MS Proteotyping of Human Cancers in Oncology Therapeutic Development
Daniel C. Liebler, Ph.D.
Protypia, Inc.
Daniel C. Liebler, Ph.D. is an internationally-recognized research leader in the fields of proteomics, cancer proteogenomics, chemical biology and toxicology. With over 30 years experience at the interface of analytical technology, chemical biology and disease research, Dr. Liebler led multidisciplinary programs at the University of Arizona and Vanderbilt University School of Medicine funded by the National Institutes of Health, industry and private philanthropy. At Vanderbilt, Dr. Liebler's team laid the groundwork for the integration of proteomic technologies into cancer therapeutics and diagnostics. Dr. Liebler left Vanderbilt in 2016 to launch Protypia, which provides drug target and system analysis to leading pharmaceutical and biotechnology companies in therapeutic development.
In this discussion, Dr. Dan Liebler, President of Protypia, Inc., will highlight his research on MS proteotyping of human cancers in oncology therapeutic development using mass spectrometry.
Quantitative Analysis of the TIGIT/DNAM1 and PD-1/PD-L1 Axes in Primary Non-Small Cell Lung Cancers (NSCLC) and Lymph Node Metastases
Matt Westfall1, Salisha Hill1, Ryan D. Morrison1, Daniel C. Liebler1*, and Alexander Haragan2*
1 Protypia, Inc, Nashville, TN, USA
2 Royal Liverpool University Hospital, Department of Pathology, Liverpool, UK
New therapies targeting immune checkpoint (IC) proteins have revolutionized oncology therapeutics, but heterogeneous expression of IC proteins between individuals and tumor types complicates development of cancer immunotherapies. Although typically framed in the context of companion diagnostics, the need to reliably quantify drug targets is critical in the preclinical and clinical development of new drugs, especially for the design and interpretation of clinical trials. Quantification of drug target status can inform interpretation of target abundance and outcomes. Targeted mass spectrometry (MS) uniquely enables sensitive and precise measurement of IC proteins, coregulators and immune cell markers. MS measurements can be performed in formalin-fixed, paraffin-embedded (FFPE) samples and are multiplexed, thereby enabling simultaneous analysis of multiple IC proteins, immune cell markers, and related pathway markers in the same sample.
New immunotherapeutics targeting the IC protein TIGIT are in clinical development with PD-1/PD-L1 inhibitors for solid tumor indications, but without reliable TIGIT protein biomarkers to guide trial design and interpretation. We used targeted mass spectrometry (MS) to precisely quantify TIGIT, DNAM1, PVR, PVRL2, PD-1, PD-L1, and PD-L2 in 97 primary non-small cell lung cancers (NSCLC) and matched tumor draining lymph node metastases (TDLN). Only 56% of NSCLC cases expressed TIGIT, which was quantifiable almost exclusively in TDLN. TIGIT, DNAM1 and PVR abundance varied over approximately 25-fold and they were co-expressed only in some tumors. PD-1/PD-L1 axis proteins were quantified in virtually all samples over an even broader abundance range than TIGIT/DNAM1 axis proteins. Combined quantitation of TIGIT/DNAM1 and PD-1/PD-L1 axis proteins may indicate the sufficiency of the target system to respond to combined anti-TIGIT anti-PD-1/PD-L1 therapeutics.
Learn More
• Protypia, Inc.
• daniel.liebler@protypia.com
Transitioning from nanoflow to standard flow LC/MS: High throughput protein biomarker quantification for clinical research
Linfeng Wu, PhD
Agilent Technologies
Liquid chromatography mass spectrometry-based proteomics has been widely used for protein biomarker discovery and validation. When transitioning from discovery proteomics to targeted protein biomarker quantification, the MRM-based LC/MS method plays an important role in clinical research. To ensure analytical reproducibility and robustness, implementing standard flow-based triple quadrupole LC/MS system has tremendous benefit when involving a large cohort. This webinar will discuss the analytical performance under standard-flow and low LC flow conditions using the Agilent 6495 triple quadrupole LC/MS system.
For Research Use Only. Not for use in diagnostic procedures.
Learning Objectives:
· Quantitative sensitivity, precision and accuracy of standard flow-based dynamic MRM method for targeted protein biomarker analysis using the Agilent 6495 LC/TQ
· Successful transfer of PromarkerD method for diabetic kidney disease research from nanoflow to standard flow
· When sample limited, a low flow LC system, Evosep One, coupled to Agilent 6495 LC/TQ could be used for high throughput studies
For Research Use Only. Not for use in diagnostic procedures.
How is the emergence of hemp affecting the Clinical space? Synthesis, certification and clinical evaluation of 7-Hydroxy and 7-Carboxy Cannabidiol Certified Reference Materials in plasma samples by LC-MS/MS
Heather Lima, PhD
MilliporeSigma
I joined Cerilliant Corporation at MilliporeSigma as a Senior Scientist in 2012 after earning a Ph.D. in Chemistry at the University of Texas at Arlington. My graduate research focused on the total synthesis of imidazole-containing natural products, and a manufacturing technology internship at Abbott Laboratories focused on API manufacturing process improvements and scale up. I earned a B.S. in Biochemistry in 2005 also at the University of Texas at Arlington.
