Over the past five decades, scientists have described more than 80,000 protein structures, most of which are now publicly available and provide important information to medical researchers searching for targets for drug therapy. However, a similar effort to catalogue RNA structures has mapped only a few hundred RNA molecules. As a result, the potential of RNA molecules has just barely been developed as targets for new therapeutics.

“To effectively target these molecules, researchers often need a three-dimensional picture of what they look like,” says Nikolay Dokholyan, PhD, professor in the department of biochemistry and biophysics, and the project’s co-leader.

“With Dr. Kevin Weeks’ lab, we have developed a way to create a three-dimensional map of complex RNAs that are not amenable to study through other methods. It builds on information from a routine laboratory experiment, used in the past to evaluate RNA models from a qualitative standpoint. Our team has created a sophisticated quantitative model that uses this simple information to predict structures for large, complex RNA molecules, which have previously been beyond the reach of modeling techniques,” he adds.

Dokholyan, who is a member of UNC Lineberger Comprehensive Cancer Center and director of the UNC Center for Computational and Systems Biology, hopes that the method will help researchers who are trying to target RNAs molecules to change cellular metabolism in a way that ultimately reduces the effects of cellular diseases like cancer. He notes, “Rational, cost-effective screening for small molecules requires a good understanding of the targeted structure. We hope that this method will open doors to new findings applicable to a wide range of human diseases.”
Other members of the research team include Feng Ding, PhD, Research Assistant Professor of biochemistry and biophysics, Christopher Lavendar, a graduate student of in the department chemistry, and study co-leader Kevin Weeks, PhD, Kenan Distinguished Professor of Chemistry and UNC Lineberger member.
The research was funded by the National Institutes of Health and the University of North Carolina Research Council.
source: University of North Carolina School of Medicine

In this newly published data, researchers identify two distinct autophagy regulated pathways downstream from the von Hippel-Lindau tumor suppressor gene, or VHL. This specific tumor suppressor is lost in the majority of renal cell carcinomas.

UC researchers report these findings in Cancer Cell.

Maria Czyzyk-Krzeska, MD, PHD, corresponding author of the study, says the discoveries could guide researchers to more effective treatment approaches for kidney cancer, particularly metastatic disease, based on knowledge of these specific autophagic processes. UC collaborators in this study include David Plas, PhD, assistant professor of cancer and cell biology, and Jarek Meller, PhD, associate professor of environmental health.

“VHL has emerged as a master controller of access to intracellular nutrients through autophagy and to extracellular nutrients through formation of blood vessels. Our work shows that there are different autophagic programs – pro-and anti-oncogenic. Drugs that inhibit the final stages of autophagy non-specifically, such as derivatives of chloroquine, may not be as beneficial as hoped,” explains Czyzyk-Krzeska, a professor of cancer and cell biology at the UC College of Medicine and researcher with the UC Cancer Institute.

She says the challenge is to understand the molecular mechanisms of these diverse autophagic pathways and identify targets that are specific to the pro-oncogenic pathway but not affecting tumor-suppressing pathways.

“Current drugs for metastatic kidney cancer target angiogenesis – blocking the formation of blood vessels that feed the tumor – but they typically only increase survival by a matter of months,” says Czyzyk-Krzeska. “We hope this new body of evidence can help pave a new path to more effective treatment options for this disease.”

According to the American Cancer Society, incidence rates of kidney cancer are increasing steadily by 2 to 3 percent each year. The disease is curable when it is identified early and isolated to the kidney. Treatment options for metastatic disease are limited.
The study was sponsored by grants from the National Cancer Institute, U.S. Department of Veterans Affairs and U.S. Department of Defense.
source: University of Cincinnati Academic Health Center

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In research published online in the journal Cancer Cell, CSHL Assistant Professor Mikala Egeblad and her team report using “live” microscopy to observe how cancer cells in mouse tumors react to the widely used chemotherapeutic agent doxorubicin. They found that selective inhibition of two factors that regulate the tumor microenvironment – enzymes called matrix metalloproteinases (MMPs) and a class of immune signaling molecules called chemokines – made breast tumors in mice more responsive to the drug.

