Luis Carvajal-Carmona receives award to investigate ethnic differences in diagnosis and treatment of gastric cancer

Study seeks to improve cancer survival for Latinos, Asians and Blacks

UC Davis leads University of California precision medicine effort to address vast cancer health disparities

(SACRAMENTO)

UC Davis Comprehensive Cancer Center has received a $6.3 million grant from the National Cancer Institute’s (NCI) Center to Reduce Cancer Health Disparities for a 5-year study to tease out why some ethnic and racial minority groups fare worse than whites when they get cancer and to find more precise treatments to improve their chances of survival.

Chong-xian Pan

The new, collaborative study engages four of the University of California’s NCI-designated comprehensive cancer centers: UC Davis Comprehensive Cancer Center, Jonsson Comprehensive Cancer Center at UCLA, UCSF Helen Diller Family Comprehensive Cancer Center and the Chao Family Comprehensive Cancer Center at UC Irvine. The four centers are part of the recently created UC Cancer Center Consortium, and their patient population is among the most diverse in the U.S.

Under the grant, entitled “University of California Minority Patient-Derived Xenograft (PDX) Development and Trial Center” or UCaMP, tumor samples from patients will be delivered to UC Davis for use in the research. A minimum of 60 percent of the tumor samples will be drawn from minority patients to grow tumors (or xenografts) in mice; the rest will be from non-Hispanic whites and used as controls. Once a PDX is established, it can be replicated so that a single patient tumor can be used to test numerous drugs at the same time. The goal is to generate at least 200 PDXs for use in two research projects. The findings will be shared with the NCI and other scientists to aid in the development of more precise cancer treatments.

The study will focus on four types of cancer that disproportionately affect minorities:  lung, liver, gastric (stomach) and bladder. The first project in the study will focus on gastric and liver cancer among Latinos and Asian Americans, Pacific Islanders and Native Hawaiians, and the second will examine lung and bladder cancers among African Americans. Researchers will use PDXs to discern their genetic characteristics and to test potential targeted drugs to treat them.

Moon Chen

“UCaMP is one of the only two programs funded by NCI nationwide to address cancer health disparities using patient-derived cancer models,” said Chong-xian Pan, a study principal investigator. Pan is a medical oncologist and physician-scientist specializing in genitourinary cancers. He will coordinate the study’s annual report to the NCI and oversee the bladder and lung cancer project.

When compared with non-Hispanic whites, African Americans have lower survival from lung and bladder cancer, even when diagnosed at the same stage of the disease.

“We are trying to address why this happens,” Pan said. “Socio-economics could be a factor, but we also want to see if there are biological factors contributing to this disparity. PDXs are a great model, not only to study the biological differences of cancers from non-Hispanic whites and African Americans, but also to facilitate cancer drug development and precision medicine.”

Luis Carvajal-Carmona, a UC Davis cancer genomicist, expert in the genetics of Latinos and a principal investigator, will lead the stomach and liver cancer project. He said the study is an effort to correct a major discrepancy in existing cancer genomics research to date – the lack of minority patient representation, which is essential for the development of targeted, or personalized, treatments.

Luis Carvajal-Carmona

“Minority patients have the worst cancer outcomes for multiple reasons. One of them is because they come in with more advanced tumors because many don’t have proper access to health care. But also because there are not enough data and models for the scientific community to develop precision medicine studies in them. So we want for this NCI-funded research to be a magnet for minority-focused clinical trials.”

Carvajal-Carmona said that while gastric cancer is a leading cancer killer of Latinos, the largest gastric cancer genetic sequencing study to date, which analyzed 300 tumors, included only three tumor samples from patients of Latino ancestry.

“Sequencing studies are done to find targets (genetic mutations) to help develop new therapies, and because Latinos have different genetic backgrounds and may have different lifestyles and environmental risk factors, their tumors are likely to be different, too, which will affect the targets for treatment.”

Moon Chen, a UC Davis population scientist, expert in Asian cancer health disparities and a principal investigator, said PDXs have advantages over other research tools because they can be used to screen for and enhance the effectiveness of cancer therapies or to develop novel therapies.

“In so doing, they contribute to a better understanding of the underlying mechanisms of resistance and elucidate potential biological determinants of treatment responses and cancer health disparities for these tumor sites,” he said.

UC Davis researchers have used PDX models to study potential cancer therapies for many years, mostly in collaboration with The Jackson Laboratories, an NCI-designated cancer research center. Although all of the mouse work for the current study will be done at UC Davis and UCSF, The Jackson Laboratories also was awarded an NCI grant to serve as the coordinating center for this and other PDX research.

Other investigators involved in the study are Ralph de Vere White, David J. Segal, Regina Gandour-Edwards, K.C. Kent Lloyd, John Albeck, David R. Gandara, Kit S. Lam, Ai-Hong Ma, Edward N. Pugh, David M. Rocke, Susan Leroy Stewart and Clifford G. Tepper of UC Davis; Roshan Bastani, Samuel French and Richard S. Finn at UCLA; Robert E. Bristow, Farshid Dayyani and Marian Waterman at UC Irvine; and Rosemary J. Akhurst, Robert A. Hiatt, John Gordan, R. Kate Kelley and Tung Nguyen at UCSF.

The project will be funded with NCI grant No. 1 U54 CA233306-01.

Email this to someoneTweet about this on TwitterShare on FacebookShare on Google+Share on LinkedInShare on RedditShare on TumblrPrint this page
Posted in Highlights, News

Upcoming Talks and Events

Events on January 14, 2019
WCMC: Hands-on LC-MS Data processing and Statistics
Starts: 12:00 am
Ends: January 19, 2019 - 12:00 am
Location: UC Davis Conference Center, 550 Alumni Ln, Davis, CA 95616, USA
Description: Registration: http://ucanr.edu/survey/survey.cfm?surveynumber=15575

This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation.

We will instruct using a variety of software, workflows, and algorithms but also give theoretical background information and overviews. We will focus on utilizing open source software and only refer to commercial or vendor software when necessary.

All participants will be trained on laptops that were specifically purchased for course training, with all software already installed and data available to use.

The course will include:

untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
The course fees are $ 2,500 per participant to cover expenses for instructors, organization, materials and meals.

more Info:

Jeannette Martins

email: jmartins@ucdavis.edu

phone: +1-530-754-5357

Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.
Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:


1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.

Categories