Attacking cancer from all angles
Genomics
Attacking cancer from all angles

Brandon Mistretta and Asha Palat, both Ph.D. students at the University of Houston’s Department of Biology and Biochemistry, are working on novel ways to interfere with cancer cell signaling and, in the process, stop tumors from growing and metastasizing. Using next-generation sequencing (NGS) techniques, their aim is to develop more effective and more humane cancer therapies.

Asha Palat and Brandon Mistretta are looking into novel ways to fight cancer from different angles – to accomplish what they think is the key to treating the disease – with the help of FastSelect RNA Removal Kits to gain insights from challenging samples.

Coming from opposite ends of the globe – Mistretta from Buffalo, New York, and Palat, from Chennai, India – the two researchers experienced very similar situations when someone close to them was diagnosed with and treated for cancer: “Whether it’s you or someone you care about, it will change your world,” Brandon Mistretta says, thinking about his college roommate who had been diagnosed with cancer years before. “Having seen someone I care about go through cancer treatment, and the hardships he faced while doing it, I know how important it is to have better therapy options out there.”

That’s why both he and Palat joined the laboratory of Preethi Gunaratne, Ph.D., a researcher who worked directly on the National Cancer Institute’s Human Cancer Genome Atlas.

“Most cancer therapy approaches look at the tumor, not the microenvironment it grows in,” explains Palat. “By targeting the microenvironment, we have the opportunity to come up with therapies that can maybe even prevent cancer from occurring in the first place.”

Preethi Gunaratne, Ph.D.
is a professor in the Department of Biology and Biochemistry at the University of Houston, with a dual appointment at the Baylor College of Medicine’s Human Genome Sequencing Center. She contributed to the National Cancer Institute’s pioneering Cancer Genome Atlas Program; a massive database of cancer-related genetic information, which is helping researchers across the globe identify ways to better prevent, diagnose and treat various forms of cancer.

Moving beyond chemotherapy

While conventional treatments like chemotherapy can be effective in the earliest stages of cancer, they often don’t work as well with more advanced disease and a lot of patients don’t respond to these treatments at all. And the side effects – ranging from nausea to heart complications – can be daunting. “What’s needed are new therapies that don’t take that large of a toll on a person,” Mistretta says, “the main problem with chemotherapy is we are not seeing the success rates that we want, as well as it being a very harsh living situation for the patient. It also targets every cell in your body, so if you have a tumor cell, it can now progress to cancer even more because of the toxins that you are adding to your system.” As an alternative to chemotherapy, he is trying to figure out ways to use a patient’s own immune system to fight the cancer.

A treatment with limitations
A 2015 study led by Dr. Condeelis at the Albert Einstein College of Medicine in New York showed that transmembrane proteins (TMEM) loosen the normally tight connection that exists between endothelial cells during chemotherapy, creating a temporary opening in the wall of a blood vessel for the tumor cell to squeeze through and migrate to other parts of the body. Chemotherapy can also lead to a more aggressive form of cancer when the chemo-resistant tumors are the only ones remaining, and the treatment can even trigger new cancers to grow. Additionally, fat cells have been known to absorb commonly used chemotherapy drugs, removing the drug from the immediate environment around the tumor cells. In some cases, the fat cells break the drug down into a less potent form, potentially reducing its efficacy in treating the tumor.

Mistretta is specifically looking at T-cells, the fierce, fighting immune cells the human body relies on to attack all types of bodily invaders and damaged cells – including tumor cells. “Approximately one-third of the population will develop a cancer,” he starts to explain. “Two-thirds won’t because their immune systems are doing their job. We think, for those who are getting cancer, it is most likely due to the fact that T-cells can’t get into the tumor microenvironment. So I’m using NGS techniques to try to determine if there are T-cells that match the tumor cells in the body – and we think there are – and if so, how we could assist them into the tumor microenvironment so they can get to work.”

Brandon Mistretta
is a third-year doctoral student at the University of Houston’s Department of Biology and Biochemistry. He holds an undergraduate degree in Biology from the University of Buffalo.

The primary challenge in his research work is the fact that a lot of the cancer samples come in formalin-fixed paraffin-embedded (FFPE) blocks to help preserve the tissue. Removal of unwanted RNA from low-yield, FFPE RNA is especially challenging and can lead to further loss of sample. “FFPE blocks make the quality of RNA we can extract out pretty poor, which directly affects our sequencing,” says Mistretta. The presence of unwanted RNA species such as ribosomal RNA and globin mRNA in the RNA sample complicates RNA sequencing. Mistretta continues to explain that using the QIAseq FastSelect RNA Removal Kit allows him to easily remove unwanted RNA from those samples with a single pipetting step. “Fifteen minutes later, we are ready to prep the samples.”

