Stimulated Raman Histology and Machine learning provides an alternative approach in brain tumor diagnosis

The study published in Nature Medicine examined the diagnostic accuracy of brain tumor image classification through artificial intelligence tool, compared with the accuracy of pathologist interpretation of conventional histologic images. The results for both methods were comparable: the artificial intelligence based diagnosis was 94.6% accurate, compared with 93.9% for the traditional pathologist-based assessment and interpretation. This research was conducted at NYU Langone Health.

The imaging technique known as stimulated Raman histology (SRH), reveals tumor infiltration in human tissue by collecting scattered laser light, illuminating essential features not typically seen in standard histologic images. Using deep convolutional neural network (CNN) with more than 2.5 million samples from 415 patients researchers trained a machine-learning algorithm to classify tissue into 13 histologic categories that represent the most common brain tumors, including malignant glioma, lymphoma, metastatic tumors, and meningioma.

Researchers note advantages with this method include quicker and almost realtime results (two and half minutes) with this method compared to traditional pathological examination (twenty to thirty minutes). This can be very useful especially during intraoperative decision making. In addition, researchers found that diagnostic errors due to this method are different from traditional pathology and combining both methods would increase diagnostic accuracy to 100%.

Malaria drug Chloroquine helps fight treatment resistant brain cancer

After her brain cancer became resistant to chemotherapy and then to targeted treatments, 26-year-old Lisa Rosendahl’s doctors gave her only a few months to live. Now a paper published in the journal eLife describes a new drug combination that has stabilized Rosendahl’s disease and increased both the quantity and quality of her life: Adding the anti-malaria drug chloroquine to her treatment stopped an essential process that Rosendahl’s cancer cells had been using to resist therapy, re-sensitizing her cancer to the targeted treatment that had previously stopped working. Along with Rosendahl, two other brain cancer patients were treated with the combination and both showed similar, dramatic improvement.

The science behind the innovative, off-label use of this malaria drug, chloroquine, was in large part built in the lab of Andrew Thorburn, PhD, deputy director of the CU Cancer Center, where Mulcahy-Levy worked as a postdoctoral fellow, starting in 2009. Thorburn’s lab studies a cellular process called autophagy. Autophagy is a process of cellular recycling in which cell organelles called autophagosomes encapsulate extra or dangerous material and transport it to the cell’s lysosomes for disposal. In fact, the first description of autophagy earned the 2016 Nobel Prize in Medicine or Physiology for its discoverer, Yoshinori Ohsumi.

Mulcahy-Levy’s work with Thorburn (among others), showed that cancers with mutations in the gene BRAF, and specifically those with a mutation called BRAFV600E, were especially dependent on autophagy. In addition to melanoma, in which this mutation was first described, epithelioid glioblastomas are especially likely to carry BRAFV600E mutation.

With this new understanding, Mulcahy-Levy became an essential link between Thorburn’s basic science laboratory and the clinical practice of oncologist, Nicholas Foreman, MD, CU Cancer Center investigator and creator of the pediatric neuro-oncology at Children’s Hospital Colorado, who had been overseeing Lisa’s care.

After many surgeries, radiation treatments and chemotherapy, Lisa had started the drug vermurafenib, which was originally developed to treat BRAF+ melanoma and is now being tested in pediatric brain tumors. Lisa’s experience on the drug was typical of patients with BRAF+ cancers who are treated with BRAF inhibitors such as vemurafenib – after a period of control, cancer develops additional genetic mechanisms to drive its growth and survival and is able to progress past the initial drug.

At that point, one promising strategy is to predict and/or test for new genetic dependencies and then treat any new dependency with another targeted therapy. For example, many BRAF+ cancers treated with BRAF inhibitors develop KRAS, NRAS, EGFR or PTEN changes that drive their resistance, and treatments exist targeting many of these “escape pathways”. However, some cancers develop multiple resistance mechanisms and others evolve so quickly that it can be difficult to stay ahead of these changes with the correct, next targeted treatment.

