Computer simulations help understand lung cancer drug resistance

Scientists from the Universities of Bristol and Parma, Italy, have used computer simulations to understand drug resistance to osimertinib. Findings of this study are published in journal Chemical Science.

Osimertinib works by binding to epidermal growth factor receptor (EGFR), which is over expressed in many tumors. EGFR is involved in a pathway that signals for cell proliferation, and so is a target for drugs. Blocking the action of EGFR (inhibiting it) can switch it off, and so is a good way to treat tumors. Osimertinib is used to treat non-small-cell lung cancer (NSCLC), in cases where the cancer cells have a particular (T790M) mutant form of EGFR.

Osimertinib drug resistance computer simulations
Credit: University of Bristol

Although patients generally respond well to osimertinib, most acquire drug resistance within one year of treatment, so the drug stops working. Drug resistance arises because the EGFR protein mutates, so that the drug binds less tightly. One such mutation, called L718Q, was recently discovered in patients in the clinic by the Medical Oncology Unit of the University Hospital of Parma. In this drug resistant mutant, a single amino acid is changed. Unlike other drug resistant mutants, it was not at all clear how this change stops the drug from binding effectively, information potentially crucial in developing new drugs to overcome resistance.

Using a range of advanced molecular simulation techniques which included modelling chemical step using combined quantum mechanics/molecular mechanics and recognition step using molecular dynamics simulations and free energy calculations.  These calculation gave researchers understanding of molecular basis for the drug resistance. Such knowledge could be exploited in future to find solution to problem.

Citation: Callegari, D., K. E. Ranaghan, C. J. Woods, R. Minari, M. Tiseo, M. Mor, A. J. Mulholland, and A. Lodola. “L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.” Chemical Science, 2018. doi:10.1039/c7sc04761d.

Adapted from press release by University of Bristol.

Using ribosomal protein expression patterns as cancer biomarker

A research team at the University of Basel’s Biozentrum has investigated the expression of ribosomal proteins in a wide range of human tissues including tumors and discovered a cancer type specific signature. The study is reported in journal Genome Biology. Researchers think that these signature could be used for predicting progression and survival.

Gene expression level of individual ribosomal proteins (RP) in different types of cancer (blue: lower level; red: higher level compared to normal tissue). Credit: Mihaela Zavolan and Joao Guimaraes, University of Basel, Biozentrum

Prof. Mihaela Zavolan’s research group at the Biozentrum of the University of Basel has now discovered that about a quarter of the ribosomal proteins have tissue-specific expression and that different cancer types have their own individual expression pattern of ribosomal proteins. In the future, these patterns may serve as a prognostic marker for cancer and may point towards new therapeutic opportunities.

Mihaela Zavolan and her co-worker Joao Guimaraes have systematically analyzed ribosomal protein expression in thirty tissue types, three hundred different cell types and sixteen different types of tumors, such as lung and breast cancer. In contrast to previous assumptions, they found a wide variability in ribosomal protein gene expression. In particular, hematopoietic and tumor cells display the most complex expression pattern.

“For us, it was really impressive to see that consistent signatures emerged for the different cancer types after the analysis of distinct data sets including patient samples,” explains first author Guimaraes. “The pattern of the dysregulated proteins is very striking, whereby the expression of some ribosomal proteins is systematically reduced, and of others increased in cancer cells. This suggests that individual ribosomal proteins can either suppress or promote tumorogenesis.”

Furthermore, the scientists discovered a strong relationship between the “signature” in breast cancer and the relapse-free survival. “We were quite surprised to find that the expression level of just three ribosomal proteins allows a fairly accurate prognosis of disease progression, comparable to the best predictive markers that are currently known”, Zavolan points out.

“Our study demonstrates the potential of such expression signatures for the prognosis and perhaps a diagnosis of cancer. We are especially interested in studying the functions of individual ribosomal proteins and hopefully opening the door for new therapeutic options,” explains the scientist.
Citation: Guimaraes, Joao C., and Mihaela Zavolan. “Patterns of ribosomal protein expression specify normal and malignant human cells.” Genome Biology 2016 17:236.
DOI: 10.1186/s13059-016-1104-z
Adapted from press release by University of Basel.

