Shared Resources

Biospecimen processing is performed in two different sections:

1. The histopathology section (led by the designated pathologist) for processing normal, pretumoral, and tumoral tissue,
2. The “non tissue biospecimen laboratory” (led by the designated laboratory scientist), which processes all other biospecimens, such as blood and derivatives, buccal samples, stool, etc.

The laboratories are located at Louisiana Cancer Research Center (LCRC) in New Orleans, LA. The Core consists of the "Histopathology section" which processes the tumoral and nontumoral tissue and the "Nontissue biospecimen laboratory" that processes all other specimens. 

The Biobank links the prospectively collected biospecimens to the Louisiana Tumor Registry (LTR) which is a statewide population-based registry that collects a complete, high-quality, and timely population-based cancer data in Louisiana and participates in both the Surveillance, Epidemiology, and End Results (SEER) Program of the National Cancer Institute and the National Program of Central Cancer Registries (NPCR) of the Centers for Disease Control and Prevention (CDC). The LTR is one of only 10 Specialized Registries that are funded by the NPCR to collect enhanced data to support Comparative Effectiveness Research. Therefore, collected biospecimens are associated with robust clinical information. 

The BPC currently holds approximately 11,000 biospecimens from 5,000 participants and regularly accrues new specimens. Of the donors to date, 2,352 are African American, and of those, 1,220 are male and 1,132 are female. 

In addition, the BPC collects samples from malignancies and nontumoral tissues in HIV+ patients. The Core currently holds samples from approximately 380 participants with matching peripheral blood. All biospecimens are collected after obtaining written informed consent from the patient. These include a variety of biospecimens, including:

• Fresh-frozen tumor samples and corresponding nontumoral tissue
• Paraffin-embedded tissue
• Blood/plasma/serum
• Serum and urine
• Buccal swab
• Stool

• CryoPlus Liquid Nitrogen Storage system, which has a storage capacity of 13,000 vials (2.0 ml) 
• Leica CM 1860 cryostat used for sectioning frozen tissues at sub-zero temperatures as a QA/QC  
• Two -80˚C freezers for liquid (blood/urine) products and cryopreserved cells from patient blood
• Tissue processor Leica 6021 or similar     
• Microtome                                                          
• -80 to -86oC freezer                                           
• Centrifuge Eppendorf 5810R                        
• Olympus upright microscope                    
• Inverted tissue culture microscope  

Biostatisticians in the Biostatistics and Bioinformatics Core have collective experience analyzing and planning hundreds of studies. They serve as a first counselor to study design, help disseminate results via publication, brainstorm future helpful projects/process implementation, and connect researchers from various fields. Specific services that biostatisticians in the BBC can provide are:

• Analysis of datasets, including large-scale electronic health record data, spatial data, repeated measures, and tumor registry data. 
  
• Help with planning studies, including outcome/data collection choices, sample size determination/power calculations, and adaptive decision-making processes.
  
• Clinical trial design, including stopping rules, treatment allocation, dose-finding, enrichment designs, and subgroup-based decision-making. This service includes all phases of research (pre-clinical bench work, animal studies, phase I, phase II, phase III, and hybridized designs). 
  
• Artificial Intelligence Applications: Biostatistics members have experience implementing statistical and machine learning methods in decision-making software. This could include implementing modeling procedures into patient electronic medical records like EPIC to provide better clinical decision-making, coding up error prompts in data entry, and many other applications. Some of these may need careful collaboration with a software engineer. Members have experience in various statistical fields (Frequentist, Bayesian, and Machine Learning Methods) that can be leveraged for the prediction and inference of complex biological relationships.
  
• Software Design: Through the use of R Graphical User Interfaces, Biostatisticians can develop user-friendly software to tackle problems that are frequently seen by various researchers. With the help of software engineers, these user interfaces can be adapted to provide an optimal experience for researchers.

Hardware Capabilities 

The Bioinformatics and Genomics (BIG) Research and Training Program is the research and academic component of the LSU Health New Orleans School of Medicine and Department of Genetics. The BIG was established as a multidisciplinary program in 2015 with funding from the School of Medicine and grants. This program, directed by Dr. Chindo Hicks, is highly interdisciplinary, involving many schools and departments across the LSU Health New Orleans campus and the Tulane University campus. 

