Over the years, hunting for cancer-related genes and understanding how they work has been an important, although time-consuming, exercise.

At Cold Spring Harbor Laboratory (CSHL), five different research groups have now combined their expertise to speed up the rate of discovering cancer-related genes and validating their function in living animals.

The result of the collaborative effort is a large-scale, rapid, cost-effective genetic screen that in a preliminary test succeeded in uncovering 13 new tumor suppressors - genes that inhibit the activity of cancer genes. Tumor suppressors are important in cancer development generally, and specifically in liver cancer, where they frequently have been found to be missing in people who develop the illness.

These discoveries, published online ahead of print on Nov.17 and scheduled to appear in the November 26 issue of Cell , "are a huge step forward in understanding the genetics of cancer and open up a host of new strategies to improve its diagnosis and treatment," according to CSHL Professor Scott W. Lowe, Ph.D., the corresponding author of the study. Other authors include Scott Powers, Ph.D., Director of the Human Cancer Genome Center at CSHL, and CSHL Professors Gregory J. Hannon, Ph.D., W. Richard McCombie, Ph.D., and Michael Wigler, Ph.D.

Pinpointing Tumor Suppressor Genes

Tumor suppressors are a crucial component of intracellular signaling networks that protect against uncontrolled cell proliferation. The benefits of such genes can be lost when DNA undergoes alterations, including mutations or deletions of entire stretches of chromosomes. A highly efficient genome-sequencing technique developed several years ago in the Wigler laboratory has made it possible to scan the genome of cancerous cells for, among other things, deleted portions of chromosomes where tumor suppressors are likely to reside.

Dr. Powers performed a genomic analysis of human liver cancer samples that provided a basis for the work of the combined teams. Powers' lab scanned the genomes of liver cancers from more than 100 patients to compile a list of deletions of chromosomal regions. These regions were hypothesized to be the location of most of the missing tumor suppressor genes. A comparison of this list with the genome sequence of a normal human cell revealed the identity of approximately 300 genes within the deleted chromosomal segments.

Chromosomal deletions aren't limited to cancer-related genes alone; any number of "passenger" or unrelated neighboring genes can inadvertently also be lost. The team therefore had to pinpoint the tumor suppressors among the 300 genes. "Genomic analysis of human tumors is important," Powers observed," but combining it with functional screening in mouse models is a notable step forward."

The usual route of characterizing a gene's function is to mutate it in mouse embryos and then create lines of mice that can then be examined for the mutation's effects. Lowe's group bypassed this step, which is time-consuming, by engineering mutations into the genome of adult mouse cells and then re-injecting these cells into adult mice. The team used a method honed by Dr. Hannon of introducing stable mutations into mouse cells via RNA interference, or RNAi, a technique in which small RNA molecules are introduced into cells to shut off specific genes.

RNA sequences that corresponded to all the 300 or so deleted genes were obtained from an RNAi "library" compiled by the Hannon lab. Lowe's team introduced these RNAi tools (known as "short-hairpin RNAs, or shRNAs) into progenitor cells that develop into mature liver cells, albeit ones engineered to over-produce a cancer gene product called Myc.

In cells with these Myc mutations, an additional "trigger" such as the shutting off of a tumor suppressor gene via RNAi would be sufficient to cause cancer. The engineered cells that carried a Myc mutation and an shRNA were injected into mice. Dramatically, those that received cells in which a tumor suppressor gene had been "silenced" by an shRNA developed tumors within a month.

The scientists homed in on the identity of the silenced tumor suppressors by simply isolating and analyzing the genetic material from the tumors. Their strategy identified 13 new tumor suppressor genes, most of which had not been linked to cancer before.

A rich and unexpected payoff

"The nature of these new genes is not obvious and we wouldn't have guessed their relationship to cancer if we hadn't followed this approach," says Lowe. "They may now allow us to make headway into poorly understood areas of cancer."

The newly identified tumor suppressor genes affect a wide array of cellular activities, including maintenance of cell structure, cellular metabolism, cell proliferation and control of the levels of various tumor growth-enhancing proteins in the cell's nucleus. In one instance, the team's strategy also uncovered not genes in isolation but an entire network of genes that go awry in liver cancer. "Given that the cancer puzzle involves multiple genes in various combinations, we need to find all the hits that make the cell tip over the edge," says Lowe, explaining one advantage of his team's broad strategy.

Some of the genes identified might also lead to new strategies for cancer therapy. For example, some of the newly discovered tumor suppressor genes "code" for proteins that are secreted, which indicates that their ability to prevent cancer is dependent on their presence outside the cell. Reversing the loss of such proteins - by replenishing their levels via injections - is an easier fix than having to correct a defect in the genome via gene therapy.