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 lung cancer biomarker Protein PD-1 for predicting survival

The biomarker PD-1, a protein, could potentially be used to predict survival or disease-free survival of lung cancer patients who have had the tumor surgically removed. This is substantiated by the results of a study conducted under the direction of the Comprehensive Cancer Center (CCC) of MedUni Vienna and Vienna General Hospital, together with MedUni Graz and the University of Novi Sad. The paper was presented at the 17th World Conference on Lung Cancer (Dec 2016)

PD-1 protein expression predicts survival in resected adenocarcinomas of the lung. Credit: Medical university of Vienna

In Austria, around 4,000 people develop lung cancer every year. Around three-quarters of these cases involve so-called Non-Small Cell Lung Cancer (or NSCLC). In turn, half of these, that is to say around 1,400 people, are diagnosed as having adenocarcinomas, the commonest subtype of NSCLC. The earlier the disease is detected, the better the patient’s chances of recovery. Essentially, the options for treatment are surgery, radiotherapy, chemotherapy (before and after surgery), a combination of these methods and, very recently, immunotherapy.

Scientists led by Martin Filipits, a cancer researcher at MedUni Vienna’s Institute of Cancer Research and member of CCC Vienna, has now been able to show that PD-1, a protein that occurs on the surface of the body’s immune cells, could serve as a biomarker for predicting the survival of patients with adenocarcinomas. PD-1 is a so-called immune checkpoint protein. Immune checkpoints monitor the correct functioning of the immune response and check an ongoing immune reaction. That is important, as otherwise the immune response could overshoot and give rise to autoimmune diseases.

In the study, the researchers examined cancer cells and immune system cells from 159 patients. All of these patients had previously had cancer resected and some of them had received chemotherapy afterward. PD-1 was found on the immune cells of 45% of the patients and PD-L1 on the cancer cells in 37% of them. The investigation clearly showed that both survival and disease-free survival was longer in the patients in which PD-1 was found than in those where it was not. On the other hand, it made no difference to the prognosis whether PD-L1 was present on the cancer cells or not.

Filipits: “Our results indicate that PD-1 could serve as a biomarker for predicting the survival of patients with an operable adenocarcinoma of the lung. This finding still needs to be confirmed in further studies but it indicates the direction for further research.”

Citation: Zaric, Bojan, Luka Brcic, Anna Buder, Christian Tomuta, Anita Brandstetter, Jorun O. Buresch, Stefan Traint, Vladimir Stojsic, Tomi Kovacevic, Branislav Perin, Robert Pirker and Martin Filipits. “PD-1 protein expression predicts survival in resected adenocarcinomas of the lung.” 17th World Conference on Lung Cancer, Vienna, Dec 2016.
Adapted from press release by the Medical University of Vienna.

Liquid biopsies for lung cancer could predict best treatment

A blood test could predict how well small-cell lung cancer (SCLC) patients will respond to treatment, according to new research published in Nature Medicine today. Scientists, based at the Cancer Research UK Manchester Institute at The University of Manchester, isolated tumor cells that had broken away from main cancer known as circulating tumor cells (CTCs) – from the blood of 31 patients with this aggressive form of the disease. When researchers analyzed these cells, they discovered that patterns of genetic faults measured before treatment were linked to how well and how long a patient might respond to chemotherapy.

Obtaining a tumor sample from lung cancer patients using an operation, known as a biopsy, can be difficult because the tumor is hard to reach and samples are often too small to reveal useful clues on how best to treat patients. Liquid biopsies offer an alternative to taking tumor samples, providing a snapshot of the disease from a blood sample.

The team also investigated the genetic changes that occurred in patients who initially responded well to treatment but later relapsed. The pattern in these cells was different from patients who didn’t respond well to chemotherapy, suggesting different mechanisms of drug resistance had developed.

Lead researcher Professor Caroline Dive, based at the Cancer Research UK Manchester Institute, said: “Our study reveals how blood samples could be used to anticipate how lung cancer patients may respond to treatments”. Unfortunately, we have very few treatment options for patients with SCLC and none at all for those whose cancer is resistant to chemotherapy. “By identifying differences in the patterns of genetic faults between patients, we now have a starting point to begin to understand more about how drug resistance develops in patients with this aggressive form of lung cancer.”