It is well known that genetic mutations and epigenetic changes in cancer cells contribute to a tumor’s capacity to resist treatment. But tumors contain many other cells besides cancer cells and surprisingly little is known about how factors secreted from these non-cancerous cells – “stromal” cells, which constitute the tumor microenvironment influence drug resistance. Such cells include white blood cells, some of which are inflammatory.

Egeblad’s team used real-time microscopic imaging to scrutinize how cancer cells react to doxorubicin in the context of different tumor microenvironments. The resulting time-lapse movies revealed how drugs flowed through – and leaked out of – blood vessels feeding tumors; the manner and rate at which drugs killed cancer cells in tumors of different stages of advancement; and dynamics of the interactions between cells of the tumor and those of the surrounding stromal tissue, before, during and after drug administration.

“We were able to see clearly that the microenvironment contributes critically to drug response,” Egeblad says, “specifically via regulation of the permeability, or ‘leakiness,’ of blood vessels running through and around the tumor, and also by impacting the local recruitment of inflammatory cells.”

When viewed at the microscopic level, resistance to doxorubicin was found to be associated with tumor stage. Observing tumors continuously following drug administration led to the discovery that this response correlated with the ability of blood vessels to transport doxorubicin to the cancer cells, which was comparatively greatest not early or late, but at intermediate stages of tumor development.

Mice engineered to lack the gene that encodes the MMP9 enzyme, which helps regulate the permeability of blood vessels, “had significantly leakier blood vessels, and this corresponded strikingly with a better response to doxorubicin,” according to Egeblad.

Existing chemical inhibitors of MMP enzymes have failed in clinical trials, she noted. “But our data suggest that these or other drugs that affect vascular permeability could be used to achieve better responses to chemotherapies.”

Another important discovery gleaned from the CSHL team’s real-time imaging was that myeloid cells – inflammatory cells that are one of the most common kinds of non-cancerous cells in tumors – were consistently recruited to the tumor site during chemotherapy. Myeloid cells tend to be drawn to places where cells have died. The team found that this attraction, called chemotaxis, is the result of the activation of signaling by CCL2, a member of a class of immune cell recruiting molecules called chemokines.

By knocking out the gene encoding the receptors (called CCR2) for this chemokine, the team was able to diminish myeloid cell recruitment to the tumor. Importantly, this also resulted in a significantly improved response to doxorubicin and to another commonly used chemotherapy drug, cisplatin. This observation is important because it points to a novel way of potentially boosting the cancer cell-killing effectiveness of chemotherapeutic drugs.

The CSHL team now has the goal of finding additional ways to boost the response chemotherapy by determining how the myeloid cells that are recruited to tumors during chemotherapy contribute to the response of cancer cells to drug treatment.
“Imaging tumor-stroma interactions during chemotherapy reveals contributions of the microenvironment to resistance” appears in Cancer Cell on April 17, 2012. The authors are: Elizabeth S. Nakasone, Hanne A. Askautrud, Tim Kees, Jae-Hyun Park, Vicki Plaks, Andrew J. Ewald, Miriam Fein, Morten G. Rasch, Ying-Xim Tan, Jing Qiu, Juwon Park, Pranay Sinha, Mina J. Bissell, Eirik Frengen, Zena Werb, and Mikala Egeblad. The paper can be obtained online at: DOI 10.1016/j.ccr.2012.02.017.
source: Cold Spring Harbor Laboratory

“It was not immediately obvious that MCL1 was such an attractive therapeutic target in cancer,” said Todd Golub, director of the Broad’s Cancer Program and Charles A. Dana Investigator in Human Cancer Genetics at the Dana-Farber Cancer Institute. Golub is also a professor at Harvard Medical School and investigator at Howard Hughes Medical Institute. “But once it became clear that MCL1 was something that we wanted to turn off in tumor cells, we faced two additional problems: we didn’t know which tumors depend on it for survival and there wasn’t an obvious path to drug discovery. This paper addresses those two challenges.”

