IISER Bhopal: strategies to fight breast cancer
The first study of DNA methylation causing alternative splicing in cancer cells
Inhibiting the growth and accelerating the death rate of breast cancer cells may be possible by starving the cancer cells of glucose or by inhibiting the energy production process (aerobic glycolysis). Aerobic glycolysis confers a proliferative advantage to the cancer cells. The results were published in the Proceedings of the National Academy of Sciences.
A team of researchers led by Dr. Sanjeev Shukla from the Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, has been able to reverse aerobic glycolysis by inhibiting DNA methylation or reducing the expression of BORIS (Brother of Regulator of Imprinted Sites) gene.
Alternative splicing
In normal cells, exon 9 gets included while exon 10 is excluded when precursor messenger RNA (pre-mRNA) is spliced or edited into mature messenger RNA (mRNA). The researchers found that splicing was different in the case of cancer cells — instead of exon 9, exon 10 gets included when the pre-mRNA is spliced into mRNA. “The methylation at exon 10 allows BORIS to bind to the exon 10 and leads to the inclusion of exon 10 in the mature mRNA,” says Dr. Shukla. “Due to aberrant alternative splicing, exon 10 gets included in the mature mRNA leading to the formation of PKM2, a cancer-specific isoform of pyruvate kinase.”
The PKM2 isoform is seen in cancer cells and is responsible for proliferation of cancer due to aerobic glycolysis while the PKM1 isoform is found in normal cells. The DNA methylation along with BORIS regulates the switch from PKM1 to PKM2 isoform.
This is the first time DNA methylation causing alternative splicing in cancer cells has been studied. DNA methylation also silences tumour suppressor genes.
“The BORIS gene is predominantly expressed in germ cells and gets over-expressed in cancer cells but not in somatic cells. So BORIS is a potential target for cancer therapy,” says Dr. Shukla.
The team studied two breast cancer cell lines and found increased exon 10 in both cancer cell lines but exon 9 was found to be increased in normal, primary cells. The presence of exon 10 in breast cancer cell lines led to higher expression of cancer-specific PKM2 isoform.
Unlike in normal breast tissue, the researchers found overexpression of BORIS in breast cancer subtypes in the Cancer Genome Atlas and Oncomine.
Potential targets
Inhibition of DNA methylation led to reduced binding of BORIS at exon 10 leading to reduced exon 10 and increased exon 9 in the mature mRNA. There was also a reduction in the cancer-specific PKM2 isoform and increase in the PKM1 isoform.
Similarly, depletion of BORIS gene led to reduced BORIS binding and decreased inclusion of exon 10 with a concomitant increase in exon 9 inclusion.
To rule out other factors responsible for alternative splicing of PKM, the researchers mutated the BORIS binding site at the PKM exon 10 region. “There was reduced exon 10 and increased exon 9 in the mutant cells. Also, there was reduced BORIS enrichment which resulted in reduced exon 10 inclusion in the mutant cells,” Dr. Shukla says.
As predicted, BORIS depletion reduced the consumption of glucose in breast cancer cells. Inhibition of DNA methylation, too, decreased glucose uptake. Interestingly, BORIS depletion went beyond reduction in glucose consumption — it resulted in reduced cancer cell growth and cell viability.
“When BORIS is down regulated it affects alternative splicing of several genes which are associated with cancer hallmark (cancer growth, reduced apoptosis abnormal metabolism). So targeting BORIS will have a great impact for cancer therapy,” says Smriti Singh from the Department of Biological Sciences, IISER, Bhopal, and the first author of the paper. “BORIS binds after DNA methylation. So we must determine whether inhibiting DNA methylation or BORIS is more effective in cancer therapy.”
Herpes treatment could be the key to curing deadliest brain cancers
THE solution to stopping an incurable brain tumour could lie with a drug now used to treat a common herpes virus.
Australian scientists are hoping to trial this, but desperately need funding from the government.
Cytomegalovirus (CMV) is a member of the herpes family that is present in half of all adults, although it shows no signs or symptoms as a healthy immune system keeps it in check.
