A New Approach for Prostate Cancer Diagnosis by miRNA Profiling of Prostate-Derived Plasma Small Extracellular Vesicles

Vesicular miRNA has emerged as a promising marker for various types of cancer, including prostate cancer (PC). In the advanced stage of PC, the cancer-cell-derived small extracellular vesicles (SEVs) may constitute a significant portion of circulating vesicles and may mediate a detectable change in the plasma vesicular miRNA profile. However, SEVs secreted by small tumor in the prostate gland constitute a tiny fraction of circulating vesicles and cause undetectable miRNA pattern changes. Thus, the isolation and miRNA profiling of a specific prostate-derived fraction of SEVs can improve the diagnostic potency of the methods based on vesicular miRNA analysis. Prostate-specific membrane antigen (PSMA) was selected as a marker of prostate-derived SEVs. Super-paramagnetic beads (SPMBs) were functionalized by PSMA-binding DNA aptamer (PSMA–Apt) via a click reaction. The efficacy of SPMB–PSMA–Apt complex formation and PSMA(+)SEVs capture were assayed by flow cytometry. miRNA was isolated from the total population of SEVs and PSMA(+)SEVs of PC patients (n = 55) and healthy donors (n = 30). Four PC-related miRNAs (miR-145, miR-451a, miR-143, and miR-221) were assayed by RT-PCR. The click chemistry allowed fixing DNA aptamers onto the surface of SPMB with an efficacy of up to 89.9%. The developed method more effectively isolates PSMA(+)SEVs than relevant antibody-based technology. The analysis of PC-related miRNA in the fraction of PSMA(+)SEVs was more sensitive and revealed distinct diagnostic potency (AUC: miR-145, 0.76; miR-221, 0.7; miR-451a, 0.65; and miR-141, 0.64) than analysis of the total SEV population. Thus, isolation of prostate-specific SEVs followed by analysis of vesicular miRNA might be a promising PC diagnosis method.

Tumor Biomarker In-Solution Quantification, Standard Production, and Multiplex Detection

The diagnosis and monitoring of cancer have been facilitated by discovering tumor “biomarkers” and methods to detect their presence. Yet, for certain cancers, we still lack sensitive and specific biomarkers or the means to quantify subtle concentration changes successfully. The identification of new biomarkers of disease and improving the sensitivity of detection will remain key to changing clinical outcomes. Patient liquid biopsies (serum and plasma) are the most easily obtained sources for noninvasive analysis of proteins that tumor cells release directly and via extracellular microvesicles and tumor shedding. Therefore, an emphasis on creating reliable assays using serum/plasma and “direct, in-solution” ELISA approaches has built an industry centered on patient protein biomarker analysis. A need for improved dynamic range and automation has resulted in the application of ELISA principles to paramagnetic beads with chemiluminescent or fluorescent detection. In the clinical testing lab, chemiluminescent paramagnetic assays are run on automated machines that test a single analyte, minimize technical variation, and are not limited by serum sample volumes. This differs slightly from the R&D setting, where serum samples are often limiting; therefore, multiplexing antibodies to test multiple biomarkers in low serum volumes may be preferred. This review summarizes the development of historical biomarker “standards”, paramagnetic particle assay principles, chemiluminescent or fluorescent biomarker detection advancements, and multiplexing for sensitive detection of novel serum biomarkers.

Multi-frequency impedance sensing for detection and sizing of DNA fragments

Electronic biosensors for DNA detection typically utilize immobilized oligonucleotide probes on a signal transducer, which outputs an electronic signal when target molecules bind to probes. However, limitation in probe selectivity and variable levels of non-target material in complex biological samples can lead to nonspecific binding and reduced sensitivity. Here we introduce the integration of 2.8 μm paramagnetic beads with DNA fragments. We apply a custom-made microfluidic chip to detect DNA molecules bound to beads by measuring Impedance Peak Response (IPR) at multiple frequencies. Technical and analytical performance was evaluated using beads containing purified Polymerase Chain Reaction (PCR) products of different lengths (157, 300, 613 bp) with DNA concentration ranging from 0.039 amol to 7.8 fmol. Multi-frequency IPR correlated positively with DNA amounts and was used to calculate a DNA quantification score. The minimum DNA amount of a 300 bp fragment coupled on beads that could be robustly detected was 0.0039 fmol (1.54 fg or 4750 copies/bead). Additionally, our approach allowed distinguishing beads with similar molar concentration DNA fragments of different lengths. Using this impedance sensor, purified PCR products could be analyzed within ten minutes to determine DNA fragment length and quantity based on comparison to a known DNA standard.

SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS

Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.