The program is home to the Bioinformatics and Computational Genomics (BCG) Laboratory, which is equipped with:

• Four Dell Precision Workstations, Tower 5810 XCTO Base (210-ACQM) 32GB (4x8GB) 2133MHz DDR4 RDIMM ECC (370-ABUP) 3.5 inch 2TB SATA 7.2k RPM HDD, FPWS (400-AIJK). Each workstation has 8TB of storage space. 
• Three newly acquired Mac Pros, each powered by a 12-Core and Dual GPU 3.5GHz 6-Core Intel Xeon E5 processor 64GB 1866MHz DDR3 ECC memory Dual AMD FirePro D500 with 3GB GDDR5 VRAM each with 30TB data storage. These systems are used for small-scale and medium-scale computing. 

For large-scale bioinformatics, computational genomics, and big data analysis, the BIG/BCG staff have access to LSU’s “SuperMike-II,” a $2.6 million Dell, Inc. supercomputer with:

• Peak performance capability in excess of 212 TeraFlops (or 212 thousand-billion floating-point operations per second). 
• A total of 440 compute nodes (servers), each of which has two Intel Sandy Bridge 8-core processors running at 2.6GHz.
• A total of 7040 computational cores.
• Nodes that are interconnected by a 40Gbps Mellanox InfiniBand network. While most of the nodes (382) have 32GB of memory, 8 are equipped with 256GB each and joined via Scale MP software to give a single SMP machine with 128 processing cores and 2TB of memory. Fifty nodes are each equipped with 64GB of memory and two NVIDIA Tesla M2090 GPUs. 

SuperMike is housed on the LSU campus and operated in conjunction with the High Performance Computing Group of LSU’s Office of Computing Services. 

Software Capabilities

All workstations and Mac Pros in the Bioinformatics and Genomics Program’s Bioinformatics and Computational Genomics Laboratory are equipped with various software and pipelines to analyze omics, genotype, sequence, and clinical data. These include:

• The Galaxy system
• SAM and BWA Tools
• GenePattern
• Bioconductor
• SAS
• In-house Perl, Java, C++, and R scripts

The software is regularly updated. In addition, the workstations are equipped with the Ingenuity Pathway Analysis (IPA, Qiagen) software, which will be deployed for network and pathways analysis for the proposed projects. 

The Cellular Immunology and Immune Metabolism Core (CIMC) facility supports investigators from the New Orleans metropolitan area: LSU Health New Orleans School of Medicine, LSU Health New Orleans Dental School, Tulane University School of Medicine, Ochsner Health System, and Xavier University.

The Core provides assistance in sample processing and instrument operation, as well as consultation in experimental design, troubleshooting, data analysis, and interpretation of the results.

Additionally, the CIMC Core organizes group and individual trainings, workshops, and seminars for all members of the LSU LCMC Health Cancer Center.

Equipment is available 24/7 for trained investigators, with the exception of the FACS Aria and the Amnis. During regular working hours, a Core member is available to assist with setup, running samples, and troubleshooting. After-hours, only trained users have access to the Core. Equipment is protected by a user-specific password, which enables the CIMC to monitor equipment usage.

The equipment scheduling, billing, and reporting are performed using Agilent iLab.

Flow Cytometers:  

• FACS ARIA II, which has five lasers: 355nm, 405nm, 488nm, 561nm, and 633nm. The sorter is used for the isolation of specific cell populations based on their cellular markers. It can sort up to four different cell populations into 5 ml tubes. Additionally, cells can be sorted into 6-,24-,48-,96-, 384-well plates or slides. Operated only by Core personnel.
  
• Beckman Coulter 10 color Gallios flow cytometer, purchased in 2010. Gallios is equipped with three lasers: 405nm; 488nm, and 638nm. Available to be operated by a user after training.
  
• BD FACSymphony A3; 28-parameter flow cytometer recently purchased (2019). Equipped with five lasers: 355nm; 405nm; 488nm, 561nm, and 633nm. Available to be operated by a user after training.
  
• Amnis ImageStreamX Mark II combines flow cytometry with fluorescent microscopy technology. This flow cytometer is equipped with a camera, which takes pictures of every cell passing through the flow cell using 20x, 40x, or 60x magnification lenses. It is equipped with four lasers: 405nm; 488nm, 561nm, and 633nm. Aside from regular cell phenotyping, this configuration allows analysis of cell-to-cell interactions, cell signaling, internalization and co-localization, translocations, shape change, and chemotaxis and nanoparticles analysis. LSU LCMC Health Cancer Center shares it with Tulane Cancer Center. Operated only by Core personnel.
  