In other words, the CSHL team's new strategy now makes it possible to rapidly filter from genomic information those genes that specifically impact cancer development in living animals, and thus focus follow-up studies on those that might be most clinically useful.

http://www.cshl.org/

Dilon Technologies, Inc., the leader in molecular breast imaging, announced today that they have formed an alliance with Terason Ultrasound to offer an expanded imaging capability when molecular breast imaging and ultrasound may be required.

BSGI is a molecular breast imaging technique that can see lesions independent of tissue density and discover very early stage cancers, particularly for women with high risk factors or that present with questionable mammograms. With BSGI, metabolic activity is assessed and cancerous cells generally display as "hot spots."

Terason is the innovator and world leader in integrating patented microsystem technology with an Apple MacBook Pro PC. The Terason t3000(TM) Ultrasound System offers premium imaging performance with the portability and functionality of a laptop. When used as a complement to the Dilon 6800 Gamma Camera, physicians are able to move from BSGI to ultrasound without leaving the exam room.

Bob Moussa, President and CEO of Dilon Technologies said, "We are proud to partner with Terason to complement BSGI with ultrasound when appropriate. Through innovative products and partnerships such as this, Dilon continues to expand its offerings to be the best in patient care and cancer detection."

The Terason t3000 offers best-in-class image quality; ease of use with a dual user interface; and an integrated information management and communications protocol in one system. For quick on-the-spot, accurate scanning in a wide array of clinical applications, transducers quickly connect to the system allowing technicians to perform an ultrasound exam at the point of patient care. Terason's patented high-density, beam-forming architecture provides a superior performance cost-effective ultrasound solution.

The ultrasound system is built upon an industry respected combination of the Apple PC coupled with Windows Operating System to provide seamless networking capabilities, compatibility with various applications, standard connections, and software updates. The system includes DICOM, Wireless, Integrated CD/DVD, and USB capability. The ergonomically designed slide out dual-user interface is extremely easy to use. The Terason t3000(TM) Ultrasound System is a powerful ultrasound designed to work smarter, enhance workflow, and promote efficiency and diagnostic confidence.

"BSGI has proven to be an important adjunct to mammography and ultrasound in the diagnosis of breast cancer. We are excited to be in a partnership with Dilon as we both continue to offer important advances in care," said Alice Chiang, Ph.D., Terason's CEO.

http://www.dilon.com/

An abstract presented at the American Association for Cancer Research's Seventh Annual International Conference on Frontiers in Cancer Prevention Research shows that lower socioeconomic status reduced the chance of early stage diagnosis and survival of colorectal cancer in Colorado.

"Diagnosis of colorectal cancer at an early stage can lead to better survival. Good screening tests for early stage diagnosis of colorectal cancer are available," Alma Palisoc, M.D., a preventive medicine resident physician at the University of Colorado Denver and lead author of the study, said. "However, those in the lower socioeconomic groups and those having no health insurance or only Medicaid coverage are more likely to be diagnosed with colorectal cancer at a later stage of disease when survival is worse."

In the study, Palisoc, and her co-authors from the Colorado School of Public Health and the Colorado Department of Public Health and Environment, used data from 21,212 colorectal cancers reported to the Colorado Central Cancer Registry over a 12-year period. Using information from the 2000 U.S. census on block group socioeconomic characteristics, they then examined differences in early-stage diagnosis and five-year, cause-specific survival by socioeconomic status.

They found early-stage diagnosis was less common for all three socioeconomic groups among those with no health insurance or only Medicaid coverage. They also observed that early-stage diagnosis was less common among those younger than 65 among lower socioeconomic groups. "In contrast, for those 65 and older, Medicare covers colorectal cancer screening tests and so earlier-stage diagnosis was observed to be similar among the three groups." More important, for those under the age of 65, there was a 19 percent decrease in five-year survival between the higher and lower groups.

"We concluded that both lack of health insurance and being in a lower socioeconomic strata are important risk factors for later stage colorectal cancers and for poorer survival from colorectal cancer," Palisoc said.

Colorectal cancer incidence rates have declined considerably over the last two decades, due to increased screening, which allows physicians to detect and remove colorectal polyps before forming cancer. "Later detection and, therefore, lower survival of colorectal cancer among those in the low socioeconomic strata were most likely due to barriers in accessing screening tests," Palisoc said.

"These findings can hopefully raise more awareness to the importance of removing barriers to lifesaving health services such as screening tests and treatment for colorectal cancer, " Palisoc said. "We need to identify ways to provide such services in Colorado and across the nation, even for people without health insurance."

http://www.aacr.org/

Using a novel technique developed by Mitchell Sogin of the Marine Biological Laboratory (MBL) to identify different types of bacteria, scientists have completed the most precise survey to date of how microbial communities in the human gut respond to antibiotic treatment.

