Dan L Duncan Comprehensive Cancer Center

Cancer Shared Resources


DLDCCC Shared Resources Retreat Slide Deck


This is the entirety of the presentations that were shown at the DLDCCC Shared Resources Retreat Oct. 23, 2023.

View slides (Baylor login required)

The Shared Resources of the Dan L. Duncan Comprehensive Cancer Center provide technical support services essential for basic and clinical research studies of Cancer Center members. The NCI-designated Cancer Center Support Grant provides funding support for advanced technologies, high-end instrumentation, data analysis, biostatistics and informatics services that would be difficult and too expensive for individual investigators or programs to develop and maintain on their own. Below are short descriptions of the Shared Resources with links to websites with more detailed information.

Advanced In Vivo Cancer Models Shared Resource

Leader: Michael Lewis, Ph.D.

Co-Leaders: Hugo Villanueva, Ph.D. and Jason D. Heaney, Ph.D.

The Advanced In Vivo Cancer Models Shared Resource is constructed to meet the needs of Cancer Center investigators wishing to use experimentally demanding, state-of-the-art, in vivo cancer models that require specialized techniques, and a high degree of experimental ingenuity. These models include genetically engineered mice (“knockout,” “knockin,” and transgenics), and patient-derived tumor xenografts (PDX) grown either in immunocompromised mice, or in alternative platforms such as the chicken egg chorioallantoic membrane (CAM). Both mouse and human-derived models require substantial validation work to “credential” that they are reflective of the biology of the disease or process under study. Since patient-derived tissues used to generate the models have considerable associated clinical and “omic” information, computational infrastructure is supported to abstract, store, organize, retrieve, and display such information so that investigators can make rational choices as to which model(s) to use, and to help interpret their results. AICM is a merger and restructuring of Genetic Engineered Mouse (GEM) and Patient-Derived Xenograft and Advanced In Vivo Models (PDX-AIM) Shared Resources supported by Baylor College of Medicine and the DLDCCC. For more information, visit the GERM and PDX-AIM websites.

Advanced Microscopy and Image Informatics Shared Resource

Leader: Michael Mancini, Ph.D.
Co-Leader: Fabio Stossi, Ph.D.

The Advanced Microscopy and Image Informatics Shared Resource provides high-quality microscopy and analytics services to DLDCCC members through availability of state-of-the-art imaging instrumentation, custom image analysis, one-on-one training by expert staff, plus consultation for experimental setup, data acquisition and analysis. AMII covers most of investigators needs for light microscopy with particular emphasis on fully-assisted services for super-resolution microscopy, high throughput/high content imaging-based phenotypic or mechanistic screening, assay development, live imaging, multi-dimensional spatial analysis, imaging of 3D culture models and custom image analysis pipelines and data analytics. AMII is also invested in education and training through graduate level teaching, symposia and seminar organization, and via one-on-one training for most of the services. The original Integrated Microscopy Core was renamed AMII to highlight enhanced capabilities in super-resolution, live imaging, and high throughput microscopy coupled with image analysis. For more information, visit the Advanced Microscopy and Image Informatics Shared Resource website. 

Cell Processing and Vector Production Shared Resource 

Leader: Natalia Lapteva, Ph.D.
Co-Leader: Zhuyong, Mei, Ph.D.

The Cell Processing and Vector Production Shared Resource provides manufacturing of therapeutic grade cellular therapy products and viral vector for use in early phase clinical trials. These must be prepared according to current Good Manufacturing Practices as mandated by the Food and Drug Administration. This CPVP provides the infrastructure and environment to prepare, test, and release these products for use. It consists of a state-of-the-art facility with 22 manufacturing clean rooms and support facilities and highly experienced manufacturing and quality control and assurance staff. This Shared Resource works with investigators to develop clinical scale manufacturing procedures, and release test specifications, testing procedures, quality assurance oversight, and regulatory assistance for IND submissions. The CPVP facilitates the transition of cellular and gene therapy products from the basic science laboratories into early-phase clinical trials. The CPVP currently supports more than 50 clinical trials (21 actively accruing, 18 in follow-up, and 11 in stages of translation to investigational new drug applications [INDs]) held by DLDCCC investigators and does so at a much-reduced cost compared to commercial manufacturing and testing entities. For more information, visit the Cell Processing and Vector Production Shared Resource website. 

Gene Modulation in Cancer Cell Models Shared Resource

Leader: Jun Xu, Ph.D.
Co-Leader: Aleksandar Bajic, Ph.D.

