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City of Hope, Duarte, California – Combining Science with Soul to Create Miracles at a Comprehensive Cancer Center designated by the National Cancer InstituteAn Interview with the Provost and Chief Scientific Officer of City of Hope, Steven T. Rosen, M.D.

Author: Gail S. Thornton, M.A.

Co-Editor: The VOICES of Patients, Hospital CEOs, HealthCare Providers, Caregivers and Families: Personal Experience with Critical Care and Invasive Medical Procedures

 

City of Hope (https://www.cityofhope.org/homepage), a world leader in the research and treatment of cancer, diabetes, and other serious diseases, is an independent, biomedical research institution and comprehensive cancer center committed to researching, treating and preventing cancer, with an equal commitment to curing and preventing diabetes and other life-threatening diseases. Founded in 1913, City of Hope is one of only 47 comprehensive cancer centers in the nation, as designated by the National Cancer Institute.

City of Hope possesses flexibility that larger institutions typically lack. Innovative concepts move quickly from the laboratory to patient trials — and then to market, where they benefit patients around the world.

As a founding member of the National Comprehensive Cancer Network, their research and treatment protocols advance care throughout the nation. They are also part of ORIEN (Oncology Research Information Exchange Network), the world’s largest cancer research collaboration devoted to precision medicine. And they continue to receive the highest level of accreditation by the American College of Surgeons Commission on Cancer for their exceptional level of cancer care.

As an innovator, City of Hope is a pioneer in bone marrow and stem cell transplants with one of the largest and most successful of its kind in the world. Other examples of its leadership and innovation include,

  • Numerous breakthrough cancer drugs, including Herceptin, Rituxan, Erbitux, and Avastin, are based on technology pioneered by City of Hope and are saving lives worldwide.
  • To date, City of Hope surgeons have performed more than 10,000 robotic procedures for prostate, kidney, colon, liver, bladder, gynecologic, oral and other cancers.
  • They are a national leader in islet cell transplantation, which has the potential to reverse type 1 diabetes, and also provide islet cells for research at other institutions throughout the U.S.
  • Millions of people with diabetes benefit from synthetic human insulin, developed through research conducted at City of Hope.
  • Their scientists are pioneering the application of blood stem cell transplants to treat patients with HIV- and AIDS related lymphoma. Using a new form of gene therapy, their researchers achieved the first long-term persistence of anti-HIV genes in patients with AIDS-related lymphoma — a treatment that may ultimately cure lymphoma and HIV/AIDS.

 

Additionally, City of Hope has three on-campus manufacturing facilities producing biologic and chemical compounds to good manufacturing practice (GMP) standards.

City of Hope launched its Alpha Clinic, thanks to an $8 million, five-year grant from the California Institute for Regenerative Medicine (CIRM). The award is part of CIRM’s Alpha Stem Cell Clinics program, which aims to create one-stop centers for clinical trials focused on stem cell treatments for currently incurable diseases. The Alpha Clinics Network is already running 35 different clinical trials involving hundreds of patients, 17 of which are being conducted at City of Hope. Current clinical trials include transplants of blood stem cells modified to treat patients with AIDS and lymphoma, neural stem cells to deliver drugs directly to cancers hiding in the brain, and T cell immunotherapy trials.

Located just northeast of Los Angeles, landscaped gardens and open spaces surround City of Hope’s leading-edge medical and research facilities at its main campus in Duarte, California. City of Hope also has 14 community practice clinics throughout Southern California.

COH robotic (1)COH Helford H (1)COH1 Dr__Rosen_Clinic-2 (2)COH8 Janice_Huss-7COH7 COH_1369COH6 GMP_0454COH4 DSC_9279

Image SOURCE: Photographs courtesy of City of Hope, Duarte, California. Interior and exterior photos of the City of Hope, including Dr. Steven T. Rosen and his team.

 

Below is my interview with the Provost and Chief Scientific Officer of City of Hope, Steven T. Rosen, M.D., which occurred in April, 2017.

 

What sets City of Hope apart from other hospitals and research centers?

Dr. Rosen: City of Hope offers a unique blend of compassionate care and research innovation that simply can’t be found anywhere else.

We’re more than a medical center, and more than a research facility. We take the most compassionate patient-focused care available, combine it with today’s leading-edge medical advances, and infuse both with a quest to deliver better outcomes.

I’m proud to say that we’re known for rapidly translating scientific research into new treatments and cures, and that our technology has led to the development of four of the most widely used cancer-fighting drugs, Herceptin (trastuzumab), Avastin (bevacizumab), Erbitux (cetuximab), and Rituxin (rituximab).

City of Hope is a family. Our special team of experts treats the whole person and the family, not just a body, or a case or a disease. In fact, some of our patients have shared their stories of success. It is gratifying for me and our many health professionals to be able to make a positive difference in their lives.

Eleven years ago, Los Angeles firefighter Gus Perez was facing a battle far greater than any he’d ever known. He was diagnosed with CML (chronic myelogenous leukemia). Gus began receiving the drug Gleevec, which put him into remission. Given the drug’s success, he almost resigned himself to staying on it, yet was drawn to another option: undergoing a bone marrow transplant at City of Hope. “I went to my favorite ocean spot,” Gus recalls. “I put on my wetsuit, like I’ve done thousands of times, and paddled out. Every wave was special because I wasn’t sure if I was ever going to be back. And I remember getting out of the water and counting the steps to my car, thinking, ‘I’m going to beat this. I’m going to retrace those steps.’ And I’m happy to say I was able to do it.” Gus and his family recently celebrated the 10th anniversary of his bone marrow transplant. “City of Hope is more than just medical treatment,” Gus says. “They have to put you back together from the ground up. And to me, that’s truly a miracle.”