• The Incucyte SX5 Live-Cell Analysis System is a real-time cell monitoring and surveillance system that automatically captures high resolutions of fluorescent and bright field images. It analyzes images of living cells around the clock for days, weeks, or months, while cells remain undisturbed inside a standard tissue culture incubator. The stage accommodates up to six multi-well plates, which are scanned automatically according to the investigator-defined schedule. The IncuCyte enables real-time monitoring of a variety of live cell assays including viability, differentiation, proliferation, migration, invasion, metabolism, neurite outgrowth, and a wide range of phenotypic cell-based assays. Incucyte is placed in the cell culture incubator to maintain the required cell culture environment. Available to operate by a user after training.
  
• XFe24 and XFe96 bio analyzers (previously named Seahorse) measure real-time cell respiration in 24 or 96 well plates. It is used to perform assays like Glycolysis Stress, MitoStress, ATP Rate, and many others. The XFe96 unit is placed inside a hypoxia chamber, which allows the creation of different oxygen conditions. XFe96 is equipped with a Cytation 1 microscope for cell counting to normalize the results. Available to be operated by a user after training. Kits and reagents can be found here. 
  
• Luminex -MagPIX for cytokines level measurement. MagPIX technology is a beads-based versatile multiplexing platform performing quantitative and qualitative analysis of proteins and nucleic acids in a variety of sample matrices. It is capable of measuring up to 60 analytes/samples in a single well. Available to be operated by a user after training. Kits and reagents can be found here. 
  
• The IVIS® SpectrumCT by Perkin Elmer is a preclinical in vivo imaging system, which allows simultaneous molecular and anatomical non-invasive imaging of small live animals. It is used in the monitoring of disease progression, cell trafficking, and gene expression patterns. IVIS Spectrum CT offers 2D and 3D imaging capabilities and includes integrated low-dose microCT. Available to operate by a user after training. Please contact Dr. Bin Yi for assistance with training and operation.
  
• Malvern Panalytical Inc.-NanoSight NS300 is a system for detecting and measuring the concentration of extracellular vesicles (EV). Equipped with a 532nm laser. Available to be operated by a user after training.
  
• Milteny gentleMax Octo Dissociator with heaters for preparation of single-cell suspension from tissues and tumors. Available to everyone without training.
  
• Nikon fluorescent microscope. Operated by a user after training.
  
• ECHO Revolve microscope. A hybrid microscope, combining four microscopes into one that easily converts between upright and inverted. 

Please contact the Core before planning an experiment to make sure fluorophores are compatible with the systems in the Core.

All equipment is under the service contract, and all calibration is performed daily, which allows instruments to be well-maintained and, in case of malfunction, repaired quickly. 

The CIMC provides support for the analysis and interpretation of the data obtained in the Core. 

The following analysis software is available: 

• Kaluza
  
• Flowjo
  
• ModFit
  
• Ideas, Wave
  
• Excel
  
• Graph Pad software

The Molecular Histopathology and Analytical Microscopy Core (MHAM) is a state-of-the-art facility created to provide advanced histopathology and microscopy services to investigators and clinicians conducting research at LSU LCMC Health Cancer Center, including promising junior investigators of the Center for Translational Viral Oncology (CTVO). 

The MHAM provides researchers with access to archival clinical samples, experimental planning design, and imaging studies on the histology and pathology of tissues, the expression of cell surface, and intracellular molecules including viral proteins, using bright field and confocal microscopy, immunohistochemistry, immunohistofluorescence, multiplexing, in situ hybridization, and in situ proximity ligation (DuoLink). These multiple methods are used to determine protein expression patterns and localization, mRNA levels, their subcellular localization, and protein-protein and RNA-protein interactions in the cells and tissues. Moreover, the MHAM Core assists investigators in developing the necessary imaging and data for the submission of manuscripts and grants.

The Molecular Histopathology section of the Core is prepared to handle conventional tissue processing through a Leica tissue processor, TP1020, with a capacity of 80 cassettes per load and different time programs. Paraffin blocks are prepared manually in a TBS Embedding Station. Tissue sections are cut in three Thermo HM340E Microtomes, one for human samples, one of which is dedicated to viral PCR procedures, and one exclusively reserved for experimental animal tissue. Average sections are 3-5 microns in thickness.