In a major breakthrough, researchers at Duke University in the US have found this virus concentrates in the lethal brain tumour glioblastoma. By using a vaccine to attack the CMV, the Duke University trial has prolonged the lives of the trial subjects four-fold.
Three of the 11 patients are still alive and others lived for more than five years, compared to the average of 15 months post-diagnosis with glioblastoma.
University of NSW Associate Professor Kerrie McDonald said CMV proteins were abundant in glioblastoma tumours but absent in surrounding brain cells.
Her team has found a peptide (an amino acid) that can attack the CMV proteins and therefore attack the tumour without harming surrounding brain tissue.
“Because CMV concentrates in the tumour, it is a viable target and it’s a small peptide so it crosses the blood-brain barrier,” Prof McDonald said.
RELATED VIDEO
John McCain insists cancer diagnosis hasn't changed him
Mother-of-five Felicity Plew was diagnosed with glioblastoma in May this year. Her baby son Jesse was delivered at 33 weeks so that she could have surgery to remove 80 per cent of the tumour.
The 32-year-old has not responded to chemotherapy or radiotherapy and her husband Simon said the tumour had grown back.
“Flip is having surgery again tomorrow (Monday) to have more tumour removed because it has grown back to 4cm. We’ve asked what else there is in the world and we’ve been told if we want further treatment, like experimental treatment, we have to go overseas and you’re up for hundreds of thousands of dollars,” Mr Plew said.
The surgery was to “buy time”, Mr Plew said, adding he hoped such a trial could come to Australia.
Simon, and children, Alexander, 8, Gracie, 6, Sophia, 4, Charlie, 2 and baby Jesse are by Felicity’s side praying for a cure.
As is the case with most new brain cancer treatments, Prof McDonald needs funding and is applying for government grants of up to $1.5 million to run a peptide trial next year.
“We need money to run the trial with 26 adult brain cancer patients next year. The adult trial will be first but then we want to trial it on children, which will be funded by the Love For Lachie foundation,” she said.
Lachie Muldoon, 10, died of glioblastoma brain cancer in October 2015 and his parents set up the foundation to fund potential cancer treatments.
“I strongly believe this trial will work in patients and I’m confident we will see patient survival shift,” Prof McDonald said.
Brain cancer remains the number one disease killer of children and survival rates have not changed in three decades due to a lack of funding for research.
The current Senate Inquiry into Funding For Research Into Cancers With Low Survival Rates has heard that research funding from the National Health and Medical Research Council goes mainly to high-profile cancers. Dozens of applications for brain cancer research get knocked back each year.
* To help the Plew family, donate at gofundme.com/felicity-simon-fight-brain-cancer or help fund brain cancer research at loveforlachlie.com.au
Scientists reveal the relationship between sugar, cancer
A nine-year joint research project conducted by VIB, KU Leuven and VUB has led to a crucial breakthrough in cancer research. Scientists have clarified how the Warburg effect, a phenomenon in which cancer cells rapidly break down sugars, stimulates tumor growth. This discovery provides evidence for a positive correlation between sugar and cancer, which may have far-reaching impacts on tailor-made diets for cancer patients. The research has been published in the leading academic journal Nature Communications.
This project was started in 2008 under the leadership of Johan Thevelein (VIB-KU Leuven), Wim Versées (VIB-VUB) and Veerle Janssens (KU Leuven). Its main focus was the Warburg effect, or the observation that tumors convert significantly higher amounts of sugar into lactate compared to healthy tissues. As one of the most prominent features of cancer cells, this phenomenon has been extensively studied and even used to detect brain tumors, among other applications. But thus far, it has been unclear whether the effect is merely a symptom of cancer, or a cause.
Sugar awakens cancer cells
While earlier research into cancer cell metabolism focused on mapping out metabolic peculiarities, this study clarifies the link between metabolic deviation and oncogenic potency in cancerous cells.