 

As an active 14-year-old, Nicole Schulz loved cheerleading and hanging out with her friends. Then her whole world changed. Nicole learned that her fatigue and other symptoms weren’t “just the flu,” but the effects of acute myelogenous leukemia (AML), an aggressive disease that rendered her bone marrow 97 percent cancerous. Nicole spent the next three and a half months at City of Hope, fighting the cancer with a daily regimen of chemotherapy and blood and platelet transfusions. “It put me into remission,” Nicole says. “But I wasn’t cured. And I wanted a cure.” Fortunately, Nicole was a candidate for a bone marrow transplant. Her malfunctioning marrow cells would be replaced with healthy marrow from a matching unrelated donor. “I never gave up — and neither did City of Hope,” Nicole says. After two bone marrow transplants and tremendous perseverance, Nicole is back to living the life she once knew and quickly making up for lost time.

 

When Jim Murphy’s doctor called and asked to see him on Christmas Eve, Jim knew it wasn’t going to be good news. And he was right. “The diagnosis was esophageal cancer,” Jim says. “Once they tell you that, there’s nothing you can do but formulate your action plan.” Jim would need to undergo chemotherapy, radiation and surgery to remove the tumor from his esophagus. It would require taking two-thirds of his esophagus and a third of his stomach. Despite the intense treatment, Jim was determined to keep his life as normal as possible. Throughout his chemotherapy and radiation therapy, he never missed a day of work, even riding his mountain bike to and from City of Hope to take his treatments. “I needed to show myself one victory after another,” Jim says. “I know City of Hope appreciated the fact that I was fighting as hard as they were.” Now cancer-free for several years, Jim credits City of Hope with giving him the best chance to fight his disease. “What really impressed me was that the research was right there at City of Hope. If they have something experimental, it goes from the researcher, right to the doctor and right to you. It’s the ultimate weapon — doctors reaching out for researchers, researchers reaching out for doctors. And the patient wins.”

 

City of Hope is a pioneer in the fields of bone marrow transplantation, diabetes and breakthrough cancer drugs based on technology developed at the institution.  How are you transforming the future of health care by turning science into a practical benefit for patients? 

Dr. Rosen: This is a distinctive place where brilliant research moves rapidly from concept to cure. That’s what we do—we speed breakthroughs in the lab to benefit patients in the clinic

Many know us for our leadership in fighting cancer, but fighting cancer is only part of our story. For decades, we’ve been making history in the fight against diabetes and other life-threatening illnesses that can be just as dangerous, and shattering, to patients and their families.

Every year, we conduct 400+ clinical trials, enrolling 6,000+ patients; hold 300+ patents and submit nearly 30 applications to the U.S. Food and Drug Administration (FDA) for investigational new drugs; and offer comprehensive assistance for patients and their families, including patient education, support groups, social resources, mind-body therapies and patient navigators.

We also translate breakthrough laboratory findings into real, lifesaving treatments and cures, and manufacture them at three on-campus facilities. Our goal is to get patients the treatments they need as fast as humanly possible.

We are in the race to save lives – and win. In our research efforts, we are teaching immune cells to attack tumors and Don J. Diamond [Ph.D.], Vincent Chung, [M.D.], and other City of Hope researchers launched a clinical trial seeking ways to effectively activate a patient’s own immune system to fight his or her cancer. The team is combining an immune-boosting vaccine with a drug that inhibits tumor cells’ ability to grow — to encourage immune cells to attack and eliminate tumors such as non-small cell lung cancer, melanoma, triple-negative breast cancer, renal cell carcinoma and many other cancer types.

City of Hope’s Diabetes & Metabolism Research Institute is committed to developing a cure for type 1 diabetes (T1D) within six years, fueled by a $50 million funding program led by the Wanek family. Research is already underway to unlock the immune system’s role in diabetes, including T cell modulation and stem cell-based therapies that may reverse the autoimmune attack on islet cells in the pancreas, which is the cause of T1D. City of Hope’s Bart Roep [Ph.D.], previously worked at Leiden University Medical Center in the Netherlands, where he was instrumental in launching a phase 1 clinical trial for a vaccine that aims to spur the immune system to fight, and possibly cure, T1D. Plans are developing for a larger, phase 2 trial to launch in the future at City of Hope.

 

What makes your recent alliance with Translational Genomics Research Institute (TGen) different from other efforts in precision medicine around the country and within our Government to identify treatments for cancer?

Dr. Rosen: Precision medicine is the future of cancer care. Since former Vice President’s Joe Biden’s Moonshot Cancer program was launched to achieve 10 years of progress in preventing, diagnosing and treating cancer, within five years, federal cancer funding has been prioritized to address these aims.

City of Hope and the Translational Genomics Research Institute (TGen) have formed an alliance to fast-track the future of precision medicine for patients. Our clinical leadership as a comprehensive cancer center combined with TGen’s leadership in molecular cancer research will propel us to the forefront of precision medicine and is further evidence of our momentum in transforming the future of health.

