Cancer Causing Gene Protein Found

Dr. Tak Mak and scientists at The Campbell Family Institute for Breast Cancer Research at Princess Margaret Hospital have discovered the role of two "cousins" in the genetic family tree of cancer development.

The findings, published online today in the journal Genes and Development, plant the seed for a critical new branch of scientific inquiry, says Dr. Mak, principal investigator. Dr. Mak, Director of The Campbell Family Institute is also a Professor, University of Toronto, in the Departments of Medical Biophysics and Immunology.

The cousins are proteins related to the gene p53 family – the patriarch known for two decades to be the master gatekeeper that controls all cancer development. When gene p53 is defective, it loses its ability to regulate healthy cells and suppress cancer.

"Until now, we thought these cousins (TAp73 protein isoforms) were not involved in cancer. Our results prove that they are. This is fundamental to understanding every human cancer and furthering the science."

In the lab, Dr. Mak and his team challenged traditional thinking about the role of these proteins. "Before, scientists studied only whether these proteins were present or absent. We decided to study how they interact with each other and discovered that they actually have a split personality. When we turn one 'on' or 'off', the other changes behavior and becomes part of the cancer-causing process. The key is understanding the ratio of the interaction."

"The next step is to understand how the ratio affects cell division that leads to human cancer," says Dr. Mak, whose work was supported by the Canadian Institutes for Health Research.
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Genome analysis reveals new protein associated with breast cancer progression

A novel systems-based approach that combines comprehensive gene expression profiling with genome-wide transcription factor analysis and protein-protein interaction has led researchers to an important genetic marker that can help physicians know which breast cancer patients are at highest risk and will require more aggressive treatment, a research team based at the University of Chicago Medical Center reports in the April 15, 2008, issue of the journal Molecular Systems Biology.

The researchers found that high expression of a protein known as H2A.Z, which is associated with the expression of genes within the nucleus, can help physicians predict which patients are most at risk for disease spread and death. It could also serve as a new target for therapy.

“Elevated H2A.Z expression is significantly associated with metastasis and shorter survival, and it could quickly help doctors make better predictions and treatment choices for their patients,” said study director Kevin White, PhD, professor of human genetics and director of the Institute for Genomics and Systems Biology at the University of Chicago and Argonne National Laboratory. “It could also provide clues to new therapies.”

“But, perhaps more important,” he added, “we think we have developed an integrated approach to genomic analysis that can be applied to a wide range of cancers.”

Instead of a standard whole-genome analysis, looking for genetic variations that correlate with disease risk, White and colleagues integrated multiple genetic technologies to measure the effects of estrogens, which play a crucial role in many breast cancers, on multiple cellular pathways, what they refer to as a “transcriptional regulatory cascade.”

The female hormone estrogen acts by binding to the estrogen receptor, which carries the hormone’s signal to a cell’s nucleus, where it activates many other genes. One of those genes is a known cancer-related gene called c-MYC, which in turn regulates its own cascade of gene targets.

White’s team set out to map out the many sequential genetic events that occur in breast cancer cells after estrogen binding, using a series of innovative technologies. They ultimately found that estrogen-stimulated c-MYC enhanced production of H2A.Z, which altered the positioning and activation of various genes in ways that increased the odds that a cancer would spread to the lymph nodes and ultimately to distant sites, often resulting in the patient’s death.

This is not a simple process. In tumor cells from patients with estrogen-dependent breast cancers, the researchers found estrogen affected 1,615 genetic regions. One of those was the promoter for the gene for c-MYC, which, when activated, could bind another set of overlapping 311 genetic regions.

Both estrogen and c-MYC interact with the gene for H2A.Z, leading to increased production of this protein in breast cancer cells. When the researchers looked at tumor tissue samples collected from 500 patients, they found that elevated levels of H2A.Z were highly correlated with the spread of the cancer to lymph nodes and decreased patient survival. Adding H2A.Z expression to other known risk factors provided “significant prognostic information,” the authors note, “beyond what these factors alone provide.”

“Although it has been implicated in genomic stability and gene transcription, H2A.Z has never been reported to be associated with cancer,” said White. “We would not have found this clinically important factor without taking such a large-scale integrated approach.”

“We suspect this integrated systems approach will lead us to a number of previously unsuspected genes that play a role in disease initiation and progression,” he said. “Many of these could become targets for new treatments.”

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A Protein that Triggers Aggressive Breast Cancer

SATB1 is a nuclear protein well known for its crucial role in regulating gene expression during the differentiation and activation of T cells, making it a key player in the immune system. But SATB1 has now revealed a darker side: it is an essential contributing factor in the most aggressive forms of breast cancer.

SATB1 forms a three-dimensional cage-like structure within the cell nucleus (left) that binds to DNA specific sites within genes, reorganizes chromatin, and recruits enzymes that promote the expression or suppression of genes (right).