“Pre-clinical and clinical experience invariably shows that tumor cells rapidly evolve ways around inhibition of mutated kinase pathways like the BRAF pathway targeted here,” the paper writes.

“However, based on our results, we hypothesize that by targeting an entirely different cellular process, i.e. autophagy, upon which these same tumor cells rely, it may be feasible to overcome such resistance and thus re-establish effective tumor control.”

In other words, knowing that Lisa Rosendahl’s tumor was positive for BRAFV600E mutation, and that this marked the tumor as especially dependent on autophagy – and also knowing that traditional options and even clinical trials were nonexistent – the group worked with Rosendahl and her father, Greg, to add the autophagy-inhibiting drug chloroquine to her treatment.

“In September 2015, the previous targeted drugs weren’t working anymore,” says Greg Rosendahl. “Doctors gave Lisa less than 12 months to live. We took all our cousins up to Alaska for a final trip kind of thing. Then they came up with this new combination including chloroquine.”

Vemurafenib had initially pushed Lisa’s cancer past the tipping point of survival. Then the cancer had learned to use autophagy to pull itself back from the brink. Now with chloroquine nixing autophagy, vemurafenib started working again.

“We have treated three patients with the combination and all three have had a clinical benefit. It’s really exciting – sometimes you don’t see that kind of response with an experimental treatment. In addition to Lisa, another patient was on the combination two-and-a-half years. She’s in college, excelling, and growing into a wonderful young adult, which wouldn’t have happened if we hadn’t put her on this combination,” Mulcahy-Levy says.

Research accompanying these results in patients implies that the addition of autophagy inhibition to targeted treatments may have benefits beyond glioblastoma and beyond only BRAF+ cancers.

Because chloroquine has already earned FDA approval as a safe and effective (and inexpensive) treatment for malaria, the paper points out that it should be possible to “quickly test” the effectiveness of adding autophagy inhibition to a larger sample of BRAF+ glioblastoma and other brain tumor patients, and also to possibly expand this treatment to other likely mutations and disease sites.

As Mulcahy-Levy’s early studies show, many cancers do not depend on autophagy. But at the same time, many do. Because a safe and simple drug already exists to inhibit autophagy, the time between discovering an autophagy-dependent cancer and the ability to add autophagy-inhibiting chloroquine to a treatment regimen against this cancer may be short.

Citation: Jean M Mulcahy Levy , Shadi Zahedi, Andrea M Griesinger, Andrew Morin, Kurtis D Davies, Dara L Aisner, BK Kleinschmidt-DeMasters, Brent E Fitzwalter, Megan L Goodall, Jacqueline Thorburn, Vladimir Amani, Andrew M Donson, Diane K Birks, David M Mirsky, Todd C Hankinson, Michael H Handler, Adam L Green, Rajeev Vibhakar, Nicholas K Foreman and Andrew Thorburn. “Autophagy inhibition overcomes multiple mechanisms of resistance to BRAF inhibition in brain tumors.” eLife  2017; 6:e19671.
DOI: 10.7554/eLife.19671
Research funding: National Institutes of Health, US Department of Defense, St. Baldrick’s Foundation.
Adapted from press release by University of Colorado.

Piperlongumine, chemical from Indian pepper plant inhibits enzyme in cancer cells

UT Southwestern Medical Center scientists have uncovered the chemical process behind anti-cancer properties of a spicy Indian pepper plant called the long pepper, whose suspected medicinal properties date back thousands of years. The study is published in the Journal of Biological Chemistry.

Dr. Westover’s lab used X-ray crystallography to create this molecular model of piperlongumine.
Credit: UT Southwestern

The secret lies in a chemical called Piperlongumine (PL), which has shown activity against many cancers including prostate, breast, lung, colon, lymphoma, leukemia, primary brain tumors, and gastric cancer.