In fact, most recently scientists at TGen have identified a potent compound in the fight for an improved treatment against glioblastoma multiforme (GBM), the most common and deadly type of adult brain cancer. This research could represent a breakthrough for us to find an effective long-term treatment. The compound prevents glioblastoma from spreading, and leaves cancer vulnerable to chemotherapy and radiation.  Aurintricarboxylic Acid (ATA) is a chemical compound that in laboratory tests was shown to block the chemical cascade that otherwise allows glioblastoma cells to invade normal brain tissue and resist both chemo and radiation therapy.

The goal is to accelerate the speed at which we advance research discoveries into the clinic to benefit patients worldwide.

 

As a prestigious Comprehensive Cancer Center, City of Hope was named this year as one of the top 20 cancer centers for the past 10 years. How do you achieve that designation year after year? And what specific collaborations, clinical trials and multidisciplinary research programs are under way that offer benefits to patients?

Dr. Rosen: It’s simple – we achieve this through the compassion, commitment and excellence of the City of Hope family, which includes our world-class physicians, staff, supporters and donors.

We look to find the best and brightest professionals and bring them to City of Hope to work with our amazing staff on research, treatments and cures that not only change people’s lives, but also change the world.

We also have a community of forward-looking, incredibly generous and deeply committed supporters and donors. People who get it. People who share our vision. People who take their capacity for business success and apply it to helping others. They provide the fuel that drives us forward, enabling us to do great things.

City of Hope has a long track record of research breakthroughs and is constantly working to turn novel scientific research into the most advanced medical services.

Right now, we have a number of collaborative programs underway, including: Our alliance with TGen to make precision medicine a reality for patients, The Wanek Family Project to Cure Type 1 Diabetes, and Immunotherapy and CAR-T cell therapy clinical trials, which aim to fight against brain tumors and blood cancers.

More specifically, our research team led by Hua Yu, [Ph.D.] and Andreas Herrmann, [Ph.D.], developed a drug to address the way in which cancer uses the STAT3 protein to “corrupt” the immune system. The drug, CpG-STAT3 siRNA, halts the protein’s ability to “talk” to the immune system. It blocks cancer cell growth while sending a message to surrounding immune cells to destroy a tumor, and it may also enhance the effectiveness of other immunotherapies, such as T-cell therapy.

We could also see a functional cure for HIV in the next 5 to 10 years. Gene therapy pioneer, John A. Zaia, [M.D.], the Aaron D. Miller and Edith Miller Chair in Gene Therapy, the director of the Center for Gene Therapy within City of Hope’s Hematologic Malignancies and Stem Cell Transplantation Institute, as well as principal director of our Alpha Clinic, and researchers are building on knowledge gained from the case of the so-called “Berlin patient” whose HIV infection vanished after receiving a stem cell transplant for treatment of leukemia. The donor’s CCR5 gene, HIV’s typical pathway into the body, had a mutation that blocked the virus. The team launched a clinical trial that used a zinc finger nuclease to “cut out” the CCR5 gene, leaving HIV with no place to go. Their goal: to someday deliver a one-time treatment that produces a lifetime change. Integral to the first-in-human trials are the nurses who understand the study protocols, potential side effects and symptoms.

 

Would you share some of the current science under way on breakthrough cures for cancer?

Dr. Rosen: We are achieving promising results in many innovative approaches – gene therapy, targeted therapy, immunotherapy and all aspects of precision medicine. We are also forging new partnerships and collaboration agreements around the world.

Let me share with you a few examples of our cutting-edge science.

City of Hope researchers identified a promising new strategy for dealing with PDAC, an aggressive form of pancreatic cancer. The bacterial-based therapy homes to tumors and provokes an extremely effective tumor-killing response.

Teams at City of Hope are working to load nanoparticles with small snippets of DNA molecules that can stimulate the immune system to attack tumor cells in the brain. This innovative approach can overcome the blood-brain barrier, which blocks many drugs from reaching the tumor site.

A pioneer in islet cell transplantation for the treatment of diabetes, City of Hope conducted a clinical trial to refine its transplantation protocol. Because this new protocol includes an ATG (antithymoglobulin) induction, the immune system will not harm the transplant. The immune-suppression strategy used in the trial is considered a significant improvement over the protocol used in previous islet cell transplant trials.

City of Hope physicians and scientists joined a multinational team in reporting the success of a phase II clinical trial of a novel drug against essential thrombocythemia (ET). ET patients make too many platelets (cells essential for blood clotting), which puts them at risk for abnormal clotting and bleeding. All 18 patients treated with the drug, imetelstat, exhibited decreased platelet levels, and 16 showed normalized blood cell counts.

Researchers found that the CMVPepVax vaccine — developed at City of Hope to boost cellular immunity against cytomegalovirus (CMV) — is safe and effective in stem cell transplant recipients. Building on this discovery, City of Hope and Fortress Biotech formed a company to develop two vaccines, PepVax and Triplex, against CMV, a life-threatening illness in people who have weakened or underdeveloped immune systems such as cancer patients and developing fetuses. The vaccines are the subjects of multisite clinical trials. These City of Hope vaccines could open the door to a new way of protecting cancer patients from CMV, a devastating infection that affects hundreds of thousands of people worldwide.

 

In what ways does the initial vision of Samuel H. Golter impact the work you are doing today? What does the tagline – “The Miracle of Science with Soul” – mean?

Dr. Rosen: 100+ years ago, Samuel Golter, one of the founders of City of Hope said: “There is no profit in curing the body if in the process we destroy the soul.” For decades, City of Hope has lived by this credo, providing a comprehensive, compassionate and research-based treatment approach.