Breast cancer cells need SATB1 to become metastatic; metastasis — the stage when cells break away from the original tumor and spread to other parts of the body — is the final step of solid tumor progression and is the most common cause of death in cancer patients.

"In breast tumors, SATB1 reprograms the genome to change the expression of hundreds of genes, promoting tumor growth and metastasis," says Terumi Kohwi-Shigematsu, a scientist in the Life Sciences Division of the Department of Energy's Lawrence Berkeley National Laboratory who, with her colleagues, discovered SATB1 and has since investigated its many functions. She says, "SATB1's role in breast cancer is a new paradigm for the way tumors progress."

Kohwi-Shigematsu, working with Berkeley Lab's Hye-Jung Han and Yoshinori Kohwi, and with Jose Russo of the Fox Chase Cancer Center in Philadelphia, found that when SATB1 is detected in a breast tumor, the cancer is highly likely to progress or recur.

Moreover, by introducing SATB1 into otherwise nonmetastatic breast cancer cells, invasive tumors can be induced in mice; conversely, removing SATB1 from metastatic cells not only abolishes metastasis and tumor growth in mice but also returns cells to their normal appearance in vitro. The researchers have published these and other findings in the March 13, 2008 issue of Nature.

How SATB1 works

Kohwi-Shigematsu and Kohwi originally identified a class of DNA sequences they called base-unpairing regions (BURs), a finding that led Kohwi-Shigematsu's group to the discovery of "special AT-rich sequence binding protein 1" (SATB1). SATB1 binds to BURs in double-stranded DNA by recognizing the BURs' distinctive phosphate-backbone structure. BURs contain unusual sequence contexts that readily unzip to expose DNA's individual strands.

As a nuclear architectural protein, SATB1 forms what Kohwi-Shigematsu calls a "3‑D chickenwire network" inside the nucleus of the cell. SATB1 anchors chromosomes to its cage-like structure by tethering the BURs in the target genes, thus serving as a kind of "glue" for these genes. SATB1 folds and remodels the chromatin — the intertwined DNA and proteins that form chromosomes — into new shapes, bringing even distant parts of the genome together for coordinated control of gene expression and regulation.

SATB1 also globally regulates histone status in the chromatin by recruiting histone-modifying enzymes to the target-gene loci. Histones are the proteins around which DNA in chromatin is wound like thread on a spool; histone status renders DNA sequences accessible or inaccessible for transcription.

Early on, SATB1's ability to regulate gene expression was identified as critical to T-cell development. Although Kohwi-Shigematsu and her colleagues have found several other cell types that use SATB1 to reshape chromatin and regulate gene expression in a similar way, SATB1 is not expressed in all cells. SATB1 seems particularly important in cells which must change their function — as do many progenitor cells, including the thymocytes that turn into T cells. And as cancerous cells must do to turn into metastatic cells.

"Hye-Jung Han of our group started by looking at two dozen breast-cell lines, including normal human epithelial cells" — epithelial cells are the kind that form the linings of hollow glands in the breast — "and both nonmetastatic and metastatic breast cancer cells," Kohwi-Shigematsu says. "Only the metastatic cells expressed SATB1, with the most aggressive breast cancer cells showing the highest levels of the protein."

The researchers examined over 2,000 human primary breast cancer tissue samples for which clinical follow-up studies were available. The highest levels of SATB1 were in samples from patients whose survival times had been shortest; patients whose tumor samples had no SATB1 expression generally had longer survival times.

The analysis showed that a high level of SATB1 expression by itself is an excellent indicator of poor prognosis — independent of whether breast cancer cells have already metastasized to the lymph nodes at the time of diagnosis.

SATB1 takes command

The reason why SATB1 is a good prognostic marker is because SATB1 drives breast cancer cells to become invasive, as revealed by both in vitro and in vivo studies.

The researchers performed in vitro studies of highly metastatic cell lines, reducing SATB1 expression through the use of shRNAs, "short-hairpin-interfering" RNAs, that dramatically reduced the invasive capacity of these cells and also reduced their capacity for unattached growth — a necessity if metastasizing cancer cells are to travel through the blood and lymph vessels.

With increasing stages of breast cancer, initially nonmalignant cells making up the acini in the breast become increasingly disorganized and finally metastasize (top). Breast cells cultured in a three-dimensional matrix form acinar structures, but the expression of SATB1 in these cells causes increasing disorganization. When SATB1 expression is reduced in these metastatic cells, they return to normal appearance (bottom).

Other in vitro studies used normal breast epithelial cells, the kind that form the hollow oriented structures called acini, the milk-secreting glands of the breast. Normal cells form similar, well-organized acinar structures in vitro, whereas in highly metastatic epithelial cell lines these structures are disorganized and lack polarity. When SATB1 expression is reduced in the metastatic cell lines, they too form the kind of polarized, uniform acinar structures found in normal mammary epithelial cells.