Sogin, director of the MBL's Josephine Bay Paul Center, and Susan Huse of the MBL, along with David Relman and Les Dethlefsen of Stanford University, identified pervasive changes in the gut microbial communities of three healthy humans after a five-day course of the antibiotic Ciprofloxacin. Their results are reported in the Nov. 18 issue of PloS Biology .

Using very conservative criteria, the scientists identified at least 3,300 to 5,700 different taxa (genetically distinct types) of bacteria in the human distal gut, and antibiotic treatment influenced the abundance of about a third of those taxa.

"You clearly get shifts in the structure of the microbial community with antibiotic treatment," says Sogin. "Some bacteria that were in low abundance prior to treatment may become more abundant, and bacteria that were dominant may decrease in abundance. When you get these shifts, they may be persistent. Some individuals may recover quickly, and others won't recover for many months."

In all the individuals tested in this study, the bacterial community recovered and closely resembled its pre-treatment state within four weeks after the antibiotic course ended, but several bacterial taxa failed to recover within six months.

This raises questions about the health effects of perturbations to the human-microbial symbiosis in the gut, such as may occur with antibiotic treatment. Because specific microbial populations mediate many chemical transformations in the gut-and previous studies have related these processes to cancer and obesity, among other conditions-changes in the composition of the gut microbiota could have important, but as yet undiscovered, health effects.

"When you change the microbial population structure in the gut, you may affect how that population is keeping indigenous pathogens at manageable levels," says Sogin. Bacteria that do not normally cause problems, for example, may begin to grow more rapidly, and cause disease.

The study is part of a large, international effort to fully characterize the microbiota in the human gut, which is the highest-density natural bacterial ecosystem known. Up to 100 trillion microbial cells reside in the gut, and this community plays essential roles in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses.

Until recently, descriptions of human-associated microbiota were constrained by techniques of cultivating (and thus identifying) bacteria. Less than 20-40% of the microbes in the human distal gut, for example, have been cultured in the laboratory. Since the late 1980s, however, cultivation-independent microbial surveys have been developed that identify community members by genetic sequencing. Sogin's technique, for example, which was used in this study, characterizes microbial populations by sequencing short, hypervariable regions of one gene common to all microbes, the 16S rRNA gene. This pyrosequencing technique reveals greater taxonomic richness in microbial samples at a fraction of the cost of traditional sequencing technologies.

http://www.mbl.edu/

The risk of non-AIDS cancer is higher for individuals infected with HIV than for the general population, according to a meta-analysis presented here at the American Association for Cancer Research's Seventh Annual International Conference on Frontiers in Cancer Prevention Research.

Compared with the general population, the risk for non-AIDS cancers was 2.3 times higher for men with HIV and 1.5 times greater for women with HIV. Among individuals with HIV, however, incidence rates were similar for those with AIDS and those without, relative to the general population.

Although the researchers did not examine why non-AIDS cancers may occur at a greater rate among individuals with HIV, clinicians should be aware of this potential increased risk when examining patients with HIV, said Meredith Shiels, M.H.S., an epidemiologist at Johns Hopkins School of Public Health.

"In particular, clinicians of HIV-infected patients should inquire about well-known modifiable cancer risk factors," she said. "For example, the prevalence of cigarette smoking, which is a cause of many types of cancer, is known to be higher among HIV-infected individuals."

Modern drug therapy has led to a longer life for patients with HIV. Because cancer risk increases with age, investigating the risk of cancer among patients with HIV is important. Although some cancers are known to be associated with HIV, such as Kaposi's sarcoma, non-Hodgkin's lymphoma and cervical cancer, limited research has been conducted on risk of non-AIDS cancers.

Shiels and her colleagues analyzed data from 11 U.S. and international studies comparing cancer incidence in individuals with HIV with the general population. Individual studies were excluded if they included data that overlapped with more recent studies. The meta-analysis combined standardized incidence ratios from each study and examined whether they differed by gender and prior AIDS diagnosis.

"We observed an overall elevated risk for all non-AIDS cancers combined among HIV-infected individuals compared with the general population," Shiels said. "The elevated risk appears to be greater among men than women."

Relative to the general population, the incidence of non-AIDS cancer appeared higher for individuals with and without an AIDS diagnosis. When the researchers adjusted the data for gender and study design, the estimates were similar: the risk of non-AIDS cancer was about two times greater than the general population for HIV-infected individuals both with and without AIDS.

When managing patients with HIV, clinicians should be aware of the potential for increased risk of non-AIDS related cancers. It is important for regular cancer screening to take place and for clinicians to encourage patients to modify factors that could affect cancer risk, such as cigarette use and nutrition.

The meta-analysis did not investigate possible reasons for the increased risk of non-AIDS cancers among patients with HIV. Understanding the link may lead to better management of cancer among patients with HIV and could be a topic for future study.

http://www.aacr.org/