In a paper appearing in the April issue of the journal Cancer Cell, Golub and colleagues from the Broad Institute and Dana-Farber identify several chemical compounds that tamp down the expression of the MCL1 gene and describe the relationship between MCL1 and a related pro-survival gene, BCL-xL. The research team leveraged several critical Broad Institute resources, including the recently published Cancer Cell Line Encyclopedia (CCLE) and RNAi screening capabilities, to better understand how to target MCL1.

MCL1 is frequently amplified in human cancer, meaning that multiple copies of the gene are often present in tumors. The research team suppressed MCL1 in cancer cell lines, allowing them to determine which ones depended on MCL1 for survival. The researchers then looked for a genetic signature that accurately predicted which cell lines were dependent on MCL1 for survival. The gene BCL-xL, another gene protective against cell death, was clearly the best predictor. In its presence, cancer cells can survive even when MCL1 is turned off.

“That was gratifying not only because BCL-xL was a clear winner as a predictive marker, but also because it encodes a protein in the same pathway as MCL1,” said Guo Wei, the paper’s first author. Wei is a research scientist at the Broad Institute and a research fellow in pediatrics at Dana-Farber. “It’s not just right statistically – it also makes sense given the biology.”

Drugs targeting BCL-xL are currently in clinical trials. The new study predicts that in cancer cells where both genes are highly expressed, combination therapies targeting both genes could be effective in treating the tumor.

The researchers also tested almost 3,000 chemical compounds, searching for ones that turned off the expression of MCL1. One of the compounds that this screen revealed was the natural compound triptolide. To find out how triptolide has its effect, the researchers turned to another Broad-created resource: the Connectivity Map, a database researchers can use to connect drugs, genes, and diseases.

“Based on the Connectivity Map, triptolide appears to be a classical inhibitor of transcription, meaning that it should tamp down the expression of all genes,” said Wei. “However, it disproportionately affects MCL1. If you give a dose of transcriptional inhibitor, most gene transcripts decrease at a gentle rate, but MCL1 levels decline sharply.”

Transcriptional inhibitors like triptolide may be useful tools for probing MCL1 biology, but Golub emphasizes that specific, targeted therapies for MCL1 are also needed. “We used clever chemical genomic approaches to find a way to inhibit MCL1, but the results further our resolve to find more specific MCL1 small molecule inhibitors,” Golub, senior author of the study, said.

“The work suggests a path for the clinical development of an MCL1 inhibitor,” said Wei. “A number of anti-cancer drugs currently in use have the effect of turning off MCL1 expression. Our study suggests that we’re beginning to get a handle on which tumor types might be most responsive to these drugs. And, as newer MCL1-specific drugs are developed, this study suggests the patient population to focus on in clinical trials.”
This work was supported by NIH grant P01 CA068484 and 5U54CA112962, the Novartis Institutes of Biomedical Research, and by a postdoctoral fellowship from the Damon Runyon Cancer Research Foundation. Other researchers who contributed to this work include Adam A. Margolin, Leila Haery, Emily Brown, Lisa Cucolo, Bina Julian, Shyemaa Shehata, Andrew L. Kung, and Rameen Beroukhim.
source: Broad Institute of MIT and Harvard

The study, published in Journal of Clinical Oncology, is the largest prospective evaluation of cancer pain and related symptoms ever conducted in an outpatient setting.

Almost 20 years ago, Charles Cleeland, Ph.D., professor and chair of the Department of Symptom Research at MD Anderson, published the first comprehensive study to look at the adequacy of pain management in cancer care.