Dr. Emma Smith, Cancer Research UK’s science information manager, said: “Lung cancer causes more than one in five of all cancer deaths in the UK and it’s vital that we find effective new treatments to fight the disease and save more lives. “These liquid biopsies are an incredibly exciting area of research. Studies like this help build a bigger picture of the disease, pointing the way to developing new treatments that are urgently needed for people with lung cancer.”

Citation: “Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer”. Louise Carter, Dominic G Rothwell, Barbara Mesquita, Christopher Smowton, Hui Sun Leong, Fabiola Fernandez-Gutierrez, Yaoyong Li, Deborah J Burt, Jenny Antonello, Christopher J Morrow, Cassandra L Hodgkinson, Karen Morris, Lynsey Priest, Mathew Carter, Crispin Miller, Andrew Hughes, Fiona Blackhall, Caroline Dive & Ged Brady. Nature Medicine 2016.
DOI: http://dx.doi.org/10.1038/nm.4239
Adapted from press release by the University of Manchester.

Synthetic binding protein called “NS1 Monobody” found to inhibit common cancer causing (RAS) mutation

Monobody NS1 binds to H-RAS or K-RAS protein and blocks
RAS function by disrupting the protein’s ability to form active
 molecular pairs. Credit: John P. O’Bryan, et al. 

Researchers at the University of Illinois at Chicago have identified a new way to block the action of genetic mutations found in nearly 30 percent of all cancers. Mutations in genes for the RAS family of proteins are present in nearly 90 percent of pancreatic cancers and are also highly prevalent in colon cancer, lung cancer and melanoma, the most dangerous kind of skin cancer. The group of proteins include three members, K-RAS, H-RAS and N-RAS.

The prevalence of RAS mutations in human cancers and the dependence of tumors on RAS for survival has made a RAS a prime target for cancer research and drug discovery. Scientists and drug developers have long studied RAS oncogenes hoping to find a new treatment for cancer, but they have not yet been able to identify drugs that safely inhibit the oncogene’s activity.

John O’Bryan, associate professor of pharmacology in the UIC College of Medicine, led a team of researchers that took a different approach to studying RAS, and discovered that a synthetic binding protein they call “NS1 monobody,” which they created in the lab, can block the activity of the RAS proteins.

“We did not look for a drug or specifically for an inhibitor,” said O’Bryan, who is also a member of the University of Illinois Cancer Center and holds an appointment at the Jesse Brown VA Medical Center in Chicago. “We used monobody technology, a type of protein-engineering technology, to identify regions of RAS that are critical for its function.” Unlike conventional antibodies, monobodies are not dependent on their environment and can be readily used as genetically encoded inhibitors, O’Bryan said. “The beauty of the technology is that when a monobody binds a protein, it usually works as an inhibitor of that protein,” he said.

Monobodies were developed by Shohei Koide, a co-author on the study who is professor of biochemistry and molecular pharmacology at New York University. They have been used to target a diverse array of proteins that include enzymes and receptors.

The researchers found that the NS1 monobody binds to an area of the RAS protein molecule that was not previously known to be important for its oncogenic activity. NS1 strongly inhibits oncogenic K-RAS and H-RAS function by blocking the ability of the protein to interact with an identical one to form a molecular pair. NS1 does not affect N-RAS.

O’Bryan says the findings, published in the journal Nature Chemical Biology, provide important insight into long-standing questions about how RAS proteins function in cells. These insights may help guide the development of new therapeutic approaches to treating cancer by interfering with mutant RAS function in cancer cells.

“Development of effective RAS inhibitors represents a ‘holy grail’ in cancer biology,” O’Bryan said. “We now have a powerful tool we can use to further probe RAS function. While future studies and trials are needed before these findings can be leveraged outside the lab, this study provides new insight into how we can potentially inhibit RAS to slow tumor growth.”

