

Newswise — Determining which strains of cancer will eventually become resistant to chemotherapy could be key in figuring out more effective and targeted forms of treatment. Finding the genes responsible for chemo-resistance is what Jeremy Chien, Ph.D., member of the Cancer Biology Program at The University of Kansas Cancer Center, is looking to do with an innovative system that draws inspiration from the early days of cancer gene research.

Two grants from the Department of Defense and the American Cancer Society will bolster his ongoing research into finding out why ovarian cancer is resistant to certain types of chemo and eventually identifying a different drug target. This would mean having a type of chemo resistant cancer would no longer be seen as an almost insurmountable roadblock in treating cancer. He’s doing this by creating what he calls a “genome-wide cancer toolkit” to determine which genes contribute to drug resistance.

“Our research focuses on the identification of “driver” genes in ovarian cancer,” Dr. Chien said. “In particular, we are interested in identifying genes that make cancer resistant to chemotherapy. Identifying these genes is a critical first step in targeting them to reverse chemotherapy resistance or make chemotherapy more effective.”

Dr. Chien is one of the few researchers working to create this particular kind of database for specific types of cancer and chemotherapeutic regimens. He noted other researchers are building libraries of tyrosine kinase mutations, which are focused just on those enzymes responsible for activating proteins. Many cancers with these mutations can be treated with tyrosine kinase inhibitors; however, some mutations cause resistance to inhibitor treatment.

Dr. Chien’s toolkit aims to look at the entire DNA of ovarian cancer, in this case, and figure out which genes are responsible for chemo resistance.

Drawing from genetic history

“Functional genomics” was first used in the early 1980s by Dr. Robert Weinberg, who discovered the first human oncogene - a gene that has the potential to cause cancer. Dr. Weinberg and his team used genomic DNA, which contains the entire genetic code for a cell that is passed on from one generation to the next from tumor cells and infected mouse fibroblast 3T3 cells. Mice 3T3 cells can reproduce indefinitely, but don’t initiate tumor growth, which helped Dr. Weinberg determine which injected genes were responsible for cancer causing abnormal cell growth.

Dr. Chien is using the same premise, but drawing from a wider pool of genetic information. His lab is instead extracting mRNA, which carries the blueprint of a protein from the cell’s DNA to its ribosomes that drive protein production, from 10 tumor samples of patients with chemo resistant ovarian cancer. Dr. Chien takes the mRNA from those tumor samples and then converts it into cDNA. This is the opposite of what normally occurs—RNA is formed from DNA. This reverse transcription process is used because he wants to express a specific protein in a cell that does not normally express in that protein.

This new cDNA is now placed in a pool cDNA expression library. Here the cDNA is put into host cells and all together they contain the RNA from the original tumor samples. Dr. Chien has deemed it a “genome-wide cancer toolkit.”

“It can be used to identify cancer genes that caused the transformed phenotype, those that promoted metastatic phenotypes or those that promoted drug resistance,” Dr. Chien said. “In our case, the phenotype we are looking for is drug-resistant, so we are interested in the genes that contribute to drug resistance.”

After the library’s creation, Dr. Chien can introduce the cDNA into an ovarian cancer cell line that is normally sensitive to chemo. From there, he is testing two types of chemo commonly used to treat ovarian cancer, carboplatin and taxol. After the treatment, the cells that are resistant to the drugs are extracted and the gene within can be sequenced and identified as chemo resistant.

From DNA to drug testing

The information collected from the cancer toolkit may be relevant to more than just helping treat ovarian cancer.

One of the major gene mutations found in ovarian cancer is in the p53 tumor suppressor gene. Dr. Chien knows a lot of these p53 mutations will be found in their library and could also be found in about 50 percent of other human cancers that also have a p53 mutation.

“So potentially whatever we find in regard to p53 may be applicable to other cancers,” he said.

After identifying the genes responsible for chemo-resistance using his toolkit, Dr. Chien can test already existing drugs or new therapies aimed at targeting these specific genes and give hope to people who cannot be treated successfully with the standard treatments.

He’s already excited about the potential treatment options for one candidate gene found in the toolkit.

“It’s a gene that may play a role in taxol resistance, which also happens to have a drug that can inhibit that gene,” says Dr. Chien. “It’s already out there being used to treat another disease; it just hasn’t yet been tested in treating ovarian cancer.“That is our hope—if we have a known drug for the candidate genes, we will start using it to treat cancer. Otherwise we will develop new drugs to target them.”

KU COLLABORATORSMegan Cooley, Ph.D., postdoctoral fellow at University of Kansas Medical Center, Department of Cancer BiologyJill Madden, Ph.D., postdoctoral fellow at University of Kansas Medical Center, Department of Cancer BiologyYanchun Guo, Ph.D., postdoctoral fellow at University of Kansas Medical Center, Department of Cancer BiologyYing Wan, Ph.D., postdoctoral fellow at University of Kansas Medical Center, Department of Cancer BiologyPingping Fang, MS, University of Kansas Medical Center Department of Pharmacology, Toxicology & TherapeuticsKay Minn, BS, lab managerLynn Magenheimmer, MS, research assistant

FUNDING SOURCESAmerican Cancer Society, Research Scholar (2014-2018)Department of Defense Ovarian Cancer Research Program, (2014-2016)National Science Foundation (2013-2015)University of Kansas Cancer Center Pilot GrantK-INBRE Pilot Award

RELEVANT PUBLICATIONSTargeting of mutant p53-induced FoxM1 with thiostrepton induces cytotoxicity and enhances carboplatin sensitivity in cancer cells. Zhang X, Cheng L, Minn K, Madan R, Godwin AK, Shridhar V, Chien J. Oncotarget. 2014 Nov 6.

Ovarian Cancer By the Numbers

45% of ovarian cancer patients survive five years or more after diagnosis.Taking oral contraceptives for 5 years or more can reduce the risk of developing ovarian cancer by about 50%.21,980 estimated new cases of ovarian cancer were diagnosed in 2014 alone.