Microscopes:

• Olympus FV1000 confocal microscope
  
• Keyence BZ-X810 all-in-one fluorescence microscope
  
• Nikon TE300 automated, inverted microscope equipped with a deconvolution software (SlideBook 5.0)
  
• Olympus LCV110U fluorescent microscope (VivaView) live imaging and time-lapse
  
• Olympus BX51 with multispectral imaging digital camera (Mantra, from Elkin-Elmer)
  
• Motic EasyScan Pro6 digital slide microscope

Techniques Offered:

• Immunohistochemistry
  
• Immunofluorescence
  
• Double labeling
  
• Deconvolution
  
• Multiplexing
  
• In situ hybridization
  
• Live imaging 
  
• Fluorescence recovery after photobleaching
  
• Comet assay
  

The Proteomics and Metabolomics Core is dedicated to developing, implementing, and providing high-quality analytical methodology for determination of molecules involved in disease development, progression, and treatment. This helps to standardize quantitative measurements and facilitate research progress that leads to a better understanding of these processes.

The standardized techniques offered by the PMC Core generate data that can be comparable and cross-referenced among specific experiments of each individual investigator. Particular attention is given to quality control. All the methods in the Core are defined by a series of steps to maximize the quality of the output and are described in Standard Operational Procedures (SOP). Reproducibility is monitored and ensured within the system with procedures implemented to identify any changes and shifts in the platform during sample analyses. This helps to standardize quantitative measurements for LSU LCMC Health Cancer Center and Louisiana Cancer Research Center members and facilitates research progress that will lead to a better understanding of these processes.

Services offered by Core facilities include sample extraction, high throughput screening, deep metabolomics and proteomics profiling using LC- and GC-MS techniques, targeted analysis, data analysis, pathway analysis, and flux analysis.

In addition, molecular imaging is also available. In this case, spatial protein and metabolite distribution is determined using newly established MALDI HiPLEX-IHC technology available through Bruker and AmberGen. It allows for intact protein imaging by combining transcriptome-relevant information from labeled protein expression mapping with advanced small molecule imaging from the same tissue section using MALDI imaging. The method combines MALDI-based mass spectrometry with immunohistochemistry (IHC) using specific antibodies labeled with a set of photocleavable mass-tags reporters. The platform is used to gain high-resolution tissue-wide and single-cell inflammatory RNA and protein expression data with two-dimensional lineage and proximity information. 

Core facilities are well equipped with cutting-edge instruments, which allows researchers to identify and quantify all proteins relevant to a project. These resources are readily available for proposed studies.

Instruments include:

• Two Thermo Fisher Q Exactive Plus Orbitrap mass spectrometers
• One Fusion Tribrid Orbitrap mass spectrometer (all connected to nanoUPLC systems)
• Bruker’s timsTOF fleX Pro 2 mass spectrometer equipped with two MALDI sources and nanoElute UPLC System for global profiling
• Agilent’s 6495C LCTQ MS System equipped with 1200 HPLC system for targeted analysis
• Agilent’s 7250 GC/Q-TOF for polar metabolite quantification
  Core also has bioinformatics capabilities with database search engines and additional data mining software. 

Download additional information about services and equipment. 

• Automated DNA sequencing using state-of-the-art instrumentation and the latest protocols to ensure high-quality results. These protocols include, among others, Sanger sequencing of fragments of up to 1,200nt and next-generation sequencing (NGS) protocols like whole genome sequencing (WGS), whole exome sequencing (WES), amplicon sequencing, microbiome (16S) and meta-genome sequencing, and chromatin immunoprecipitation (ChIP-seq).
• Transcriptome sequencing, which includes gene expression profiling to investigate the abundance of known mRNA; whole RNA-seq, which included coding and non-coding RNAs, single-cell RNA-seq, which investigates the gene profiles of individual cells from complex tissues or purified cell preparations; and miRNA-seq, which involves the identification of miRNAs in sample, either fluidic (serum, plasma) or from solid tissues.
• Microarray analysis includes array-based methylation (> 900K CpG across the human genome), GWAS, microarray-based exome analysis, and several focused arrays, among others. 
• NanoString SPRINT n-Counter for the analysis panels of genes associated with oncology, immunology, neuroscience, cell profiling, cancer metabolism, cell signaling, and DNA repair, among others.
• NanoString DSP/GeoMx for spatial transcriptomics/protein mapping in IHC slides. Includes whole transcriptome spatial profiling (18,000 genes) and Cancer Transcriptome Atlas (CTA, 1,800 genes). Up to three morphology markers for specific tissue area analysis (tumor margins, center, etc.)

• Illumina NextSeq2000 and a MiSeq (both for next generation sequencing instruments from Illumina)
• Illumina iScan for the analysis of microarray-based analyses 
• QuantStudio 12K real-time PCR systems
• Covaris DNA fragmentation instrument for the preparation of DNA for exome sequencing
• 10X Genomics Single Cell Isolator for single cell sequencing