Citation: Russell Spencer-Smith, Akiko Koide, Yong Zhou, Raphael R Eguchi, Fern Sha, Priyanka Gajwani, Dianicha Santana, Ankit Gupta, Miranda Jacobs, Erika Herrero-Garcia, Jacqueline Cobbert, Hugo Lavoie, Matthew Smith, Thanashan Rajakulendran, Evan Dowdell, Mustafa Nazir Okur, Irina Dementieva, Frank Sicheri, Marc Therrien, John F Hancock, Mitsuhiko Ikura, Shohei Koide & John P O’Bryan. “Inhibition of RAS function through targeting an allosteric regulatory site” Nature Chemical Biology 2016
DOI: http://dx.doi.org/10.1038/nchembio.2231
Research funding: Chicago Biomedical Consortium, Searle Funds at the Chicago Community Trust, Department of Veterans Affairs, National Institutes of Health
Adapted from press release by University of Illinois at Chicago

Synthetic binding protein called "NS1 Monobody" found to inhibit common cancer causing (RAS) mutation

Monobody NS1 binds to H-RAS or K-RAS protein and blocks
RAS function by disrupting the protein’s ability to form active
 molecular pairs. Credit: John P. O’Bryan, et al. 

Researchers at the University of Illinois at Chicago have identified a new way to block the action of genetic mutations found in nearly 30 percent of all cancers. Mutations in genes for the RAS family of proteins are present in nearly 90 percent of pancreatic cancers and are also highly prevalent in colon cancer, lung cancer and melanoma, the most dangerous kind of skin cancer. The group of proteins include three members, K-RAS, H-RAS and N-RAS.

The prevalence of RAS mutations in human cancers and the dependence of tumors on RAS for survival has made a RAS a prime target for cancer research and drug discovery. Scientists and drug developers have long studied RAS oncogenes hoping to find a new treatment for cancer, but they have not yet been able to identify drugs that safely inhibit the oncogene’s activity.

John O’Bryan, associate professor of pharmacology in the UIC College of Medicine, led a team of researchers that took a different approach to studying RAS, and discovered that a synthetic binding protein they call “NS1 monobody,” which they created in the lab, can block the activity of the RAS proteins.

“We did not look for a drug or specifically for an inhibitor,” said O’Bryan, who is also a member of the University of Illinois Cancer Center and holds an appointment at the Jesse Brown VA Medical Center in Chicago. “We used monobody technology, a type of protein-engineering technology, to identify regions of RAS that are critical for its function.” Unlike conventional antibodies, monobodies are not dependent on their environment and can be readily used as genetically encoded inhibitors, O’Bryan said. “The beauty of the technology is that when a monobody binds a protein, it usually works as an inhibitor of that protein,” he said.

Monobodies were developed by Shohei Koide, a co-author on the study who is professor of biochemistry and molecular pharmacology at New York University. They have been used to target a diverse array of proteins that include enzymes and receptors.

The researchers found that the NS1 monobody binds to an area of the RAS protein molecule that was not previously known to be important for its oncogenic activity. NS1 strongly inhibits oncogenic K-RAS and H-RAS function by blocking the ability of the protein to interact with an identical one to form a molecular pair. NS1 does not affect N-RAS.

O’Bryan says the findings, published in the journal Nature Chemical Biology, provide important insight into long-standing questions about how RAS proteins function in cells. These insights may help guide the development of new therapeutic approaches to treating cancer by interfering with mutant RAS function in cancer cells.

“Development of effective RAS inhibitors represents a ‘holy grail’ in cancer biology,” O’Bryan said. “We now have a powerful tool we can use to further probe RAS function. While future studies and trials are needed before these findings can be leveraged outside the lab, this study provides new insight into how we can potentially inhibit RAS to slow tumor growth.”