“The Miracle of Science with Soul” refers to the lives that we save by uniting science and research with compassionate care.

“Miracle” represents what people with cancer and other deadly diseases say they want most of all.

“Science” speaks to the many innovations we’ve pioneered, which demonstrate that medical miracles happen here.

“Soul” represents our compassionate care. We’re an untraditional health system — and our people, culture and campus reflect this.

 

Can you please describe how City of Hope has evolved throughout its 100-year history from a tuberculosis sanitorium into a world-class research-centered institution? 

Dr. Rosen: City of Hope is a leading comprehensive cancer center and independent biomedical research institution. Over the years, our discoveries have changed the lives of millions of patients around the world.

We pioneered the research leading to the first synthetic insulin and the technology behind numerous cancer-fighting drugs, including Herceptin (trastuzumab), Avasatin (bevacizumab), Erbitux (cetuximab), and Rituxin (rituximab).

As previously mentioned, we hold 300+ patents, have numerous potential therapies in the pipeline at any given time, and treat 1,000+ patients a year in therapeutic clinical trials.

These numbers reflect our commitment to innovation and rapid translation of science into therapies to benefit patients.

We are home to Beckman Research Institute of City of Hope, the first of only five Beckman Research Institutes established by funding from the Arnold and Mabel Beckman Foundation. It is responsible for fundamentally expanding the world’s understanding of how biology affects diseases such as cancer, HIV/AIDS and diabetes.

Recognizing our team’s accomplishments in cancer research, treatment, patient care, education and prevention, the National Cancer Institute has designated City of Hope as a comprehensive cancer center. This is an honor reserved for only 47 institutions nationwide. Our five Cancer Center Research Programs run the gamut from basic and translational studies, to Phase I and II clinical protocols and follow-up studies in survivorship and symptom management.

City of Hope’s Diabetes & Metabolism Research Institute offers a broad diabetes and endocrinology program combining groundbreaking research, unique treatments and comprehensive education to help people with diabetes and other endocrine diseases live longer, better lives.

Our dedicated, multidisciplinary team of healthcare professionals at the Hematologic Malignancies & Stem Cell Institute combine innovative research discoveries with superior clinical treatments to improve outcomes for patients with hematologic cancers.

Working closely with the City of Hope comprehensive cancer center’s Developmental Cancer Therapeutics Program and other cancer centers, the Medical Oncology & Therapeutics Research multidisciplinary program includes basic, translational and clinical research and fosters collaborations among scientists and clinicians.

City of Hope’s Radiation Oncology Department is on the forefront of improving patient care, and our staff is constantly studying new research technologies, clinical trials and treatment methods that can lead to better outcomes and quality of life for our patients.

What attracted you to City of Hope? And how do you define success in your present role as provost and CSO?

Dr. Rosen: Helping cancer patients and their families gives me a sense of purpose. I encourage everyone to find a passion and find an organization that fits their passion. City of Hope is a special place. What we do is bigger than ourselves.

I define success as finding cures and helping patients live stronger, better lives. I am focused on leading a diverse team of scientists, clinicians and administrative leaders committed to discovering breakthroughs and specialized therapies.

COH2 Dr__Steve_Rosen_

Image SOURCE: Photograph of Provost and Chief Scientific Officer Steven T. Rosen, M.D., courtesy of City of Hope, Duarte, California.

 

Steven T. Rosen, M.D.
Provost and Chief Scientific Officer

City of Hope
Duarte, California

Steven T. Rosen, M.D., is provost and chief scientific officer for City of Hope and a member of City of Hope’s Executive Team. He also is director of the Comprehensive Cancer Center and holds the Irell & Manella Cancer Center Director’s Distinguished Chair, and he is director of Beckman Research Institute (BRI) and the Irell & Manella Graduate School of Biological Sciences.

Dr. Rosen sets the scientific direction of City of Hope, shaping the research and educational vision for the biomedical research, treatment and education institution. Working closely and collaboratively with City of Hope’s scientists, clinicians and administrative leaders, he develops strategies that contribute to the organization’s mission.

As director of BRI, he works with faculty across the institution to help shape and direct the scientific vision for BRI while leading the vital basic and translational research that is fundamental to our strategic plan and mission. He focuses on opportunities for expanding and integrating our research initiatives; recruiting and leading talented scientists; helping our talented researchers achieve national and international recognition; and promoting our national standing as a premier scientific organization.

Prior to joining City of Hope, Dr. Rosen was the Genevieve Teuton Professor of Medicine at the Feinberg School of Medicine at Northwestern University in Chicago. He served for 24 years as director of Northwestern’s Robert H. Lurie Comprehensive Cancer Center. Under his leadership, the center received continuous National Cancer Institute (NCI) funding beginning in 1993 and built nationally recognized programs in laboratory sciences, clinical investigations, translational research and cancer prevention and control. The center attained comprehensive status in 1997.

Dr. Rosen has published more than 400 original reports, editorials, books and book chapters. His research has been funded by the National Cancer Institute, American Cancer Society, Leukemia & Lymphoma Society of America and Multiple Myeloma Research Foundation.

Dr. Rosen also has served as an adviser for several of these organizations and on the external advisory boards of more than a dozen NCI-designated Comprehensive Cancer Centers. He is the current editor-in-chief of the textbook series “Cancer Treatment & Research.”