“QIAseq FastSelect has really been phenomenal with the RNA sequencing in my project. The RNA was degraded and almost unusable, but QIAseq FastSelect really removes the ribosomal RNA in these degraded samples and has improved our sequencing libraries.”
Brandon Mistretta, University of Houston’s Department of Biology and Biochemistry

The QIAseq FastSelect RNA Removal Kit seamlessly integrates into QIAGEN’s suite of RNA-seq technologies, including the QIAseq UPX 3’ Transcriptome Kits for high-throughput 3' transcriptome NGS, the QIAseq miRNA Library Kit for small RNA sequencing and QIAseq Stranded RNA Library Kits for stranded whole transcriptome RNA sequencing – allowing researchers like Mistretta the ability to have a higher throughput of samples without sacrificing the quality of their data.

Intercepting the signals

Asha Palat is on a different track with her investigations and is targeting ways to disrupt the tumor microenvironment so cancer cells can’t get the nutrients they need to grow and proliferate.

Asha Palat
is a fifth-year doctoral candidate at the University of Houston’s Department of Biology and Biochemistry. She holds an undergraduate degree in Advanced Zoology and Biotechnology from the Women’s Christian College and a Master’s degree in Human Genetics from Sri Ramachandra University, both in Chennai, India.

“While Brandon’s work focuses on equipping the immune system with the means of tracking down the tumor and attacking it, I’m trying to directly intercept signals in the microenvironment to make the tumor more vulnerable for any kind of cancer therapy,” Asha says with an air of certainty. “I use a microRNA drug which reduces how much glucose the tumor can absorb, and these cells rely heavily on glucose to proliferate and metastasize.”

“By combining both of our approaches, the tumor environment is now more hospitable, and the immune cells are now equipped with the means to actually infiltrate into the tumor.”
Asha Palat, University of Houston’s Department of Biology and Biochemistry

Glucose absorption is vital for tumors to grow. If Palat can successfully derail a tumor cell’s ability to take in energy, it will weaken the cell, making the tumor microenvironment more welcoming to the immune invasion that Mistretta hopes to initiate. By attacking the problem from two different angles, the two researchers hope that novel immunotherapies could help all patients, regardless of their cancer type.

“If we can target cell metabolism to sensitize tumors to treatment, we can do that for all types of tumors,” says Palat. “Right now, many therapies are restricted to a single type of cancer or a specific type of mutation. Our approaches would be applicable to all patients.”

Tumor microenvironment
Tumors don’t grow in a vacuum. They depend on the body’s own resources to help them grow and metastasize to other parts of the body. The tumor microenvironment, or the neighboring blood vessels, immune cells and signaling molecules, can directly interact with cancerous cells. As such, the tumor can hijack these signals to help it thrive – or, if scientists understood such interactions better, they could potentially be harnessed to help fight off cancer cells before they spread.

Quality without sacrifice

Both Mistretta and Palat say they rely on QIAGEN products to help them with their research projects. The Gunaratne laboratory is actively using QIAGEN’s RNA and DNA extraction kits, the QIAcube, as well as various library preparation kits. But Mistretta, in particular, says that the QIAseq FastSelect RNA Removal Kit has been instrumental in advancing his research.

“Once QIAseq FastSelect is introduced, you are able to mix that with your RNA from the cells and it depletes all the ribosomal RNA that’s clogging up the system, vastly improving your results,” he says. “It’s incredibly easy to use too. It takes no time to add to a sample and then a quick 15-minute reaction takes care of all that ribosomal RNA. Using this kit saves me easily eight hours of benchwork, which allows us to be super high-throughput on our samples.”

“I don’t have a lot of cells remaining at the end of the experiment. So it’s important that the kit is good at extracting the RNA from a limited sample size. I found that QIAGEN Kits are great for this kind of extraction, and the quality of the RNA extracted is great as well.”
Asha Palat, University of Houston’s Department of Biology and Biochemistry

Palat explains that QIAGEN’s quality makes their RNA extraction kits the lab’s go-to product. “Nothing else matches the consistency, quality and concentration of RNA that I get from these kits,” she says. “And that’s important because, after treatment, I don’t have a lot of samples from which to collect the RNA. I need to efficiently extract it and know that I’ll have quality at the end.”

The combination of quality and more efficient workflows provided by various QIAGEN products allow both Mistretta and Palat to pursue their innovative research paths with greater ease – and will hopefully yield results that will provide the basis for more humane cancer treatments in the future. That is the ultimate goal for everyone in Gunaratne’s lab: To help provide safer and more effective cancer therapeutics for patients. Mistretta, for his part, says that if he can translate his work into a viable therapy, he will feel like he’s made a true difference: “It would be incredibly rewarding.”

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