These in vitro results were confirmed in vivo, in mice. Nine weeks after human aggressive breast cancer cells were injected into the tails of test mice, these cells developed into metastatic nodules (tumors) on the lungs. But when SATB1 expression was reduced or removed from the injected cancer cells, the mice developed fewer or even no nodules, depending on the remaining levels of SATB1. Once SATB1 is greatly reduced, these cells no longer form tumors when injected directly into breast fat pads.

In vivo studies also established that cancer cells which do not normally express SATB1, and do not normally metastasize, can become aggressive if they are modified to express SATB1. Once SATB1 is expressed, they form large tumors when injected into breast fat pads; they then invade the blood circulatory system and form metastatic tumors in lungs.

The tests of human breast cancer cell lines in mice allowed the researchers to establish that, for these cells, SATB1 is necessary and sufficient for tumor growth and metastatic activity.

"SATB1 is a key player in the metastasis of breast cancer cells, controlling expression of over a thousand genes," says Kohwi-Shigematsu. "It increases the expression of genes that promote tumor growth and reduces the expression of tumor suppressors. Among the regulated genes are numerous growth-factor genes and genes affecting cell adhesion, cell signaling, cell-cycle regulation, and other functions."

Among the important genes regulated by SATB1, the researcher identified many that are already known to play a role in aggressive breast cancers, including the epidermal growth factor gene ERBB2, otherwise known as HER2.

"What we have found is a new model of altered gene regulation during the progression of tumors, which depends on SATB1's reprogramming of the gene expression profile," Kohwi-Shigematsu says. "What results is a new and aggressive cancer phenotype that promotes both tumor growth and metastasis."

The discovery of SATB1's key part in aggressive breast cancer has profound implications for prognosis and for possible new treatments for cancer's most malignant forms. At the same time, the discovery opens a wide field of fundamental scientific inquiry, beginning with the most basic questions. What determines the particular sets of genes affected by SATB1 in specific tissues? What other factors may work together with SATB1?

"An important question is what turns on SATB1 during breast cancer progression," says Kohwi-Shigematsu. "That's just the beginning of the things we really want to know."

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Biologists identify key protein in cell’s 'self-eating' function

Molecular biologists at the University of California, San Diego have found one piece of the complex puzzle of autophagy, the process of “self-eating” performed by all eukaryotic cells -- cells with a nucleus -- to keep themselves healthy.

Their finding, published in the March 11 issue of the journal Developmental Cell, is important because it allows scientists to control this one aspect of cellular autophagy, and may lead to the ability to control other selective “self-eating” processes. This, in turn, could help illuminate autophagy’s role in aging, immunity, neurodegeneration and cancer.

All eukaryotic cells dispose of bacteria, viruses, damaged organelles and other non-essential components through this self-eating process. A part of the cell called the lysosome engulfs and degrades subcellular detritus. The ability of cells to recycle and reuse the cellular raw materials, as well as to “re-model” themselves in response to changing conditions, allows them to adapt and survive.

Autophagy was first described about 40 years ago, but has recently become a topic of great interest in cell biology because it is linked to cell growth, development aging and homeostasis -- helping cells to maintain a balance among synthesis, degradation and recycling.

The UC San Diego researchers report in their paper that they identified a novel protein called Atg30 (one of 31 required for autophagy-related processes) from the yeast Pichia pastoris, that controls the degradation of a sub-compartment of cells, the peroxisomes.

Peroxisomes generate and dispose of harmful peroxides that are by-products of oxidative chemical reactions.

Different organelles within the cell are degraded by lysosomes when the organelles are damaged or not necessary, said Jean-Claude Farré, the biologist who identified Atg30. The team is investigating peroxisomes, and working to understand how and why they are selected by the lysosome for degradation.

What the biologists found, he said, is that “this new protein can mediate peroxisome selection during pexophagy – that is, it is necessary for pexophagy, but not for other autophagy-related processes.”

Suresh Subramani, a professor of biology who headed the team, said they have established that Atg30 is a “key player” in the selection of peroxisomes for delivery to “the autophagy machinery” for re-cycling.

“For the first time, we can use a protein to control the process,” Subramani said. “It’s an important step in understanding the workings of cells.”

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Protein in Embryonic Stem Cells Controls Malignant Tumor Cells

A protein that governs development of human embryonic stem cells (hESCs) also inhibits the growth and spread of malignant melanoma, the deadliest skin cancer, Northwestern University researchers have discovered. Metastatic melanoma, which develops from the transformation of skin pigment cells or melanocytes, has a death rate of more than 80 percent and a median survival of less than 7.5 months.