I have extensive experience in reference material development and certification. My expertise includes design and synthesis of drugs, their metabolites, API impurities and stable isotope labelled internal standards, particularly steroids, cannabinoids, opiates and opioids. In June 2021, I took on the role of Senior R&D Manager of the Synthesis Department. Currently, I oversee synthesis operations of catalog and new products supporting the manufacture of Certified Reference Materials (CRM’s) at the Round Rock site as well as a diverse portfolio of custom synthesis projects.
Raymond Suhandynata, PhD DABCC
University of California, San Diego
Dr. Suhandynata is an Assistant Professor at the University of California San Diego with appointments in the Skaggs School of Pharmacy and Department of Pathology. He serves as the Associate Laboratory Director for the CMCR reference laboratory and the Associate Director of the UCSD ComACC clinical chemistry fellowship. He completed his Clinical Chemistry fellowship training at the UC San Diego Center for Advanced Laboratory Medicine, under the direction of Dr. Robert Fitzgerald. He has extensive experience with applications of mass spectrometry in research, pre-clinical, and clinical laboratories. Areas of interest include phospho-proteomics to identify novel kinase targets by LC-MS/MS, SUMO proteomics to identify cellular signals involved in chromosome segregation, utilization of MALDI-TOF MS in to identify antibiotic resistant bacteria in the clinical specimens, and development of targeted LC-MRM/PRM assays for small molecules and peptides. Addtionally, he as made significant contributions during the COVID-19 pandemic, validating several COVID-19 serology LDTs at UCSD Health.
Cannabidiol (CBD), a non-psychoactive constituent of hemp, has been increasingly promoted and studied for pharmacological uses as regulations regarding cannabis and hemp evolve rapidly at a state and federal level. In response to these recent regulations, novel Cannabinoid Certified Reference Materials (CRMs) and testing methods have been developed for the main human metabolites of CBD, 7-hydroxy cannabidiol (7-OH CBD) and 7-carboxy cannabidiol (7-COOH CBD). We will touch on recent legal changes for cannabinoid testing in a Clinical setting, as well as discuss the synthesis, certification, and evaluation of these cannabinoid CRMs in patient whole blood samples at the Center for Advanced Laboratory Medicine at UCSD.
Perspectives on Future LC-MS/MS Developments for the Routine Clinical Lab, with Special Focus on 25-OH Vitamin D Testing
Lorin Bachmann, PhD, DABCC
VCU Health System
Lorin Bachmann joined the VCU Department of Pathology in 2007. She currently serves as Co-Director of Clinical Chemistry, Co-Director of Point-of-Care Testing, Director of the New Kent Emergency Department Laboratory, Technical Advisor for the Operating Room Laboratory, Pathology Outreach and Clinical Trials, and Laboratory Director for multiple VCUHS outreach laboratories. Dr. Bachmann received her PhD in Molecular Medicine from the University of Virginia, followed by a fellowship in clinical chemistry and proteomics research at the University of Virginia. Dr. Bachmann is certified by the American Board of Clinical Chemistry.
Dr. Bachmann is active within the American Association for Clinical Chemistry (AACC), where she serves on the Board of Directors. She also serves as the Chair of the Chemistry and Toxicology Expert Panel for the Clinical Laboratory and Standards Institute (CLSI).
Dr. Bachmann’s research interests include evaluation and validation of new clinical laboratory assays, clinical laboratory analyzer design, development of mass spectrometry-based assays for the clinical laboratory and standardization of laboratory testing. She serves as the Chair of the National Kidney Disease Education Program (NKDEP)/International Federation of Clinical Chemistry Laboratory (IFCC) Joint Lab Working Group, whose goal is to accomplish standardization of urine albumin methods to enable utility of clinical decision thresholds.
Dr. Bachmann has received numerous awards for her contributions to professional societies, education and research. She serves as principal investigator for multiple industry-sponsored studies.
Accurate 25-OH Vitamin D measurements are important for assessment and management of patients with hypovitaminosis D. LC-MS/MS measurement procedures are more selective than immunoassay measurement procedures for 25-OH Vitamin D and generally exhibit improved recovery of 25-OH Vitamin D2. However, challenges related to increased labor requirements for preanalytical processing, additional method validation requirements for LDTs and lack of complete automation of quality assurance monitoring have presented significant barriers for implementation of LC-MS/MS in the routine clinical laboratory. Hear from a clinical laboratory and LC-MS/MS expert about the quality assurance needs of the routine clinical laboratory, the challenges associated with managing laboratory developed tests (LDTs) and the perspectives on future LC-MS/MS developments.
*Thermo Fisher Scientific products are distributed globally so uses, applications, and availability of product in each country depend on local regulatory marketing authorization status.
