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.

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

Noninvasive test to find fat in feces to diagnose Colorectal cancer

Scientists at Washington State University and Johns Hopkins Medical School have discovered a fast, noninvasive method that could lead to the early diagnosis of colorectal cancer. Using ultrasensitive, high-speed technology, the researchers identified a suite of molecules in the feces of mice that signifies the presence of precancerous polyps. This “metabolic fingerprint” matches changes in both mouse and human colon tumor tissues and suggests a potential new diagnostic tool for early detection of colorectal cancer in a clinical setting.

Herbert Hill, WSU Regents professor, and graduate student Michael Williams conducted the study in collaboration with Raymond Reeves, WSU School of Molecular Biosciences, and Linda Resar, Johns Hopkins University School of Medicine. The findings were reported this month in the Journal of Proteome Research.

Hill and Williams discovered the molecular fingerprint for colon cancer using a technology called ion mobility-mass spectrometry. Ion mobility-mass spectrometry is found in sensor devices worldwide that sniff out illicit drugs, chemical warfare agents and explosives in airports. Hill has been an innovator in the field for nearly 40 years. In this case, ion mobility-mass spectrometry was coupled with ultraperformance liquid chromatography.

The researchers first identified metabolic products from normal colon tissue in both humans and mice. Ion mobility-mass spectrometry can measure hundreds of metabolites simultaneously, such as enzymes, fats, glucose and amino acids. The scientists then compared this normal profile to that found in cancerous colon tissues from humans and research mice with polyps in their colons that mimic those in humans.

In both cases, the scientists found that colon cancer caused significant changes in fat metabolism, especially for lipids and fatty acids. These abnormalities created a molecular fingerprint that was similar in humans and mice, said Hill.

Next, Hill and Williams examined droppings from transgenic and control mice to see if the molecular fingerprint could be found in feces as well. Indeed ion mobility-mass spectrometry detected many of the same metabolic abnormalities seen in the previous study and could clearly distinguish between healthy mice and those with colorectal cancer.

“The feces was not exactly the same as the tissue samples, but it had a lot of similarities to the tissue,” said Hill. “We found the lipids and fatty acids were changing — and there were also changes in the amino acids.” Specifically, an important class of fats called lysophospholipids changed dramatically, said Williams. “These types of lipids are known to be important in the development of cancer and are particularly tied to colorectal cancer.”

Their next step, if funded, is to evaluate human stool samples to see if the molecular fingerprint is present with colorectal cancer in people.

Citation: The Fecal Metabolome in Hmga1 Transgenic Mice with Polyposis: Evidence for Potential Screen for Early Detection of Precursor Lesions in Colorectal Cancer.
Authors: Williams, Michael David, et., al.
DOI: http://dx.doi.org/10.1021/acs.jproteome.6b00035
Journal: Journal of Proteome Research
Research funding:
Adapted from press release by Washington State University

Improving participation in cancer screening should be a priority

Early diagnosis of cancer is linked to better survival rates. Unfortunately, participation rates for cancer screening worldwide are low even when screening programmes are free. The ESMO 2016 Congress is showcasing five studies (1) on this important area of cancer management which look at alternative ways to overcome barriers and improve screening rates

Professor J-F Morére who conducted the EDIFICE1 survey, intended to improve insight into participation in screening programmes in France, explains, “Population commitment and physician implication in promoting screening are both necessary criteria for reaching the recommended participation goals. In this Fourth Nationwide Observational Survey, we hypothesized that individual opinions may affect physicians’ and laypersons’ attitudes toward prescribing or participating in screening; we assessed physicians’ and laypersons’ opinions, focusing on colorectal (CRC), breast (BC), cervical (CC), prostate (PC) and lung (LC) cancer screening.”

“In general, screening was more reassuring than worrying, more so for physicians than for laypersons. The official guidelines for CRC and BC screening are a good setting for GPs’ medical practice. The most widely used screening programmes (CRC, BC, CC) enable GPs to make objective prescriptions, regardless of individual opinions.  In the absence of guidelines (PC), prescription rates are correlated with physicians’ confidence in screening.  Reassurance in screening was found to have a positive impact on laypersons’ participation rates.”

In Australia, a patient-centred approach to improving screening participation rates was the subject of a study by Dr Amanda Bobridge at the University of South Australia.  She comments, “The aim of this study was to investigate enablers and barriers to cancer screening and how screening participation may be improved. An overwhelming percentage of respondents to our questionnaires would support a combined cancer screening service. Offering a combined, co-located service – a ‘one stop cancer screening shop’ – has the potential to address barriers to screening (such as time constraints), improve participation rates and maximize utilization of public health resources.”

A significant proportion of cancer patients across Europe are diagnosed with their disease as the result of an emergency presentation (EP) to acute secondary care services . This route to diagnosis is associated with poorer survival and worse patient experience. Previous work has shown that EP patients usually describe a long history of symptoms (>12 weeks), and that 70% had seen their general practitioner (GP) in the days and weeks prior to presentation. Tackling EP of cancer is important when improving the outcomes of patients across Europe. In the majority of cases there are opportunities for earlier diagnosis and hence prevention of EP. Dr. Tom Newsom-Davis led a one-year pilot of a nurse-led Acute Diagnostic Oncology Clinic (ADOC) in a district general hospital. Based in the oncology department with consultant supervision of every case, the service was targeted at primary care referrals.

Newsom-Davis describes the results of this pilot, “ADOC is a novel, effective and efficient pathway for patients who might otherwise be diagnosed as part of EP. This pilot shows the feasibility of a nurse-led service based in an oncology department, and a high level of user satisfaction. This model of acute diagnostic oncology clinic should be considered as an addition to existing outpatient cancer diagnostic pathways.” 