Recognized as one of the Best Doctors in America, Dr. Rosen is a recipient of the Martin Luther King Humanitarian Award from Northwestern Memorial Hospital and the Man of Distinction Award from the Israel Cancer Research Fund. He earned his bachelor’s degree and medical degree with distinction from Northwestern University from which he also earned the Alumni Merit Award, and is a member of the Alpha Omega Alpha Honor Society.

Editor’s Note: 

We would like to thank Mary-Fran Faraji, David Caouette, and Chantal Roshetar of the Communications and Public Affairs department at the City of Hope, for the gracious help and invaluable support they provided during this interview.

 

REFERENCE/SOURCE

The City of Hope (https://www.cityofhope.org/homepage), Duarte, California.

Other related articles

Retrieved from https://www.cityofhope.org/people/rosen-steven

Retrieved from https://www.cityofhope.org/research/beckman-research-institute

Retrieved from https://www.cityofhope.org/research/comprehensive-cancer-center

Retrieved from https://www.cityofhope.org/research/research-overview/diabetes-metabolism-research-institute

Retrieved from https://www.cityofhope.org/patients/departments-and-services/hematologic-malignancies-and-stem-cell-transplantation-institute

Retrieved from https://www.cityofhope.org/patients/departments-and-services/medical-oncology-and-therapeutics-research/medical-oncology-research

Retrieved from https://www.cityofhope.org/patients/cancers-and-treatments/departments-and-services/radiation-oncology/radiation-oncology-research

                        

Other related articles were published in this Open Access Online Scientific Journal include the following: 

2017

Expedite Use of Agents in Clinical Trials: New Drug Formulary Created – The NCI Formulary is a public-private partnership between NCI, part of the National Institutes of Health, and pharmaceutical and biotechnology companies

https://pharmaceuticalintelligence.com/2017/01/12/expedite-use-of-agents-in-clinical-trials-new-drug-formulary-created-the-nci-formulary-is-a-public-private-partnership-between-nci-part-of-the-national-institutes-of-health-and-pharmaceutical-and/

The top 15 best-selling cancer drugs in 2022 & Projected Sales in 2020 of World’s Top Ten Oncology Drugs

https://pharmaceuticalintelligence.com/2017/01/03/projected-sales-in-2020-of-worlds-top-ten-oncology-drugs/

2016

Funding Opportunities for Cancer Research

https://pharmaceuticalintelligence.com/2016/12/08/funding-opportunities-for-cancer-research/

Recent Breakthroughs in Cancer Research at the Technion-Israel Institute of Technology- 2015

https://pharmaceuticalintelligence.com/2016/02/03/recent-breakthroughs-in-cancer-research-at-the-technion-israel-institute-of-technology-2015/

New York Times Articles on Cancer Immunotherapy and Cancer Treatment Options

https://pharmaceuticalintelligence.com/2016/08/09/new-york-times-articles-on-immunotherapy-and-cancer-treatment-options/

  • Cancer Biology & Genomics for Disease Diagnosis, on Amazon since 8/11/2015

http://www.amazon.com/dp/B013RVYR2K

https://pharmaceuticalintelligence.com/biomed-e-books/series-c-e-books-on-cancer-oncology/volume-2-immunotherapy-in-oncology/

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Personalized Medicine: Clinical Aspiration of Microarrays

Reporter, Writer: Stephen J. Williams, Ph.D.

 In this month’s Science, Mike May (at http://www.sciencemag.org/site/products/lst_20130215.xhtml) describes some of the challenges and successes in introducing microarray analysis to the clinical setting.  Traditionally used for investigational research, microarray is now being developed, customized and used for biomarker analysis, prognostic and predictive value, in a disease-specific manner.

Challenges in data interpretation

      In an interview with Seth Crosby, director of the Genome Technology Access Center at Washington University School of Medicine in St. Louis, “the biggest challenge” in moving microarray to the clinical setting is data interpretation.  The current technology makes it possible to evaluate expression of thousands of genes from a patient’s sample however as Crosby describes is assigning clinical relevance to the data.  For example Crosby explains that Washington University had validated a panel of 45 oncology genes by next generation sequencing and are using these genes to develop diagnostic tests to screen patient tumors for the purpose of determining a personalized therapeutic strategy. Seth Crosby noted it took “hundreds of Ph.D. and M.D. hours” to sift through the hundreds of papers to determine which genes were relevant to a specific cancer type. However, he notes, that once we better understand which changes in the patient’s genome are related to a specific disease we will be able to narrow down the list and be able to produce both economical and more disease-relevant microarrays.

Is this aberration pathogenic or not?

     Microarrays are becoming an invaluable tool in cytogenetics, as eluded by Andy Last, executive vice president of the genetic analysis business unit at Affymetrix.  Certain diseases like Down syndrome have well characterized chromosomal alterations like additions or deletions of parts or entire chromosomes.  According to Affymetrix, the most common use of microarrays is for determining copy number variation.  However according to James Clough, vice president of clinical and genomic services at Oxford Gene Technology, given the hundreds of syndromes associated with chromosomal rearrangements, the challenge will be to determine if a small chromosomal aberration has pathologic significance, given that microarray affords much higher diagnostic yield and speed of analysis than traditional microscopic techniques.  To address this challenge, Oxford Gene Technologies, PerkinElmer, Affymetrix, and Agilent all have custom designed microarrays to evaluate disease specific copy number and SNP (single nucleotide polymorphism) microarrays.  For example PerkinElmer designed OncoChip™ to evaluate copy number variation in more than 1.800 cancer genes.  Agilent makes microarrays that evaluates both copy number variation such as its CGH (comparative genomic hybridization) plus SNP microarrays.  Patricia Barco, product manager for cytogenetics at Agilent, notes these arrays can be used in prenatal and postnatal research and cancer, and “can be customized from more than 28 million probes in our library”.

