StromaLiquid Biopsy™ Whitepaper-January2022
Thiswhitepaper highlights the importance of the systemic inflammatoryresponse to the presence of cancer anywhere in the body. It alsodescribes how the vast circuitry of cascading proteolytic events,requires suitable regulation in order to resolve innate immunity andaccommodate the adaptive T-cell responsein cancer. From this, new strategies for more durable therapeuticefficacy will be uncovered.
Biotech Support Group and Leiden University Medical Center Report on a Gene Signature Ratio derived from Stroma Liquid Biopsy™ that Predicts Survival in Colon Cancer
Ravensbergen, Cor J., et al. "The Stroma Liquid Biopsy Panel Contains a Stromal-Epithelial Gene Signature Ratio That Is Associated with the Histologic Tumor-Stroma Ratio and Predicts Survival in Colon Cancer." Cancers 14.1 (2022): 163.
Liquid biopsy has emerged as a novel approach to tumor characterization, offering advantages in sample accessibility and tissue heterogeneity. However, as mutational analysis predominates, the tumor microenvironment has largely remained unacknowledged in liquid biopsy research. The Stroma Liquid Biopsy™ (SLB) proteomics panel comprises a set of 13 proteins from interconnected stromal pathways (i.e., coagulation, complement, acute phase inflammation) and is believed to capture a plasma proteomic blueprint indicative of a deranged systemic response in cancer. As such, it encompasses the importance of the tumor microenvironment (TME) compartment in liquid biopsy. Within similar context, the histologic tumor-stroma ratio (TSR), a stroma-derived biomarker developed by LUMC, has been validated as an independent predictor of patient survival in various primary tumor types. The current work provides an explorative gene transcriptomic characterization of the SLB proteomics panel in colon carcinoma by integrating single-cell and bulk transcriptomics data from publicly available repositories.
APreliminary Investigation Using Targeted LC-MS Proteomic MethodsDemonstrates Unique Serum Profiles of Hospitalized SARS-CoV-2Patients
DouglasD Fraser1;Haiyan Zheng2;Swapan Roy3; MattKuruc3;Amenah Soherwardy2;Devjit Roy4;Sowmya Avadhani 3
1LawsonResearch Institute, London, Ontario; 2RutgersUniversity Proteomics Center, Piscataway, New Jersey; 3BiotechSupport Group LLC, Monmouth Junction, NJ; 4NathanLittauer Hospital, Gloversville, New York CorrespondingAuthor:[email protected]
Briefdescription: For serum samples, targeted LC-MS is challenging, mainlydue to the presence of highly abundant proteins. So it becomescritical to pair target peptides to sample depletion methods to bestestablish differentiated profiles between samples. In thispreliminary investigation, we use unique methods described here tocharacterize the functionality of the innate immune response inhospitalized Covid-19 patients, more precisely than current methods.
High-throughput,Automated INTip™ SPE Combined with AlbuSorb™ Products forEfficient Albumin and Albumin/IgG Depletion
MatthewFitts 1;William E. Kemnitzer 1;Paul Meeh 1; MattKuruc2;Swapan Roy 2;Sowmya Avadhani 2
1DPXTechnologies, Columbia, SC; 2BiotechSupport Group LLC, Monmouth Junction, NJ Corresponding Author:[email protected]
Briefdescription: We report here new methods to incorporate beads fordepletion of Albumin, IgG and Hemoglobin, into pipette tips known asXTRaction tips or XTR tips. The XTR tip format improves ease of useand scalability to process multiple samples in parallel, utilizing96-well plates and automated liquid handlers. The incorporated BSGbeads are consumable, and not derived from immuno-affinity.
JournalPublications
AlbuminRemoval Kits
Serum
Swapan Roy, Matthew Kuruc. The Functional Subproteomes of Serpin Protease Inhibitors are Now Open for LC-MS Biomarker Discovery. MOJ Proteomics Bioinform 2016, 3(6): 00106
The authors consider that the conformational variants of the unique family of protease inhibitors annotated as SERPINs, are most often underrepresented in proteomic analyses. This limits understanding the complex regulation that this family of proteins presents to the networks within the protease web of interactions. Using bead-based separation provided by the NuGel™ family of proteomic enrichment products - notably AlbuVoid™ & AlbuSorb™, the authors demonstrate their utility to satisfy investigations of serum SERPINs. The authors also suggest their use to develop functional profiles of the SERPIN Proteoform, and how those can establish relationships to disease phenotypes, gene mutations, and deregulated mechanisms.
Featured Application - Functional Proteomics
Sun, Zhenyu, Xiaofeng Chen, Gan Wang, Liang Li, Guofeng Fu, Matthew Kuruc, and Xing Wang. "Identification of functional metabolic biomarkers from lung cancer patient serum using PEP technology." Biomarker Research 4, no. 1 (2016): 1.