Using x-ray crystallography, researchers were able to create molecular structures that show how the chemical is transformed after being ingested. Piperlongumine (PL) converts to hPiperlongumine (hPL), an active drug that silences a gene called GSTP1. The GSTP1 gene produces a detoxification enzyme Glutathione S-Transferase Pi 1 that is often overly abundant in tumors.

“We are hopeful that our structure will enable additional drug development efforts to improve the potency of PL for use in a wide range of cancer therapies,” said Dr. Kenneth Westover, Assistant Professor of Biochemistry and Radiation Oncology. “This research is a spectacular demonstration of the power of x-ray crystallography.”

Dr. Westover, a member of the Harold C. Simmons Comprehensive Cancer Center, used cutting edge technologies in UT Southwestern’s Structural Biology Core (SBC) – the University’s world-renowned facility for X-ray crystallography, to better understand the anticancer properties of Piperlongumine (PL). X-ray crystallography allows scientists to determine molecular structures that reveal how molecules interact with targets – in this case how Piperlongumine (PL) interacts with GSTP1. Viewing the structures helps in developing drugs for those targets.

Citation: Harshbarger, Wayne, Sudershan Gondi, Scott B. Ficarro, John Hunter, Durga Udayakumar, Deepak Gurbani, William Singer, Yan Liu, Lianbo Li, Jarrod A. Marto and Kenneth D. Westover. “Structural and Biochemical Analyses Reveal the Mechanism of Glutathione S-Transferase Pi 1 Inhibition by the Anti-cancer Compound Piperlongumine.” Journal of Biological Chemistry (2016): jbc-M116.
DOI: 10.1074/jbc.M116.750299
Research funding: V Foundation for Cancer Research, Welch Foundation, and Cancer Prevention and Research Institute of Texas.
Adapted from press release by UT Southwestern Medical Center.

New biomarker based on expression of SHOX2 gene for predicting survival in Gliomas

Researchers at UT Southwestern Medical Center have found a new biomarker for glioma, a common type of brain cancer, that can help doctors determine how aggressive a cancer is and that could eventually help determine the best course of treatment. The findings are published in EBiomedicine.

Researchers from the Harold C. Simmons Comprehensive Cancer Center found that high expression of a gene called SHOX2 predicted poor survival in intermediate-grade gliomas.  “As an independent biomarker, SHOX2 expression is as potent as the currently best and widely used marker known as IDH mutations,” said Dr. Adi Gazdar, Professor of Pathology in the Nancy B. and Jake L. Hamon Center for Therapeutic Oncology and a member of the Simmons Cancer Center.

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According to the National Cancer Institute, cancers of the brain and nervous system affect nearly 24,000 people annually. In 2013, there were an estimated 152,751 people living with brain and other nervous system cancer in the United States. The overall 5-year survival rate is 33.8 percent.
Knowing the probable survival status of an individual patient may help physicians choose the best treatment. In combination with IDH mutations or several other biomarkers, SHOX2 expression helped to identify subgroups of patients with a good prognosis even though other biomarkers had predicted a bad prognosis.

“Our findings are based on analysis of previously published studies. They will have to be confirmed in prospective studies, and their clinical contribution and method of use remain to be determined,” said Dr. Gazdar, who holds the W. Ray Wallace Distinguished Chair in Molecular Oncology Research.

Citation: “SHOX2 is a Potent Independent Biomarker to Predict Survival of WHO Grade II–III Diffuse Gliomas”. Yu-An Zhang1, Yunyun Zhou1, Xin Luo, Kai Song, Xiaotu Ma, Adwait Sathe, Luc Girard, Guanghua Xiao and Adi F Gazdar. EBioMedicine 2016 vol: 13 pp: 80-89.
DOI: 10.1016/j.ebiom.2016.10.040
Research funding: NIH
Adapted from press release by UT Southwestern Medical Center.