Custom Tools and Software to Handle the Onslaught of Big Data

     There is a need for FDA approved diagnostic tools based on microarrays. Pathwork Diagnostic’s has one such tool (the Pathwork Tissue of Origin test), which uses 2,000 transcript markers and a proprietary computational algorithm to determine from expression analysis, the tissue of origin of a patient’s tumor.  Pathwork also provides a fast, custom turn-around analytical service for pathologists who encounter difficult to interpret samples.  Illumina provides the Infinium HumanCore BeadChip family of microarrays, which can determine genetic variations for purposes of biological tissue banking.  This system uses a set of over 300,000 SNP probes plus 240,000 exome-based markers.

     Tools have also been developed to validate microarray results.  A common validation strategy is the use of quantitative real-time PCR to verify the expression changes seen on the microarray.  Life Technologies developed the TaqMan OpenArray Real Time PCR plates, which have 3,072 wells and can be custom-formatted using their library of eight million validated TaqMan assays.

Making Sense of the Big Data: Bridging the Knowledge Gap using Bioinformatics

          The use of microarray has spurned industries devoted to developing the bioinformatics software to analyze the massive amounts of data and provide clinical significance.  For example companies such as Expression Analysis use their bioinformatics software to provide pathway analysis for microarray data in order to translate the data into the biology.  Using such strategies can also validate the design of microarrays for various diseases.

Foundation Medicine, Inc., a molecular information company, provides cancer genomics test solutions. It offers FoundationOne, an informative genomic profile to identify a patient’s individual molecular alterations and match them with relevant targeted therapies and clinical trials. The company’s product enables physicians to recommend treatment options for patients based on the molecular subtype of their cancer.

The Canadian Bioinformatics Workshops series recently offered a course on using bioinformatic approaches to analyze clinical data generated from microarray approaches (http://bioinformatics.ca/workshops/2012/bioinformatics-cancer-genomics-bicg).   The course objectives are described below:

Course Objectives

Cancer research has rapidly embraced high throughput technologies into its research, using various microarray, tissue array, and next generation sequencing platforms. The result has been a rapid increase in cancer data output and data types. Now more than ever, having the bioinformatic skills and knowledge of available bioinformatic resources specific to cancer is critical. The CBW will host a 5-day workshop covering the key bioinformatics concepts and tools required to analyze cancer genomic data sets. Participants will gain experience in genomic data visualization tools which will be applied throughout the development of the skills required to analyze cancer -omic data for gene expression, genome rearrangement, somatic mutations and copy number variation. The workshop will conclude with analyzing and conducting pathway analysis on the resultant cancer gene list and integration of clinical data.

Successful Examples of Clinical Ventures Integrating Bioinformatics in Cancer Treatment Decision –Making

The University of Pavia, Italy developed a fully integrated oncology bioinformatics workflow as described on their website and at the ESMO 2012 Congress meeting:

http://abstracts.webges.com/viewing/view.php?congress=esmo2012&congress_id=370&publication_id=2530

ESMO

ONCO-I2B2 PROJECT: A BIOINFORMATICS TOOL INTEGRATING –OMICS AND CLINICAL DATA TO SUPPORT TRANSLATIONAL RESEARCH

Abstract:

2530

Congress:

ESMO 2012

Type:

Abstract

Topic:

Translational research

Authors:

A. Zambelli, D. Segagni, V. Tibollo, A. Dagliati, A. Malovini, V. Fotia, S. Manera, R. Bellazzi; Pavia/IT

  • Body

The ONCO-i2b2 project, supported by the University of Pavia and the Fondazione Salvatore Maugeri (FSM), aims at supporting translational research in oncology and exploits the software solutions implemented by the Informatics for Integrating Biology and the Bedside (i2b2) research centre, an initiative funded by the NIH Roadmap National Centres for Biomedical Computing. The ONCO-i2b2 software is designed to integrate the i2b2 infrastructure with the FSM hospital information system and the Bruno Boerci Biobank, in order to provide well-characterized cancer specimens along with an accurate patients clinical data-base. The i2b2 infrastructure provides a web-based access to all the electronic medical records of cancer patients, and allow researchers analyzing the vast amount of biological and clinical information, relying on a user-friendly interface. Data coming from multiple sources are integrated and jointly queried.

In 2011 at AIOM Meeting we reported the preliminary experience of the ONCO-i2b2 project, now we’re able to present the up and running platform and the extended data set. Currently, more than 4400 specimens are stored and more than 600 of breast cancer patients give the consent for the use of specimens in the context of clinical research, in addition, more than 5000 histological reports are stored in order to integrate clinical data.

Within the ONCO-i2b2 project is possible to query and merge data regarding:

• Anonymous patient personal data;

• Diagnosis and therapy ICD9-CM subset from the hospital information system;

• Histological data (tumour SNOMED and TNM codes) and receptor profile testing (Her2, Ki67) from anatomic pathology database;

• Specimen molecular characteristics (DNA, RNA, blood, plasma and cancer tissues) from the Bruno Boerci Biobank management system.