Zhenget al. AlbuVoid™Coupled to On-Bead Digestion - Tackling the Challenges of SerumProteomics. JProteomics Bioinform 2015, 8:9
Abstract
Forcancer research, serum and plasma are especially attractive sampletypes as collection of blood is common, simple and only minimallyinvasive. Yet serum samples can offer unique challenges in LC-MSproteomic analyses. The two biggest challenges being: 1) the highabundance of Albumin accounting for about 50% of the total proteinmass and, 2) proteolytic resistance, in large part due to substantialamount of glycoprotein, a modification that manifests proteolyticresistance. In this short report, we describe new methods using asurface/bead based product, AlbuVoid™, which depletes Albuminthrough a negative selection or voidance strategy, retaining the vastamount of the remaining serum proteome on the bead. We then combinethis novel enrichment, with a direct and seamless integration withTrypsin digestion, a method conventionally referred to as on-beaddigestion. We evaluated the digestion time as a parameter to identifywhether different sub-populations of peptides and proteins can beobserved by LC-MS analyses. Using 2 different allotted digestiontimes - 4 hours, and overnight, each with a singular 3 hour gradientLC-MS run, between 400-500 total proteins were observed for bothhuman and rat sera, with overlapping and distinct sub-populationsobservable at each digest time. These results support that thedescribed methods gain efficiencies over other high abundancedepletion and in-solution digestion workflows. We solicit that suchworkflows will minimize many of the inconsistencies of proteolytichydrolysis for both discovery and quantitative serum proteomicapplications.
Cleanascite™- Lipid Removal and Cell Response Applications
The“omics” revolution demanded new and different sample prepseparations that were not efficiently performed by conventionaltechnologies. While effective for many applications, these tools werenot efficient for “omics” sample preparation, asthroughput, economy and simplicity are especially required.Furthermore, these same separation tools often denatured proteinswhich limited there use in applications which demanded themeasurement of function, structure or bio-activity. For thesereasons, BSG has been dedicated to create new methods andapplications to drive efficient workflows and better data quality forall proteomic and biomarker analyses. Of special importance is thevalue created when certain families of biomolecules can be evaluatedwith respect to cell response and viability. For example,extracellular vesicles (EVs) substantially influence cultured cellbehavior. While all of our products serve cell response applications,we report here an extensive list of applications in this area forCleanascite™. Cleanascite™ is derived through aproprietary formulation of metallic oxide derivatives. However,unlikeother metallic oxides, Cleanascite™ does not have significantprotein binding, making its selectivity profile for lipids un-rivaledin the bio-research products industry. As a result, it is ideal toclear lipid-associated matrix effects - including extracellularvesicles, which may influence cell response assays.
Todownload whitepaper entitled “Cleanascite™ - LipidRemoval and Cell Response Applications"
Mutations,post-translational modification, and non-covalent binding factors allplay a role in fine tuning polypeptide sequence to final function.Because of this phenomena, populations of proteins annotated to thesame sequence nevertheless can display multiple functions withintissues and disease states. Likewise, the same or similar functionmay be presented by multiple sequences, with subcellular controlmechanisms regulating functional diversity. As a consequence,strictly abundance based biomarkers may lack the necessary dynamicrange and greater specificity provided by functional basedbiomarkers, to define the phenotype. Thus, Functional Proteomictechniques such as described here, support a top-down proteomicstrategy starting with functional annotation of the structurallyintact protein, and ending with sequence and structural annotation.
CWan, BBorgeson, SPhanse,F Tu, KDrew, GClark,et al. Panoramaof ancient metazoan macromolecular complexes.Nature Volume:525, Pages:339–344 Date published:(17 September2015). doi:10.1038/nature14877
Twoof BSG products, NRicher™ 6 and HemogloBind™, were able tocontribute to this rigorous examination of protein complexes. Whenour products were used as a pretreatment step in the overallworkflow, about twice the number of observations and annotationsbecame possible. This further validates that the sub-proteome biascharacteristics of NRicher™ 6 can simplify complex proteomes intoless complex sub-proteomes with efficiencies suitable for deepfunctional proteome characterization. Furthermore, this studydemonstrated the importance of a key feature implicit to all of ourproducts; that is the maintenance of functional and structuralintegrity after separations. Without that particular feature, theseadditional observations would not have been possible.
HemogloBind™& NuGel™ HemogloBind™ for selective binding of Hemoglobin &
HemoVoid™for negative selection or voidance of Hemoglobin with consequentenrichment of the remaining erythrocyte proteome on the bead