Prof. Johan Thevelein (VIB-KU Leuven): "Our research reveals how the hyperactive sugar consumption of cancerous cells leads to a vicious cycle of continued stimulation of cancer development and growth. Thus, it is able to explain the correlation between the strength of the Warburg effect and tumor aggressiveness. This link between sugar and cancer has sweeping consequences. Our results provide a foundation for future research in this domain, which can now be performed with a much more precise and relevant focus."
Yeast as an advantageous model organism
Yeast cell research was essential to the discovery, as these cells contain the same 'Ras' proteins commonly found in tumor cells, which can cause cancer in mutated form. Using yeast as a model organism, the research team examined the connection between Ras activity and the highly active sugar metabolism in yeast.
Prof. Johan Thevelein (VIB-KU Leuven): "We observed in yeast that sugar degradation is linked via the intermediate fructose 1,6-biophosphate to the activation of Ras proteins, which stimulate the multiplication of both yeast and cancer cells. It is striking that this mechanism has been conserved throughout the long evolution of yeast cell to human.
"The main advantage of using yeast was that our research was not affected by the additional regulatory mechanisms of mammalian cells, which conceal crucial underlying processes. We were thus able to target this process in yeast cells and confirm its presence in mammalian cells. However, the findings are not sufficient to identify the primary cause of the Warburg effect. Further research is needed to find out whether this primary cause is also conserved in yeast cells."
Journal Reference:
- Ken Peeters, Frederik Van Leemputte, Baptiste Fischer, Beatriz M. Bonini, Hector Quezada, Maksym Tsytlonok, Dorien Haesen, Ward Vanthienen, Nuno Bernardes, Carmen Bravo Gonzalez-Blas, Veerle Janssens, Peter Tompa, Wim Versées, Johan M. Thevelein. Fructose-1,6-bisphosphate couples glycolytic flux to activation of Ras. Nature Communications, 2017; 8 (1) DOI: 10.1038/s41467-017-01019-z
Immunotherapy is the newest weapon in the fight against cancer
The human immune system is both clever and powerful. But it is often foiled by cancer’s wily ways.
A new approach to cancer treatment — immunotherapy — aims to unmask the disease for the deadly threat it is, then direct the full force of the immune system on malignancies that would otherwise grow and spread unchecked.
Our multilayered immune defenses spot most foreign invaders and crush them decisively. But cancer, arising out of one or more mutations in our DNA, is a home-grown threat with a deceptively reassuring look. Even as cells multiply and spread, malignant cells cloak themselves in innocent garb.
Confused, the immune system pulls back its talons. And cancer has its way with us.
Immunotherapy can change this.
It stems from a growing understanding of how cancers start, grow and protect themselves from both medicines and our bodies’ natural defenses. It also capitalizes on researchers’ efforts to unpack the exquisite complexity of the immune system, including when and why it retreats from a fight.
The first generation of immunotherapy drugs is designed to release the “brakes” that inhibit the immune system from attacking cancers. By various means, they block an antibody that spares cancer cells from a sentence of “programmed death” issued by the immune system.
These so-called PD-1 blockers are the first of a class of immune checkpoint inhibitors. They are used to treat a wide range of advanced malignancies, including melanomas and cancers of the lung, breast, colon, bladder, thyroid and endometrium.
The first checkpoint inhibitor, a medication called Yervoy (ipilimumab), was approved for U.S. patients in 2011. The drug improved survival time for patients with metastatic melanoma from an average of six months to 10 months. Next came Opdivo (nivolumab) in 2014, which extended survival for patients with certain head and neck cancers, small-cell lung cancers, Hodgkin lymphoma, and some advanced colorectal cancers.
Half a dozen more immunotherapy drugs followed, including Keytruda(pembrolizumab) for lymphoma, metastatic head and neck cancers, non-small cell lung cancers and advanced melanoma.
These drugs tend to help more patients than standard therapy does, and with less punishing side effects. They extend average survival in large groups of patients — sometimes just by months, but generally by spans that are considered meaningful.
