Core Facilities Offer Centralized, Specialized Expertise and State-of-the-Art Equipment

(Top) Human ES cells at the undifferentiated stage. Each blue marker identifies a cell nucleus. The green identifies a human ES cell-specific marker called Tra-1-60. (Above left) The blue indicates the cell nucleus. The red labels a marker expressed in nerve cells called tyrosine hydroxylase. (Above right) The red markers identify human-specific nuclear antigen as a way to reveal the cell nucleus. Green identifies a muscle-specific protein called MF20

While the study of many types of stem cells is still in its infancy, greater understanding of their capacity and of how to direct their activity could facilitate the development of new regenerative treatments for conditions such as Parkinson's disease, diabetes, spinal cord injuries, and cancer. "Embryonic stem cells are capable of giving rise to any type of tissue," explained Memorial Sloan-Kettering stem cell biologist and Lorenz P. Studer. "They are the only cells that have such broad potential."

Memorial Sloan-Kettering created the Sloan-Kettering Institute stem cell research facility to explore the potential of these nascent cells. Center investigators are engaged in studies that range from learning how to manipulate them to repair damage caused by radiation treatment for brain tumors to the development of cell-based therapies targeting Parkinson's disease.

Support for the facility comes from The Starr Foundation, which, in 2005, made a $50 million gift to be distributed over three years to Memorial Sloan-Kettering, The Rockefeller University, and Weill Medical College of Cornell University to establish the Tri-Institutional Stem Cell Initiative. The Initiative includes basic and clinical stem cell research projects and places an emphasis on collaborative studies among the three institutions. It also supports graduate and postdoctoral training related to stem cell research and core research facilities to derive, maintain, and analyze human embryonic stem cells.

The Sloan-Kettering Institute stem cell research facility -- led by Dr. Studer, managed by Mark Tomishima, and staffed by two technicians -- will serve researchers from all three institutions. Its first task is to grow and maintain a large repository of stem cell lines, using human embryonic stem cells obtained from Weill Medical College of Cornell University, The Rockefeller University, and elsewhere.

This is no simple task, however, because by their very nature, "embryonic stem cells are extremely difficult to maintain," explained Dr. Tomishima. "They're inclined to differentiate into mature cells with specialized functions, but not usually the function you want them to have. Even for the best labs in the world, it can be a challenge. We're excited to contribute our expertise to help further this field." Sloan-Kettering Institute's stem cell facility staff will refine ways to coax embryonic stem cells to differentiate into specific types of cells -- such as nerve cells, bone, blood, or muscle -- for further study.

At various points during the process of generating embryonic stem cell lines, Memorial Sloan-Kettering scientists will test the cells to see whether they exhibit the properties that make them pluripotent embryonic stem cells. (A pluripotent cell is one that is able to develop into several different types of cells or tissues in the body.) This process is known as "characterization" and is a type of quality control in which the stem cells are checked to see if they contain specific protein markers that confirm they are undifferentiated cells -- meaning that they have not yet manufactured proteins characteristic of a specialized cell type -- and that they are genetically normal.

In addition, the stem cell core facility staff will provide training to scientists on how to grow human embryonic stem cells in their own laboratories. Consultation will also be available for researchers interested in working with embryonic stem cells from laboratory animals.

Once sufficient amounts of human embryonic stem cells have been produced, the staff will also be able to genetically modify them to mature into cells that overexpress or lack certain genes, providing useful models for studying the genetics of disease. For example, Dr. Studer has been able to introduce a gene into human embryonic stem cells that is frequently mutated in amyotrophic lateral sclerosis (ALS, also known as Lou Gehrig's disease). When the stem cells differentiate into nerve cells -- called motor neurons -- they become sensitive to the gene's toxic effects, creating a model of ALS that can essentially be studied in a laboratory dish.

"The insights gained from our work will also be relevant to understanding cancer, because the signals that guide stem cells are in many cases closely related to those that drive cancer growth," concluded Dr. Studer.

	Optical imaging equipment in the Molecular Cytology Core Facility was used to generate this detailed image of blood vessels in mouse lung tissue

Hypothesizing that cells may be behaving a certain way is one thing, but actually seeing them in action is quite another. That's what led Don Nguyen, a Research Fellow in Joan Massagué's lab, to Memorial Sloan-Kettering's Molecular Cytology Core Facility, where he was able to witness cancer metastasis in real time. Dr. Massagué is Chair of Sloan-Kettering Institute's Cancer Biology and Genetics Program.