The research infrastructure will be completed by the development of new set of components designed to enhance the ability of an i2b2 hive to utilize data generated by NGS technology, providing a mechanism to apply custom genomic annotations. The translational tool created at FSM is a concrete example regarding how the integration of different information from heterogeneous sources could bring scientific research closer to understand the nature of disease itself and to create novel diagnostics through handy interfaces.

Disclosure

All authors have declared no conflicts of interest.

NCI has under-taken a similar effort under the Recovery Act (the full text of the latest report is taken from their website http://www.cancer.gov/aboutnci/recovery/recoveryfunding/investmentreports/bioinformatics:

Cancer Bioinformatics: Recovery Act Investment Report

November 2009

Public Health Burden of Cancer

Cancer is the second leading cause of death in the United States after heart disease. In 2009, it is estimated that nearly 1.5 million new cases of invasive cancer will be diagnosed in this country and more than 560,000 people will die of the disease.

To learn more, visit:

Cancer Bioinformatics Program Overview

Over the past five years, NCI’s Center for Biomedical Informatics and Information Technology (CBIIT) has led the effort to develop and deploy the cancer Biomedical Informatics Grid® (caBIG) in partnership with the broader cancer community.  The caBIG network is designed to enable the integration and exchange of data among researchers in the laboratory and the clinic, simplify collaboration, and realize the potential of information-based (personalized) medicine in improving patient outcomes. caBIG has connected major components of the cancer community, including NCI-designated Cancer Centers, participating institutions of the NCI Community Cancer Centers Program (NCCCP), and numerous large-scale scientific endeavors, as well as basic, translational, and clinical researchers at public and private institutions across the United States and around the world.  Beyond cancer research, caBIG capabilities—infrastructure, standards, and tools—provide a prototype for linking other disease communities and catalyzing a new 21st-century biomedical ecosystem that unifies research and care. ARRA funding will allow NCI to accelerate the ongoing development of the Cancer Knowledge Cloud and Oncology Electronic Health Records (EHRs) initiatives, thereby providing for continued job creation in the areas of biomedical informatics development and application as well as healthcare delivery.

The caBIG Cancer Knowledge Cloud: Extending the Research Infrastructure

The Cancer Knowledge Cloud is a virtual biomedical capability that utilizes caBIG tools, infrastructure, and security frameworks to integrate distributed individual and organizational data, software applications, and computational capacity throughout the broad cancer research and treatment community. The Cancer Knowledge Cloud connects, integrates, and facilitates sharing of the diverse primary data generated through basic and clinical research and care delivery to enable personalized medicine. The cloud includes information generated through large-scale research projects such as The Cancer Genome Atlas (TCGA), the cancer Human Biobank (caHUB) tissue acquisition network, the NCI Functional Biology Consortium, the NCI Patient Characterization Center, and the NCI Preclinical Development Pipeline, academic and industry counterparts to these projects, and clinical observations (from entities such as the NCCCP) captured in oncology-extended Electronic Health Records.  Through the use of the caBIG Data Sharing and Security Framework, the Cloud will support appropriate sharing of information, supporting in silico hypothesis generation and testing, and enabling a learning healthcare system.

A caBIG-Based Rapid-Learning Healthcare System: Incorporating Oncology-Extended Electronic Healthcare Records (EHRs)

The 21st-century Cancer Knowledge Cloud will connect individuals, organizations, institutions, and their associated information within an information technology-enabled cycle of discovery, development, and clinical care—the paradigm of a rapid-learning healthcare system. This will transform these disconnected sectors into a system that is personalized, preventive, pre-emptive, and patient-participatory.  To be realized, this model requires the adoption of standards-based EHRs. Presently, however, no certified oncology-based EHR exists, and fewer than 3 percent of oncologists with outpatient-based practices utilize EHRs. caBIG has recently established a collaboration with the American Society of Clinical Oncology (ASCO) to develop an oncology-specific EHR (caEHR) specification based on open standards already in use in the oncology community that will utilize caBIG standards for interoperability. NCI will implement an open-source version of this specification to validate the specification and to provide a free alternative to sites that choose not to purchase a commercial system. The launch customer for the caEHR will be NCCCP participating sites. NCI will work with appropriate entities to provide a mechanism for certifying that caEHR implementations are consistent with the NCI/ASCO specification.

Bards Cancer Institute has another clinical bioinformatics program to support their clinical efforts:

Clinical Bioinformatics Program in Oncology at Barts Cancer Institute at Barts and the London School of Medicine

http://www.bci.qmul.ac.uk/cancer-bioinformatics

BCI HomeCancer Bioinformatics

Bards

Why we focus on Cancer Bioinformatics

Bioinformatics is a new interdisciplinary area involving biological, statistical and computational sciences. Bioinformatics will enable cancer researchers not only to manage, analyze, mine and understand the currently accumulated, valuable, high-throughput data, but also to integrate these in their current research programs. The need for bioinformatics will become ever more important as new technologies increase the already exponential rate at which cancer data are generated.

What we do

  • We work alongside clinical and basic scientists to support the cancer projects within BCI.  This is an ideal partnership between scientific experts, who know the research questions that will be relevant from a cancer biologist or clinician’s perspective, and bioinformatics experts, who know how to develop the proposed methods to provide answers.
  • We also conduct independent bioinformatics research, focusing on the development of computational and integrative methods, algorithms, databases and tools to tackle the analysis of the high volumes of cancer data.
  • We also are actively involved in the development of bioinformatics educational courses at BCI. Our courses offer a unique opportunity for biologists to gain a basic understanding in the use of bioinformatics methods to access and harness large complicated high-throughput data and uncover meaningful information that could be used to understand molecular mechanisms and develop novel targeted therapeutics/diagnostic tools.

