Using a genetic signature to overcome chemotherapy-resistant lung cancer

Patients with non-small cell lung cancer (NSCLC) often respond to standard chemotherapy, only to develop drug resistance later, and with fatal consequences. But what if doctors could identify those at greatest risk of relapse and provide a therapy to overcome or avoid it?

Researchers at UT Southwestern Medical Center believe they have an answer: a 35-gene signature that identifies tumor cells most likely to develop resistance to treatment. The study, published today in Cell Reports, points to a new pharmacologic approach to target chemo-resistant lung cancer and even prevent development of such resistance in the first place.

Cancer relapse after chemotherapy poses a major obstacle to treating lung cancer, and resistance to chemotherapy is a big cause of that treatment failure,” said study co-author Dr. John Minna, a Professor and Director of in the Hamon Center for Therapeutic Oncology Research at UT Southwestern. “These findings provide new insights into why resistance develops and how to overcome it.

Dr. Minna, with additional appointments in Pharmacology and Internal Medicine, also holds the Sarah M. and Charles E. Seay Distinguished Chair in Cancer Research and the Max L. Thomas Distinguished Chair in Molecular Pulmonary Oncology. Investigators studied mouse and cellular models of NSCLC, a type of lung cancer that the American Cancer Society estimates accounts for 85 percent of all lung cancer cases in the United States.

Previous studies have shown that up to 70 percent of those cancers develop resistance to standard therapy, such as the platinum-taxane two-drug combo that is often given,” said study senior author Dr. Elisabeth D. Martinez, Assistant Professor of Pharmacology and in the Hamon Center. Both she and Dr. Minna are also members of UTSW’s Harold C. Simmons Comprehensive Cancer Center.

Using long-term on/off drug cycles, lead author and former postdoctoral researcher Dr. Maithili Dalvi developed a series of cellular models of progressive tumor resistance to standard chemotherapy that ranged from very sensitive to highly insensitive. Next, the researchers identified genes commonly altered during the development of resistance across multiple cell line and mouse models and identified a 35-gene signature that indicated a higher genetic likelihood of chemotherapy resistance.

It’s like a fingerprint for resistance,” Dr. Martinez said, adding that it was predictive in both cells and mouse models.

Next, they compared this resistance biomarker using genetic profiles from human tumors in their National Cancer Institute (NCI) lung cancer Specialized Programs of Research Excellence (SPORE) database at UT MD Anderson Cancer Center in Houston. The database contained information on patient outcomes and those who had been treated with the two-drug chemotherapy. The genetic fingerprint for resistance correlated with cancer relapse in NSCLC patients in the database, she said.

Researchers discovered that as cancer cells developed greater resistance to chemotherapy, they progressively made higher amounts of enzymes called JumonjiC lysine demethylases. Dr. Martinez said these enzymes facilitate resistance by changing the expression of – or turning on and off – genes.
Cancer cells use these enzymes to change, or reprogram, gene expression in order to survive the toxic stress of the chemotherapy. By changing the expression of genes, the tumor cells can adapt and survive the toxins,” she said.

Investigators then tested two potential drugs, both JumonjiC inhibitors. One of them, JIB-04, was found by UT Southwestern researchers in the Martinez lab during a small-molecule screen conducted at the National Center for Advancing Translational Sciences’ Chemical Genomics Center in Bethesda, Maryland.

I believe this is the first report of NSCLC tumors taking advantage of multiple JumonjiC enzymes to reprogram gene expression in order to survive chemotoxic stress. In addition, and this is the most fascinating part: Dr. Dalvi found that greater chemotherapy resistance defines a new susceptibility to the JumonjiC inhibitors,” she said. “The cancer cells develop a new Achilles’ heel that we can hit.”

Because the chemo-resistant cancer cells are dependent on JumonjiC enzymes for survival, inhibiting those enzymes returns cancer cells to mortality and vulnerability to cell death, she explained.
We think these JumonjiC inhibitors have the potential to be used either to treat tumors once they become resistant to standard therapies, or to prevent resistance altogether,” she said. “In our experiments these inhibitors appear to be much more potent in killing cancer cells than normal cells.”

Later, researchers tested whether the Jumonji inhibitors JIB-04 or GSK-J4 prevented chemotherapy resistance. This strategy succeeded in cell cultures and partially prevented resistance in animal models, Dr. Martinez said.

Dalvi et al. Taxane-Platin-Resistant Lung Cancers Co-develop Hypersensitivity to JumonjiC Demethylase Inhibitors.Cell Reports, 2017;19:1669–1684 [Article]

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The intestine has a reservoir of stem cells that are resistant to chemotherapy

These comprise a small group of passive stem cells -quiescent- that are activated when needed and have the capacity to produce any kind of intestinal cell. Quiescent cells are relevant for tissue regeneration and for participation in tumor development.

After Chemotherapy, these cells change their behaviour, become active and regenerate all cell types in the intestine (in green). CREDIT Franscisco Barriga, IRB Barcelona


The intestine has a high rate of cellular regeneration due to the wear and tear originated by its function degrading and absorbing nutrients and eliminating waste. The entire cell wall is renewed once a week approximately. This explains why the intestine holds a large number of stem cells in constant division, thereby producing new cell populations of the various types present in this organ.