Improvement in cancer detection and treatment has led to an important increase of the number of long-term cancer survivors, many of them being at risk of a second cancer. Facing the lack of information on cancer screening practices in this population, second cancer screening among 5-year female cancer survivors was analysed by Marc Bendiane in France. He says, “Survivor care plans are needed to increase awareness among patients and physicians of the importance of screening patients for second cancers, which are not a recurrence of the first one. New targeted interventions must be invented to improve the participation of cancer survivors in screening programmes.”

This study found an underutilisation of mammography screening in those cancer survivors (non-breast cancer), compared with women in the general population (78% vs 87%). The study concludes that programmes to raise awareness of the risks of second cancers (which are not recurrences of their first cancer) are needed among cancer survivors and physicians.

Professor Virgilio Sacchini of the University of Milan comments, “Breast cancer screening is the most important determinant of quality of life of cancer patients after surgery. Screening decreases the chances of axillary lymph-node involvement, avoiding axillary dissections, the most worrisome sequela of cancer surgery: the arm lymphedema. We know that breast cancer screening will need more personalisation in our era of genetics, but by increasing the awareness and compliance of mammography screening, we can better identify high risk patients to involve in more specific surveillance.”

Also in France, a study assessed smokers’ intentions to take part in a hypothetical lung cancer screening (LCS) programme. Two comprehensive multivariate stepwise logistic regression analyses were performed in current and in former cigarette smokers to identify factors associated with the intention to take part in a LCS programme. The study authors conclude that intending to take part in LCS programs is a complex decision; explanatory factors differ between current and former smokers. Among current smokers, intended participation in screening was strongly associated with the intention to quit smoking.

Professor Sacchini concludes, “The studies being presented at the ESMO 2016 Congress should help encourage doctors and patients to respond to screening programmes proposed by national health services. Screening tests may help diagnose cancer at an early stage, before symptoms appear. When cancer is found early, it may be easier to treat or cure. In this particular period of extreme evaluation of cost/effectiveness ratio, screening is still the best investment for the health of our populations.”

Press release by European Society of Medical Oncology

Genetic targets in Colorectal Cancer: role of KRAS, MEK and TAK1 genes Identified.

Researchers from Boston University School of Medicine have discovered a possible strategy to treat colon cancers that are caused by the mutant KRAS gene, which is responsible for approximately half of all colon cancer cases. The findings, which appear online in the journal Molecular Cancer Research, may lead to better therapeutic agents to treat this disease.

Colon cancer is the third leading cause of cancer-related deaths in the U.S. Routine screenings by undergoing a colonoscopy have helped reduce mortality rates if the disease advances to malignancy, it can be very difficult to treat. Cancers with the KRAS gene mutation respond poorly to currently available therapeutic agents.

“Our study provides a new strategy to treat colon cancers driven by the mutant KRAS gene, which is based on targeting additional genes that cooperate with KRAS to promote tumor growth. These additional genes, notably MEK and TAK1, can be blocked by selective therapeutic agents to suppress colon cancer cellular proliferation and viability,” explained corresponding author Anurag Singh, PhD, assistant professor of pharmacology & experimental therapeutics at BUSM. The researchers tested 40 colon cancer cell lines that were derived from human colon cancer samples for sensitivity to inhibitors of MEK and TAK1.

They found that treating those cell lines with MEK and TAK1 inhibitors suppressed the growth of mutant KRAS-driven colon cancer cells significantly as compared to the control group. “With this study we have uncovered a novel pathway in a subset of colon cancers driven by mutant KRAS gene activation, representing an important axis of vulnerability with the potential to selectively treat these types of tumors in the clinic,” he added.

Press Release: Researchers investigate new strategy to block growth of colon cancer cells

Research indicates role of protein c-Cbl in Colorectal Cancer

The discovery, published online by Oncotarget journal, may lead to new therapies in managing patients with Colorectal Cancer (CRC). CRC is a complex disease caused by several genetic mutations and their consequences. In more than 80-percent of CRC patients, some of these mutations can lead to an increase in ?-catenin, a vital protein, leading to cancer initiation.

Researchers from Boston University School of Medicine, led by Vipul Chitalia, MD, PhD, assistant professor of Medicine, have identified a new role of the protein, c-Cbl that it may be capable of degrading ?-catenin in CRC patients. “We believe these findings could have clinical implications in managing patients with CRC,” explains Chitalia.

C-Cbl could be used as a biomarker of patient survival. The discovery may also lead to new strategies to suppress CRC growth.” According to Chitalia, another aspect of this study is related to the method by which researchers analyze human biopsy samples. BUSM researchers, led by Vijaya Kolachalama, PhD, principal investigator at the Whitaker Cardiovascular Institute at BUSM, developed a more accurate, automated and high-throughput image processing technique that was capable of uncovering hidden relationships between important proteins in cancer.

“We are excited about this discovery and the treatments that could improve the quality of life for CRC patients,” says Chitalia and his collaborators Kevan Hartshorn, MD, professor of Medicine, and Nader Rahimi, PhD, associate professor of Pathology and Laboratory Medicine “c-Cbl targeted therapy may provide a means to suppress the growth of CRC and possibly with lower side effects.”

Every year about 150,000 new cases of colorectal cancer are diagnosed in the United States. Despite surgery and new therapies, about one third of patients with the disease die from CRC annually, making it the second most common cause of cancer death.

Press release: New research indicates key protein may directly impact development of colon cancer