Dynamics and rheology of a super-paramagnetic chain suspension under the combined effect of a shear flow and a rotating magnetic field.

This study presents an analysis of the dynamics of a single and multiple chains of spherical super-paramagnetic beads suspended in a Newtonian fluid under the combined effect of an external...

Efficient and specific oligo-based depletion of rRNA

SummaryIn most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA or other highly abundant transcripts is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences.In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects.By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.

Robust Cell Selections and Depletions across Various Hematopoietic Cell Fractions on the Clinimacs Plus Instrument

Introduction: Cell enrichment and/or depletion by selection is critical for graft engineering in cellular and gene therapies. The semi-automated CliniMACS Plus Instrument (Miltenyi Biotec) is used in clinical cell processing to enrich or deplete a variety of hematopoietic cells including T, B, monocytes, NK cells, and/or CD34+ hematopoietic stem/progenitor cells (HSPCs). Antibody-conjugated paramagnetic beads attach to the desired cells which are separated from the rest of the apheresis or bone marrow product in a closed-system magnetic separation column. Either the selected cells retained in the separation column (positive selection) or those in the "flow-through" fraction (negative selection) may be used for downstream processing. There is sparse data comparing cell selection efficiency and purity across the various selection methods on the CliniMACS Plus Instrument. Further, the effect of donor demographics and other upstream processing events on final viable cell recovery (VCR)/ cell purity (CP) are unknown. This study systematically compared these parameters across various selection methods. Methods: From 2008 to 2018, data were obtained from 45 clinical processing protocols involving 991 consecutive adult and pediatric donor/patient apheresis products or bone marrow harvests, which underwent cell selections on the Miltenyi CliniMACS Plus device. Cell selections included 1.CD34+ (n=669), 2.CD4+ (n=179), 3.CD3-/56+ (n=79), 4.CD3+/19- (n=6), 5.CD4+/8+ (n=21), and 6.CD25- (n=37) cells. Based on protocol design or logistical needs, apheresis or bone marrow collections were processed/selected on the same day or held overnight for next day processing. Products were also either washed to remove platelets (PW) or loaded onto the selection device directly. Data on donor age, BMI, donor type (autologous vs. allogeneic), sex, race, pre-apheresis peripheral blood cell counts and concentrations, as well as apheresis bag blood counts were evaluated. Outcome variables included post-selection VCR and CP. Correlations and multivariate regression analyses were performed for the largest selection type, i.e CD34+ cell selections. Results: Summary data (means ± 1SD) on method-specific enrichments and depletions are shown in the Table. Median post-selection VCR and CP varied by selection method. VCR was the highest for the CD34+ cell selections (Fig. a). CP was the highest and most consistent for CD4+ selections (Fig. b). Platelet and red cell depletions also varied by selection method and averaged 3.9 ± 1.63 and 2.06 ± 0.74 logs, respectively. Selection procedures used for cell depletion resulted in near complete removal of the undesired cell fractions (Table). In multivariate regression analyses, products processed on the same day (compared to those held overnight) (Fig. c), those that underwent a PW (Fig. d), and had higher pre-apheresis peripheral blood CD34+ absolute cell counts and concentrations (Fig. e) were associated significantly with higher CD34+ CP (adjusted r2=0.2; p<0.0001). Higher pre-apheresis CD34+ concentrations (Fig. f) were associated with a lower CD34+ VCR (15%, CI: 5.6-25.3). Conversely, PW (Fig. g) correlated with higher CD34+ VCR (3.5%; CI: 0.8-6.28). Trends across the study period demonstrated a significant improvement in CD34+ VCR from 2008 to 2017 (Fig. h). Conclusions: This is the largest study, to our knowledge, to systematically summarize and analyze Miltenyi CliniMACS Plus selections for clinical graft engineering. Cell selections on the Miltenyi CliniMACS Plus resulted in robust enrichment with near complete depletion of the undesired cell fractions. CD34+ CP was higher in patients with higher CD34+ cells counts following mobilization. Same day processing, as well as PW further improved CD34+ CP. PW also improved CD34+ VCR. This was likely due to a reduction in non-specific platelet binding to the paramagnetic beads. Higher pre-selection CD34+ cell concentrations in the product marginally worsened VCR. This was possibly due to bead saturation in each selection method. Improved CD34+ VCR over time was likely due to increased platelet washes in the latter years. Further studies are ongoing to assess impact of cell selection variations on downstream manufacturing steps (cell transduction, expansion) and clinical (cell engraftment, GVHD incidence) outcomes. Disclosures Larochelle: Stem Cell Technologies: Patents & Royalties: StemDiff Hematopoietic Differentiation Kit.