The Northwestern scientists, led by researcher Mary J. C. Hendrix, additionally found that the protein, called Lefty, prevents aggressive breast cancer cells from metastasizing. Death from metastatic breast cancer exceeded 40,000 in 2007, with over 180,000 new cases diagnosed in the United States.

Importantly, Lefty is secreted only in hESCs, and not in any other stem cell type tested – including stem cells isolated from amniotic fluid, cord blood or adult bone marrow – or placental cells.

Results of the study, described in an article in the March 3rd online version of The Proceedings of the National Academy of Sciences, build on an elegant body of research by the Hendrix lab to identify the genes and cellular pathways involved in cancer metastasis.

Hendrix is president and scientific director of the Children’s Memorial Research Center and professor in The Robert H. Lurie Comprehensive Cancer Center of Northwestern University and at Northwestern's Feinberg School of Medicine. Lynne-Marie Postovit, who was first author on the study and a post-doctoral trainee in the Hendrix lab, is currently an assistant professor at the University of Western Ontario, Canada.

Embryonic stem cells are pluripotent, meaning they can become any of 200-plus cell types in the adult body, depending on the signals they receive from their microenvironment (surrounding cells, tissues and vasculature). During cancer progression, malignant cells also receive and release signals from their microenvironment, cues that promote tumor growth and metastasis.

Groundbreaking work by Hendrix and colleagues is elucidating how, by becoming more like unspecialized stem cells, aggressive melanoma cells gain enhanced abilities to migrate, invade and metastasize while remaining virtually undetected by the immune system.

Hendrix and co-researchers previously demonstrated that a three-dimensional matrix conditioned by hESCs induced metastatic melanoma cells to revert to a normal, skin cell-like type with the ability to form colonies in the manner of hESCs (Postovit and Seftor et al, Stem Cells 24:501-505, 2006).

“This observation allowed us to appreciate the powerful influence of the hESC microenvironment on the reprogramming of metastatic melanoma cells,” Hendrix said.

In subsequent experiments, Hendrix, Postovit and co-researchers found that aggressive melanoma and breast cancer produce a “morphogenic” protein called Nodal, which is essential for human embryonic stem cell pluripotency (Topczewska et al, Nature Medicine 12:925-932, 2006). Other researchers have found that Nodal also is present in testicular cancer.

“Thus, Nodal may serve as a prognostic marker of aggressive behaviors in human cancers,” Hendrix said.

As described in the PNAS study, the Lefty protein inhibits production of Nodal and therefore plays a major role in embryonic cell differentiation and development – under normal circumstances.

Hendrix and colleagues discovered that metastatic tumor cells do not express Lefty, allowing them to overproduce Nodal in an unregulated manner.

However, when the group exposed metastatic tumor cells to the microenvironment of hESCs containing Lefty, they witnessed dramatically reduced Nodal expression (production) in these cancer cells together with decreased tumor cell growth and invasiveness and an increase in apoptosis, or programmed cell suicide.

Although exposure to a hESC microenvironment inhibited Nodal expression and tumor growth in both metastatic melanoma and breast cancer cells, the breast cancer cells underwent more complex reprogramming. Melanoma cells responded to the hESC-derived factors within three days, but breast cancer cells required two additional days to achieve the most significant reduction in Nodal.

This discrepancy is likely due to differences in signaling mechanisms between the two cell types. Yet, despite the inherent differences between melanoma cells and breast cancer cells, these divergent tumor types both underwent cell suicide following exposure to the hESC microenvironment.

“The remarkable similarity of the responses of the two tumor types is likely attributable to the commonality of plasticity (for example, the aberrant and unregulated expression of Nodal) that indiscriminately unifies highly aggressive cancer cells, regardless of their tissue of origin,” Hendrix said.

“Further, the tumor suppressive effects of the hECs microenvironment, by neutralizing the expression of Nodal in aggressive tumor cells, provide previously unexplored novel therapeutic modalities for cancer treatment,” Hendrix said.

However, while findings from the study suggest that hESC-derived Lefty may have potential to prevent metastasis, it is not the only tumor suppressive factor within the embryonic microenvironment.

Observations from the study highlight the potential utility of isolating factors within the hESC microenvironment responsible for influencing tumor cell fate and reversing the cancerous properties of metastatic tumor cells, such as melanoma and breast cancer.

Additional contributing authors on the study include N. Margaryan; E. Seftor; D. Kirschmann; D. Abbott; W. Wheaton; A. Lipavsky; and R. Seftor.

This study was supported by grants from the Illinois Regenerative Medicine Institute; the National Institutes of Health (CA50702 and CA121205); the Charlotte Geyer Foundation (to Dr. Hendrix); and a Canadian Institutes of Health Research Postdoctoral Fellowship (to Dr. Postovit).
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