“We’ve known for years that the undertreatment of pain is a significant public health problem in the cancer treatment process, and that minorities are at greatest risk for not receiving appropriate pain care,” said Cleeland, the JCO’s study’s senior author. “This new research tells us that our progress has been limited, with only a 10 percent overall reduction in inadequacy of pain management from our findings almost two decades ago.”

The MD Anderson-led study was conducted by the Eastern Cooperative Oncology Group; it enrolled patients with invasive breast, prostate, colon and lung cancers from 38 institutions across the country, at any point during their care. All were treated on an outpatient basis at either an academic medical center or community clinic. The outpatient setting represents a unique setting, explain the researchers. While those hospitalized with significant pain may be evaluated by pain specialists, those treated on an outpatient basis are typically managed by their treating oncologists.

Patients completed a questionnaire providing their demographic and clinical information. Using a symptom assessment tool developed by Cleeland, the patients’ pain levels were assessed, as well the level of analgesic that had been prescribed, if any. Assessment was repeated approximately one month later. The study’s primary objective was to assess the prevalence of pain medication in oncology outpatient practice.

The researchers indentified 3,023 patients at risk for pain, with 2,026 (67 percent), taking analgesics, or pain medications. Approximately one fourth of those analyzed were minority patients, including Hispanic (9 percent), black (12 percent), Asian (1 percent) and other (1 percent). Of the 2,026 patients at risk for pain, 1,356, or 67 percent, had adequate pain management. For example, 20 percent of the patients who reported feeling severe pain were not receiving any analgesics, and of the 406 patients that were undertreated at an initial assessment, 31 percent received appropriate treatment by the follow-up visit. The researchers found that the odds of a non-Hispanic white patient having inadequate treatment for their pain at both initial and follow-up assessments was approximately half that of a minority patient.

While no discrepancy for age or gender was noted, interestingly, cancer survivors with pain also were less likely to be treated adequately.

“Pain is one of the most feared symptoms of cancer and it has tremendous impact on the quality of life and function of our patients,” said Michael Fisch, M.D., associate professor and chair of the Department of General Oncology at MD Anderson, and the study’s lead author. “These findings represent a significant discrepancy in treatment adequacy, with minority patients being twice as likely to be undertreated. This critical observation awakens us to a major opportunity in healthcare – to work hard to resolve this striking disparity.”

The researchers cite a number of possible reasons for the discrepancy in findings, including: cultural and communication barriers; access to care; concerns about addiction and reluctance to admit pain; expert symptom management and access to effective patient education.

Implicit stereotyping and bias among healthcare providers, even in the absence of the providers’ awareness or intention, may also be a factor, says Fisch. However, Cleeland notes that at underserved clinics, both whites and minorities were inadequately treated for their pain, thereby suggesting an overall lack of resources.

The study is not without its limitations, including the few number of disease types included, as well as that the researchers did not collect data on patients’ comorbidities or socio-economic status.

Both Fisch and Cleeland agree that better symptom control must begin with open-minded physicians, appropriately gauging the needs of their patients, as well as more engaged patients and caregivers willing to communicate their pain level and other symptoms. The researchers plan to follow up these findings by looking at additional symptoms of patients as well as their emotional distress and fatigue.
In addition to Fisch and Cleeland, MD Anderson’s Tito R. Mendeoza Ph.D., Department of Syptom Research, is also an author on the paper. Other authors include: Ju- Whei Lee and Judi B. Manola, Dana Farber Cancer Institute; Matthias Weiss, M.D., Ph.D., Marshfield Clinic; Lynne I. Wagner, Ph.D. and David Cella, Ph.D., both of Northwestern University Feinberg School of Medicine; Victor T. Chang, M.D., New Jersey Healthcare System; and Lori M. Minasian, M.D., and Worta McCaskill-Stevens, M.D., both of the National Cancer Institute (NCI).
The study was funded, in part, by grants from the NCI, National Institutes of Health and the Department of Health and Human Services. None of the authors reports potential conflicts of interest.
source: University of Texas M. D. Anderson Cancer Center