Developing Criteria for Genomic Profiling in Lung Cancer:

A Report from U.S. Cancer Centers

In a report by Pao et. al., a group of clinicians organized a meeting to standardize some protocols for the integration of microarray and genomic data from lung cancer patients into the clinical setting.[1]  There has been ample evidence that adenocarcinomas could be classified into “clinically relevant molecular subsets” based on distinct genomic changes.  For example EGFR (epidermal growth factor receptor) exon 19 deletions and exon 21 point mutations predict sensitivity to tyrosine kinase inhibitors (TKIs) like gefitinib, whereas exon 20 insertions predict primary resistance[2].

However, as the authors note, “mutational profiling has not been widely accepted or adopted into practice in thoracic oncology”.  

     Therefore, a multi-institutional workshop was held in 2009 among participants from Massachusetts General Hospital (MGH) Cancer Center, Memorial Sloan-Kettering Cancer Center (MSKCC), the Dana-Farber/Bingham & Women’s Cancer Center (DF/BWCC), the M.D. Anderson Cancer Center (VICC), and the Vanderbilt-Ingram Cancer Center (VICC) to discuss their institutes molecular profiling programs with emphasis on:

·         Organization/workflow

·         Mutation detection technologies

·         Clinical protocols and reporting

·         Patient consent

In addition to the aforementioned challenges, the panel discussed further issues for developing improved science-driven criteria for determining targeted therapies including:

1)      Including pathologists into criteria development as pathology departments are usually the main repositories for specimens

2)      Developing integrated informatics systems

3)      Standardizing new target validation methodology across cancer centers

 References

1.            Pao W, Kris MG, Iafrate AJ, Ladanyi M, Janne PA, Wistuba, II, Miake-Lye R, Herbst RS, Carbone DP, Johnson BE et al: Integration of molecular profiling into the lung cancer clinic. Clinical cancer research : an official journal of the American Association for Cancer Research 2009, 15(17):5317-5322.

2.            Wu JY, Wu SG, Yang CH, Gow CH, Chang YL, Yu CJ, Shih JY, Yang PC: Lung cancer with epidermal growth factor receptor exon 20 mutations is associated with poor gefitinib treatment response. Clinical cancer research : an official journal of the American Association for Cancer Research 2008, 14(15):4877-4882.

Other posts on this website on Cancer and Genomics include:

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Reporter: Aviva Lev-Ari, PhD, RN

 

 

HOSTS

  • Speaker - Gianrico Farrugia, M.D.

    GIANRICO FARRUGIA, M.D.HOST

    Director, Center for Individualized Medicine, Mayo Clinic

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  • Speaker - Michael P. Snyder, Ph.D.

    CECI CONNOLLYMODERATOR

    Managing Director, Health Research Institute, PwC

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  • Speaker - Ira Flatow

    IRA FLATOWMODERATOR

    Host, “Science Friday,” National Public Radio

    FOLLOW ME ON TWITTER

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THEME 1: INDIVIDUALIZING MEDICINE TODAY: A PRIMER ON INDIVIDUALIZED MEDICINE

THEME 2: INDIVIDUALIZING CLINICAL CARE

  • Speaker - Marc S. Williams, M.D.

    MARC S. WILLIAMS, M.D.OPENING SPEAKER

    Director, Genomic Medicine Institute, Geisinger Health System

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  • Speaker - Noralane M. Lindor, M.D.

    NORALANE M. LINDOR, M.D.

    Consultant, Department of Health Sciences Research, Mayo Clinic

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  • Speaker - Yves A. Lussier, M.D.

    YVES A. LUSSIER, M.D.

    Clinical Research Information Officer and Assistant Vice President for Health Affairs, University of Illinois Hospital & Health Sciences System

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THEME 3: INDIVIDUALIZING LABORATORY MEDICINE

  • Speaker - James L. Weber, Ph.D.

    JAMES L. WEBER, PH.D.OPENING SPEAKER

    President and Founder, PreventionGenetics

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  • Speaker - John Logan Black, M.D.

    JOHN LOGAN BLACK, M.D.

    Consultant, Department of Laboratory Medicine and Pathology, Mayo Clinic

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  • Speaker - Anna Wedell, M.D., Ph.D.

    ANNA WEDELL, M.D., PH.D.

    Professor and Senior Consultant, Clinical Genetics, Centre for Inherited Metabolic Diseases, Karolinska Institutet and Karolinska University Hospital

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THEME 4: ETHICAL AND REGULATORY IMPLICATIONS OF INDIVIDUALIZING MEDICINE

  • Speaker - Henry (Hank) T. Greely, J.D.

    HENRY (HANK) T. GREELY, J.D.OPENING SPEAKER

    Director, Center for Law and the Biosciences, Stanford University

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  • Speaker - Karen J. Maschke, Ph.D.

    KAREN J. MASCHKE, PH.D.

    Research Scholar, The Hastings Center

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  • Speaker - Susan M. Wolf, J.D.

    SUSAN M. WOLF, J.D.

    McKnight Presidential Professor of Law, Medicine & Public Policy and Faegre Baker Daniels Professor of Law, University of Minnesota

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THEME 5: DECISION-SUPPORT INFRASTRUCTURE FOR INDIVIDUALIZING MEDICINE

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