Citation: Russell Spencer-Smith, Akiko Koide, Yong Zhou, Raphael R Eguchi, Fern Sha, Priyanka Gajwani, Dianicha Santana, Ankit Gupta, Miranda Jacobs, Erika Herrero-Garcia, Jacqueline Cobbert, Hugo Lavoie, Matthew Smith, Thanashan Rajakulendran, Evan Dowdell, Mustafa Nazir Okur, Irina Dementieva, Frank Sicheri, Marc Therrien, John F Hancock, Mitsuhiko Ikura, Shohei Koide & John P O’Bryan. “Inhibition of RAS function through targeting an allosteric regulatory site” Nature Chemical Biology 2016
DOI: http://dx.doi.org/10.1038/nchembio.2231
Research funding: Chicago Biomedical Consortium, Searle Funds at the Chicago Community Trust, Department of Veterans Affairs, National Institutes of Health
Adapted from press release by University of Illinois at Chicago

Neoadjuvant immunotherapy using nivolumab prior to early lung cancer surgery is safe and feasible

Adapted from Press release by European Society for Medical Oncology

Neoadjuvant immunotherapy with the PD-1 inhibitor nivolumab is safe and feasible prior to surgery for early lung cancer, researchers reported at the ESMO 2016 Congress in Copenhagen.

Background

“Until now nivolumab and the other anti-PD-1 and anti-PD-L1 drug studies have only been reported in metastatic or advanced lung cancer,” said lead author Dr Patrick Forde, Assistant Professor of Oncology, Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins, Baltimore, US. “This was the first study of neoadjuvant PD-1 blockade in early stage lung cancer.”

Research Study

The primary objective of the study was to see whether it was safe and feasible to administer neoadjuvant nivolumab to patients with early stage non-small-cell lung cancer (NSCLC) prior to resection of the tumour. Treatment was considered feasible if it did not delay surgery.

Exploratory aims included extensive correlative analyses of the pretreatment biopsy and post-treatment resected tumour including PD-L1 staining, multiplex immunohistochemistry and T cell receptor sequencing. An additional exploratory analysis looked at the degree of pathological regression. This was analysed by a lung cancer pathologist using a method previously reported for use in measuring response to neoadjuvant chemotherapy in NSCLC. Major pathological regression (90% or more) was defined as a resected specimen with less than 10% remaining viable tumour cells.
The study included 20 patients who had a tumour biopsy taken. They then received two doses of nivolumab at four and two weeks prior to surgical resection of the tumour.

The results in the first 16 patients were presented today. The investigators found that there were no significant safety concerns and no delays to surgery with nivolumab. Six of 15 patients (40%) had major pathological regression of their tumour following nivolumab. All of those tumours had dense infiltration of immune cells and either a complete pathologic response or isolated remaining tumour cells. An additional five patients had some regression of their tumour noted and evidence of immune infiltration. Multiplex IHC demonstrated infiltration of cytotoxic T cells into the tumours and also detection of new T cell clones in the tumour that did not appear to be present in the pre-treatment biopsy.

Authors Note

Forde said: “We found that neoadjuvant administration of nivolumab is safe and feasible in stage I-IIIA NSCLC and also a preliminary signal that anti-PD-1 immunotherapy may have activity in early stage lung cancer. Following these initial results we are expanding the study.
One cohort will receive a third dose of nivolumab preoperatively and the other will receive the combination of nivolumab and ipilimumab preoperatively. This expanded study will continue to be conducted in collaboration with investigators at Johns Hopkins University and Memorial Sloan-Kettering Cancer Centre. Others, such as the Lung Cancer Mutation Consortium in the United States, are also conducting larger studies of neoadjuvant immune checkpoint inhibition in NSCLC.”

Commenting on the study, Professor Pieter Postmus, chair of Thoracic Oncology at the University of Liverpool, UK, said: “There is a potential for bias when comparing a small biopsy, which might not represent the whole tumour, with the resected tumour. This is not a validated way to measure response to a treatment. It describes a biological effect but whether that has any clinical impact on survival is unproven.”

Limitations

“Although we do not know for the time being if a major pathological response is correlated with improved survival, this method could first be validated in a cohort of patients with advanced disease by comparing the percentages of viable tumour cells in tumour biopsies taken before and four to eight weeks after immunotherapy,” continued Postmus. “If in this way regression – as defined in the preoperative study – correlates with survival in patients with advanced cancer, it is likely to hold true in less advanced or resectable patients. Long-term survival data will be the ultimate test for these neoadjuvant immunotherapy strategies.”