And for a small subset of patients whose prognosis is bleak, these drugs can drive cancer into outright remission. This is what instills the greatest hope in cancer doctors.
The approach doesn’t work for everybody. In rare cases, it sends the immune system into overdrive — a complication that can be uncomfortable at best and fatal at worst. This summer, the FDA halted a clinical trials in which Keytruda was being tested in conjunction with some other immune-boosting drugs to treat multiple myeloma, citing an increased risk of death.
The prices for these drugs is another drawback. Both Opdivo and Keytruda can cost $150,000 per year, a bill insurers are reluctant to pay and one that makes bioethicists concerned about unequal access.
Still, the drugs’ overall impact is clear, said Dr. Antoni Ribas, a melanoma specialist at UCLA who has conducted clinical trials on Keytruda. Immunotherapy drugs, he said, “are changing how we treat cancer.”
Just ask Kathy Thomas.
Five years ago, she was fighting a losing battle against metastatic melanoma that had spread to her breast, brain, lungs and liver. Her doctors feared she wouldn’t live to see the birth of her grandson.
Then she enrolled in one of Ribas’ clinical trials of Keytruda. Monthly infusions have made her cancer undetectable.
Last month, she celebrated her grandson’s fifth birthday.
“I would not be here if not for this drug,” said Thomas, 62.
Her experience is hardly unique. In an ongoing trial called Keystone, drug maker Merck & Co. reported this summer that close to 42% of subjects with metastatic melanoma who received Keytruda were still alive four years into the study. Some 13% of the subjects who received Keytruda had a “complete response,” and most had ceased taking the medication.
When Ribas started as an oncologist 18 years ago, “maybe one in 20 patients” lived for more than a year after being diagnosed with metastatic melanoma, he said. Now, thanks to immunotherapy drugs, “more than a third of my patients are living normal lives.”
Some cancers have proved more resistant to immunotherapy than others. Those that tend to afflict children or have weak ties to modifiable risk factors like smoking, obesity, poor diet and pollution can’t be stopped just by lifting the immune system’s brakes. To fight these cancers, the body seems to need a more specific assist.
Enter CAR-T cells.
For this approach, doctors start by harvesting a cancer patient’s T-cells, the warriors of the immune system. Scientists genetically engineer the cells to home in on the patient’s cancer and then grow millions of the modified cells in the lab. When the cells (now called chimeric antigen receptor cells, or CAR-T cells for short) are returned to the patient, they are much better equipped to hunt down and kill the cancer cells wherever they may hide.
So far, only one CAR-T immunotherapy treatment has been approved for use by the Food and Drug Administration — Kymriah, a drug designed to treat children and young adults with B-cell acute lymphoblastic leukemia who didn’t respond to standard treatment, or who suffered a relapse. Researchers tested it in 88 such patients ages 3 to 23, and it produced remission in 73 of them.
When FDA Commissioner Scott Gottlleib announced Kymriah’s approval in August, he predicted that many more CAR-T immunotherapies would follow. Dozens are currently in the pipeline, mainly aimed at treating cancers of the blood and lymph systems.
Dr. Crystal L. Mackall, a pediatric cancer specialist at Stanford, predicts that such “living drugs” will be “the beginning of a new era in medicine.” She calls them “the next frontier” in fighting cancer.
Pills and injections can target the processes by which cancers start and grow, said Mackall, who directs Stanford’s Parker Institute for Cancer Immunotherapy. But the effects of these treatments inevitably wane, and they must be renewed with another pill or injection.
“Cells can do things that drugs can’t do,” she said. “We’ve seen the dramatic effects of turning your cells into small machines, and this is just the beginning. They can be so much more sophisticated.”
Dr. Svetomir Markovic, an immunologist at the Mayo Clinic in Rochester, Minn., who specializes in melanoma, shares Mackall’s optimism.
“In many ways, we’re at the end of the beginning of immunotherapy: There’s clear benefit, but it’s still a minority of patients that get long-term benefit,” Markovic said. “We will get better at this.”
Subscribe to:
Posts (Atom)