Researchers at the Institute for Research in Biomedicine (IRB Barcelona) headed by ICREA investigator Eduard Batlle, head of the Colorectal Cancer Laboratory, have discovered a new group of intestinal stem cells with very different characteristics to those of the abundant and active stem cells already known in this organ. Performed in collaboration with the Centro Nacional de Análisis Genómico (CNAG-CRG), the study has been published in Cell Stem Cell. These new group of stem cells are quiescent, that is to say, they do not proliferate and are apparently dormant.

The researchers describe them as a reservoir of stem cells–it is estimated that there is one quiescent cell for every 10 active intestinal stem cells. In healthy conditions, these cells have no apparent relevant function. However, they are important in situations of stress, for example, after chemotherapy, in inflammatory processes, and in tissue infections–all conditions in which the population of “normal/active” stem cells is depleted. These quiescent cells would serve to regenerate the organ by giving rise to the various types of cells present in the intestine, renewing the population of “normal/active” stem cells, and restoring balance to the tissue.

Eduard Batlle explains that the discovery of quiescent stem cells in the intestine reveals that stem cell biology is more complex that previously appreciated and that it does not follow ahierarchical model of cell organisation. “In intestinal cell hierarchy, there are no cells above others, so the two populations are in a continual balance to ensure the proper function of the organ“.

Most drugs against cancer have a secondary effect on the cells that are dividing in our tissues. “Because quiescent stem cells divide infrequently, they are resistant to many types of chemotherapy and they regenerate the tissue that this treatment has damaged,” explains Eduard Batlle, head of one of the labs of international prestige in research into intestinal stem cells and their involvement in colorectal cancer.

Quiescent cells are present in many kinds of tissue. However, in spite of their relevance in tissue regeneration, increasing evidence points to their involvement in tumour development. “It is difficult to study these cells, mainly because they are scarce and there are technical limitations with respect to monitoring, straining and distinguishing them from the others,” explains Francisco Barriga, first author of the study and current postdoctoral fellow at the Memorial Sloan Kettering Cancer Center in New York.

Using advanced techniques, such as genetic tracing of cell lineages and transcriptomic analysis of individual cells, performed by CNAG-CRG and the Bioinformatics and Biostatistics Unit at IRB Barcelona, the group has identified the distinct genetic programme used by quiescent stem cells with respect to normal intestinal ones. This work has been done over six years.

The researchers have labelled this cell population with a specific marker, the Mex3a protein, which has allowed them to track it over time. “We intend to continue studying quiescent stem cells in health and disease and to discover the function of the genes that distinguish them in the colon and in other organs,” says Batlle.

Barriga et al. Mex3a marks a slowly dividing subpopulation of Lgr5+ intestinal stem cells. Cell Stem Cell (2017). doi: 10.1016/j.stem.2017.02.007 [Abstract]

Avoid eating herring and mackerel during chemotherapy

Researchers found that consuming the fish herring and mackerel, as well as three kinds of fish oils, raised blood levels of the fatty acid 16:4(n-3), which experiments in mice suggest may induce resistance to chemotherapy used to treat cancer, according to a study published online by JAMA Oncology.

Patients with cancer often adopt lifestyle changes and those changes often include the use of supplements. But there is growing concern about the use of supplements while taking anticancer drugs and the possible effect on treatment outcomes, according to the study background.

Emile E. Voest, M.D., Ph.D., of the Netherlands Cancer Institute, Amsterdam, and coauthors examined exposure to the fatty acid 16:4(n-3) after eating fish or taking fish oil.

The authors examined the rate of fish oil use among patients undergoing cancer treatment, while researchers also recruited healthy volunteers to examine blood levels of the fatty acid after ingestion of fish oils and fish. The fish oil portion included 30 healthy volunteers and the fish portion included 20 healthy volunteers.

Among 118 cancer patients who responded to a survey about the use of nutritional supplements, 35 (30 percent) reported regular use and 13 (11 percent) used supplements containing omega-3 fatty acids, according to the results.

The study found increased blood levels of the fatty acid 16:4(n-3) in healthy volunteers after the recommended daily amount of 10 mL of fish oil was administered. An almost complete normalization of blood levels was seen eight hours after the 10-mL fish oil dose was given, while a more prolonged elevation resulted after a 50-mL dose, according to the results.

Eating 100 grams of herring and mackerel also increased blood levels of 16:4(n-3) compared with tuna, which did not affect blood levels, and salmon consumption, which resulted in a small, short-lived peak.

Taken together, our findings are in line with a growing awareness of the biological activity of various fatty acids and their receptors and raise concern about the simultaneous use of chemotherapy and fish oil. Based on our findings, and until further data become available, we advise patients to temporarily avoid fish oil from the day before chemotherapy until the day thereafter,” the study concludes.

Daenen et al. Increased plasma levels of chemoresistance-inducing fatty acid 16:4(n-3) after consumption of fish and fish Oil. JAMA Oncol. 2015. doi:10.1001/jamaoncol.2015.0388 [Article]