"One of the technical challenges in cancer research is to visualize and confirm what we have until recently only assumed tumor cells are capable of doing," Dr. Nguyen said. "For example, the confocal microscopes in the Molecular Cytology Core Facility have enabled us to 'spy' on breast cancer cells invading the lungs of mice. Thanks to the expertise of the facility's staff and the powerful microscopes and software they have available, we were also able to reconstruct three-dimensional images and see how the metastatic tumor cells were interacting with the environment in the lung."

Like Dr. Nguyen, more than 280 scientists from Sloan-Kettering Institute research programs rely on the services of the Molecular Cytology Core Facility to detect and analyze molecules in cells, tissues, organs, embryos and tumors. "Our users are exploring molecular 'markers' that are important both in normal development and in cancer," explained Katia Manova, the laboratory's head.

Molecular Cytology staff members train and assist researchers and offer services that accelerate the research process -- obtaining tissues from investigators, preparing the samples for experiments to pinpoint molecules of interest, and generating detailed images.

Experiments for in situ localization of molecular markers -- that is, identifying the location of molecules in tissues -- are cumbersome and time-consuming to perform manually. They have now been automated and are performed as services of the facility. The automated detection capacity of the laboratory has been quadrupled in less than four years in order to meet the increased needs of users.

Using the facility's optical imaging equipment, investigators can examine tissue samples for molecules that provide clues about how cells grow, divide, differentiate, and die -- information that can shed light on cancer development. "Under our microscopes, you can see not only where the molecules are in the tissue, but how they relate to each other," explained Dr. Manova.

The facility's first confocal microscope -- purchased in 1998 and now referred to by Dr. Manova as the "old soldier" -- is still in use today. But it has been joined by a legion of more-sophisticated imaging systems, enabling faster generation of images with higher quality and precision. Scientists can use the "spinning disk confocal microscope," for instance, to visualize the movement of live cells over a period of more than three days.

The Molecular Cytology Core Facility continually introduces new services and acquires new equipment to stay current with advances in molecular imaging technology. "Because we serve multiple researchers from different institutional programs, we need to make sure that every time we acquire a new system, it will meet diverse user needs," Dr. Manova explained.

Yet novel technology is not a substitute for human beings. "Highly educated and dedicated staff will always be required for the most important parts of the scientific process," Dr. Manova asserted.

In the last decade, the tools of molecular biology, coupled with powerful computers and new software programs, have enabled investigators to produce a wealth of molecular data at an unprecedented rate. Along with the burgeoning data, the still-young and rapidly evolving field of bioinformatics was born. In 2003, Memorial Sloan-Kettering established a dedicated Bioinformatics Core Facility to work with Center researchers on a host of issues related to clinical and laboratory investigations. Led by Alex Lash, the facility can be used by the entire Memorial Sloan-Kettering research community. Bioinformatics professionals help investigators mine the publicly available databases and use mathematical algorithms, computational methods, and information systems to analyze, organize, and visualize their biomedical data.

Services of the Center's Bioinformatics Core Facility range from consultations with investigators about their specific research projects; hands-on workshops on bioinformatics topics (offered not only to Memorial Sloan-Kettering investigators, but also to investigators from Weill Medical College of Cornell University and The Rockefeller University); and the creation of institutional resources, such as software, databases, and image repositories.

For example, medical oncologist William Pao -- an investigator in the Human Oncology and Pathogenesis Program who is trying to identify new genetic mutations involved in lung cancer -- asked the Bioinformatics staff to create a tool to interpret data he had generated concerning a suspected new mutation. Dr. Lash and his colleagues developed a Web-based program to compare the location of the new mutation with mutations found in other cancers, either in the same gene or in analogous parts of related genes. The identification of a similar or analogous mutation would enable him to be more confident that the new mutation played a role in lung cancer.

Moreover, the tool, which they dubbed the MUTAGRATOR (for "mutation integrator"), is now freely available on the Internet for the use of the worldwide research community (at cbio.mskcc.org/~lash/mutagrator). "It's a great program for tumor mutational profiling studies, because it allows you to narrow down candidate mutations in a quick and easy way and to see if a putative variant could have biological significance," observed Dr. Pao.

The Bioinformatics Core Facility also hosts weekly "walk-in" clinics, offering clinical and basic researchers a chance to work one-on-one with Bioinformatics staff to address questions about biomedical research methods. One clinic is held in Memorial Sloan-Kettering's Library in the Rockefeller Research Laboratories, and a second clinic was recently established in The Mortimer B. Zuckerman Research Center.

"Research today is very data-driven, and bioinformatics is an essential component of this movement," explained Dr. Lash.