The Gene Modulation in Cancer Cell Models Shared Resource provides DLDCCC members with a versatile combination of cutting-edge technologies and genomic resources to facilitate mechanistic and exploratory investigations using cancer cells and cell lines as experimental models. GMCCM houses essential elements for single-gene analysis to whole-genome screens, including genome-wide libraries of short-hairpin RNAs (shRNAs), cDNAs, and CRISPR sgRNAs, as well as multiple automated robotic platforms for library manipulation. In addition, GMCCM provides highly customizable CRISPR/Cas9-mediated genome-editing services to create knock-in and knock-out cell lines derived from multiple cell types including primary cells, somatic cancer cell lines, human pluripotent stem cells (hPSCs) and cancer patient-derived induced PSCs. The ever-expanding functionalities of CRISPR/Cas9 promises to greatly benefit research of DLDCCC members that rely on cell lines as experimental systems. GMCCM represents a renaming and restructuring of the former Cell-Based Assay Screening Services (C-BASS) supported by the DLDCCC with an Institutional Human Stem Cell Core supported by BCM. By housing these resources in a single, cohesive Shared Resource allows investigators to employ myriad genomic and genetic platforms. For more information, visit the respective websites of C-BASS and Human Stem Cell Cores. 

Genomic, Transcriptomic, Epigenomic and Single Cell Shared Resource

Leader: Rui Chen, Ph.D.
Co-Leaders: Daniel Kraushaar, Ph.D.

The Genomic, Transcriptomic, Epigenomic, and Single Cell Shared Resource provides DLDCCC investigators with comprehensive next-generation (NextGen) sequencing and single-cell genomics services. Interrogating the genome, transcriptome, and epigenome are powerful approaches for studying complex biological processes and gaining insights into diseases such as cancer. The recent development of single-cell genomics technologies further enables researchers to probe tissue and cell heterogeneity at unprecedented resolution and to understand tumor progression in exciting new ways. GTESC services include consultation on experimental design, sample preparation and quality control, library construction, next-generation sequencing, single-cell sequencing, and bioinformatics support on data analysis, data distribution, and data storage. This is a dynamic Core facility with a mission of keeping pace with emerging technologies and instrumentation and the changing needs of the Cancer Center, as reflected in major investments in new state-of-the-art next-generation (NextGen) sequencing instruments and single-cell technologies. The GTESC integrates the former Genomic and RNA Profiling (GARP) shared resource supported by DLDCCC with a relatively new Institutional Single Cell Genomics Core. This change reflects the increasing emphasis of epigenetics in the DLDCCC Programs and the emergence and importance of single-cell technologies in cancer research. For more information, visit respective websites of GARP and Single Cell Genomics Cores.

Geospatial Analysis and Health Outcomes Shared Resource

Leader: Abiodun Oluyomi, Ph.D.

The Geospatial Analysis and Health Outcomes Shared Resource supports population science research at the Duncan Cancer Center and among other BCM community researchers. Primarily, the shared resource guides the incorporation of population-level data into cancer research among the DLDCCC members. We provide consultation and technical services to cancer center members and help drive catchment-focused research. For more information, visit the Geospatial Analysis and Health Outcomes Shared Resource website.

High-Parameter Cytometry Shared Resource

Leader: Christine Beeton, Ph.D.
Co-Leader: Joel Sederstrom, M.S.

The High-Parameter Cytometry Shared Resource provides a wide range of Cancer Center investigators with access to cost-effective state-of-the-art instrumentation, expertise and training for their cell sorting, and analysis needs. This technology continues to develop at a rapid pace, especially with the advent of novel tools and reagents, increased computational capacity, and more cost-effective equipment. To keep pace with changing technologies and increased utilization, the HPCSR has expanded its space with new lab renovations and acquired new major equipment utilizing mass, imaging, high-parameter, and large and small particle cytometry. Current instrumentation includes a Helios mass cytometer with Hyperion imaging, a 30+parameter BD Symphony A5 Flow Cytometer, 4 florescence-activated cell sorters, 7 flow analyzers, and magnetic and large particle cell sorters. To ensure optimal use of services, HPCSR provides extensive consultation, group and individually tailored training, and protocols for sample preparation, flow analysis, and cell sorting. This is an established Shared Resource of the Cancer Center under the previous name of “Cytometry and Cell Sorting.” The name change reflects new instrumentation and capabilities for mass and imaging cytometry and high-parameter flow cytometry. For more information, visit the Cytometry and Cell Sorting Core website. 

Integrated Biobanking Shared Resource

Leader: Michael Ittmann, M.D., Ph.D.
Co-Leader: Michael Scheurer, Ph.D.

The purpose of the Integrated Biobanking Shared Resource is to provide access to biospecimens by coordinated general and targeted biospecimen acquisition along with relevant expertise and technical resources to enhance basic, translational and clinical cancer biospecimen-based research activities of the Dan L Duncan Comprehensive Cancer Center. The IBSR personnel have extensive experience in pathology, epidemiology, biospecimen acquisition and processing, bank maintenance and distribution. In addition, personnel are trained in the various technical services offered including peripheral blood mononuclear cell preparation, DNA extraction, routine histology services, frozen sections, tissue microarray construction, immunohistochemistry, tissue microarray scanning, and multiplex image analysis. We also provide pathology consultation by expert pathologists for both human tissue specimens and mouse models, and risk factor questionnaire development and collection. IBSR is a merger of the prior Human Tissue Acquisition and Pathology and the Population Sciences Biorepository Shared Resources of the DLDCCC. This is a natural outgrowth of the close working relationship of HTAP and PSB over many years and the merger further integrates operations within a common management structure. For more information, visit the Human Tissue Acquisition and Pathology Core and Population Sciences Biorepository Core websites. 

Metabolomics Shared Resource

Leader: Nagireddy Putluri, Ph.D.

The Metabolomics Shared Resource provides advanced mass spectrometry approaches and technologies, scientific consultation, and expert data analytics required for high-quality global and targeted metabolomics studies. The MSR specializes in discovery, identification, characterization, and quantification of biomolecules, as well as measurement of activities of metabolic pathways, from a variety of biological specimens including tissues, cell lines, and body fluids. This is a dynamic facility that has kept pace with rapidly emerging technologies and instrumentation and has been a leader in the field by developing and publishing innovative technologies. Support services includes: Steady-state targeted metabolomics with a capacity for quantification of up to 700 known metabolites; Untargeted metabolomics for identification of up to 1200 metabolites; Lipidomics for up to 800 molecules and; Metabolic flux analysis to monitor changes in activities of major metabolic pathways in experimental model systems. For more information, visit the Metabolomics website.

Proteomics Shared Resource

Leader: Anna Malovannaya, Ph.D.
Co-Leader: Shixia Huang, Ph.D.

The goal of the Proteomics Shared Resource is to define perturbations of complex and dynamic protein signaling networks that are associated with development and progression of cancer and to use this information for identification of novel therapeutic targets and biomarkers that can predict response or resistance to specific therapies. Services are provided as “beginning-to-end” packages that includes study design and feasibility assessment, analysis and interpretation of data, troubleshooting, and decision-making for follow-up studies. The PSR provides two major technology platforms including: an antibody-based reverse phase protein array procedure that targets >240 known proteins from major oncogenic signaling pathways and, mass spectrometry methods for unbiased profiling of protein expression levels at global proteome coverage depths, and affinity-based enrichment and analysis of protein interaction networks, protein-DNA interactions and global protein post-translational modifications. Informatics tools have been developed for interpretation of proteomics data from mixed homologous species samples from patient-derived xenografts tumor model systems. PSR is a renaming and merger of Mass Spectrometry Proteomics and Antibody-Based Proteomics Shared Resources of the DLDCCC and reflects a more comprehensive approach to support proteomic research needs of cancer center members. For more information, visit the Mass Spectrometry Proteomics and Antibody-Based Proteomics core websites.

Quantitative Science Shared Resource

Leader: Susan Hilsenbeck, Ph.D.
Co-Leader (Multi-omics Bioinformatics): Cristian Coarfa, Ph.D.
Co-Leader (Cancer Bioinformatics): Chad Creighton, Ph.D.
Co-Leader (General Biostatistics): Charles Minard, Ph.D.
Co-Leader (Cancer Biostatistics): Tao Wang, Ph.D.

The Quantitative Science Shared Resource serves the mission of the Cancer Center through assistance with state-of-the-art design, conduct, analysis, and interpretation of clinical, translational, and basic science studies, through bioinformatics and multi-omics data analysis methods. QSSR maintains a high-performance compute (HPC) cluster for data management and support for clinical, translational and basic research. Education and training, scientific review, data monitoring, and strategic planning are also essential functions provided by QSSR. This Shared Resource has been restructured and renamed from the previous Biostatistics and Informatics Shared Resource to reflect the focus on the quantitative science of biostatistics and bioinformatics and the HPC infrastructure. For more information, visit the Biostatistics and Informatics Shared Resource website.

CPRIT Cancer Proteomics and Metabolomics

Additional services are available through CPRIT Cancer Proteomics and Metabolomics - a group funded through a grant from the Cancer Prevention Research Institute of Texas.

Instructions for Acknowledgement of Cancer Center Support Grant in Publications

Be sure to cite the NCI Cancer Center Support Grant (P30CA125123) and acknowledge the support of Shared Resources on all cancer-relevant publications. Please acknowledge the specific Shared Resource(s) used by its appropriate name.

This is important documentation for renewal of the Dan L Duncan Comprehensive Cancer Center grant and continued funding of Shared Resources