Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology

The Clinical Laboratory Improvement Amendments (CLIA) of 1988 requires that pharmacogenetic genotyping methods need to be established according to technical standards and laboratory practice guidelines before testing can be offered to patients. Testing methods for variants in ABCB1, CBR3, COMT, CYP3A7, C8ORF34, FCGR2A, FCGR3A, HAS3, NT5C2, NUDT15, SBF2, SEMA3C, SLC16A5, SLC28A3, SOD2, TLR4, and TPMT were validated in a CLIA-accredited laboratory. As no known reference materials were available, DNA samples that were from Coriell Cell Repositories (Camden, NJ) were used for the analytical validation studies. Pharmacogenetic testing methods developed here were shown to be accurate and 100% analytically sensitive and specific. Other CLIA-accredited laboratories interested in offering pharmacogenetic testing for these genetic variants, related to genotype-guided therapy for oncology, could use these publicly available samples as reference materials when developing and validating new genetic tests or refining current assays

Early, intensive marine resource exploitation by Middle Stone Age humans at Ysterfontein 1 rockshelter, South Africa

Modern human behavioral innovations from the Middle Stone Age (MSA) include the earliest indicators of full coastal adaptation evidenced by shell middens, yet many MSA middens remain poorly dated. We apply ²³⁰Th/U burial dating to ostrich eggshells (OES) from Ysterfontein 1 (YFT1, Western Cape, South Africa), a stratified MSA shell midden. ²³⁰Th/U burial ages of YFT1 OES are relatively precise (median ± 2.7%), consistent with other age constraints, and preserve stratigraphic principles. Bayesian age–depth modeling indicates YFT1 was deposited between 119.9 to 113.1 thousand years ago (ka) (95% CI of model ages), and the entire 3.8 m thick midden may have accumulated within ∼2,300 y. Stable carbon, nitrogen, and oxygen isotopes of OES indicate that during occupation the local environment was dominated by C₃ vegetation and was initially significantly wetter than at present but became drier and cooler with time. Integrating archaeological evidence with OES ²³⁰Th/U ages and stable isotopes shows the following: 1) YFT1 is the oldest shell midden known, providing minimum constraints on full coastal adaptation by ∼120 ka; 2) despite rapid sea-level drop and other climatic changes during occupation, relative shellfish proportions and sizes remain similar, suggesting adaptive foraging along a changing coastline; 3) the YFT1 lithic technocomplex is similar to other west coast assemblages but distinct from potentially synchronous industries along the southern African coast, suggesting human populations were fragmented between seasonal rainfall zones; and 4) accumulation rates (up to 1.8 m/ka) are much higher than previously observed for dated, stratified MSA middens, implying more intense site occupation akin to Later Stone Age middens

Short-Term Insulin Requirements Following Gastric Bypass Surgery in Severely Obese Women with Type 1 Diabetes

Background: In severely obese type 2 diabetes patients, gastric bypass surgery (GB) reduces body mass index (BMI) and hemoglobin A1c (HbA1c) and allows reduced doses of insulin and other medications. Data regarding the effects of GB on severely obese patients with type 1 diabetes are limited. Methods: Severely obese women with type 1 diabetes (n = 9) were studied immediately before and after GB (7.7 ± 5.8 weeks, mean ± SD). Results: On average, GB reduced mean BMI by 11 % and mean HbA1c by 0.9 % (from 8.0 to 7.1 %), with a parallel 38 % decrease in basal insulin requirements (expressed per kilogram of body weight). Conclusion: GB rapidly decreased BMI, HbA1c, and insulin requirements in severely obese women with type 1 diabetes. However, physiologic insulin replacement remains necessary in patients with type 1 diabetes

Immune response to controlled release of immunomodulating peptides in a murine experimental autoimmune encephalomyelitis (EAE) model

The effects of controlled release on immune response to an immunomodulating peptide were evaluated in a murine experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS). The peptide, Ac-PLP-BPI-NH2-2 (Ac-HSLGKWLGHPDKF-(AcpGAcpGAcp)2-ITDGEATDSG-NH2; Ac = acetyl, Acp = aminocaproic acid) was designed to suppress T-cell activation in response to PLP139–151, an antigenic peptide in MS. Poly-lactide-co-glycolide (PLGA) microparticles containing Ac-PLP-BPI-NH2-2 (8±4 μm, 1.4±0.2% (w/w)) were prepared by a powder-in oil-in water emulsion-solvent evaporation method, sterilized and administered subcutaneously (s.c.) to SJL/J (H-2s) mice in which EAE had been induced by immunization with PLP139–151. Treatment groups received Ac-PLP-BPI-NH2-2: (i) in solution by repeated i.v. or s.c. injection, (ii) in solution co-administered with blank PLGA microparticles, (iii) in solution co-administered with Ac-PLP-BPI-NH2-2 loaded microparticles, and (iv) as Ac-PLP-BPI-NH2-2 loaded microparticles. Administration of Ac-PLP-BPI-NH2-2 as an s.c. solution produced clinical scores and maintenance of body weight comparable to i.v. solution, but with reduced overall survival, presumably due to anaphylaxis. Administration as s.c. microparticles provided a somewhat less effective reduction in symptoms but with no toxicity during treatment. Thus, the results suggest that s.c. administration of Ac-PLP-BPI-NH2-2 microparticles can provide pharmacological efficacy and reduction in dosing frequency without increased toxicity

Recruitment of latent pools of high-avidity CD8+ T cells to the antitumor immune response

A major barrier to successful antitumor vaccination is tolerance of high-avidity T cells specific to tumor antigens. In keeping with this notion, HER-2/neu (neu)-targeted vaccines, which raise strong CD8+ T cell responses to a dominant peptide (RNEU420-429) in WT FVB/N mice and protect them from a neu-expressing tumor challenge, fail to do so in MMTV-neu (neu-N) transgenic mice. However, treatment of neu-N mice with vaccine and cyclophosphamide-containing chemotherapy resulted in tumor protection in a proportion of mice. This effect was specifically abrogated by the transfer of neu-N–derived CD4+CD25+ T cells. RNEU420-429-specific CD8+ T cells were identified only in neu-N mice given vaccine and cyclophosphamide chemotherapy which rejected tumor challenge. Tetramer-binding studies demonstrated that cyclophosphamide pretreatment allowed the activation of high-avidity RNEU420-429-specific CD8+ T cells comparable to those generated from vaccinated FVB/N mice. Cyclophosphamide seemed to inhibit regulatory T (T reg) cells by selectively depleting the cycling population of CD4+CD25+ T cells in neu-N mice. These findings demonstrate that neu-N mice possess latent pools of high-avidity neu-specific CD8+ T cells that can be recruited to produce an effective antitumor response if T reg cells are blocked or removed by using approaches such as administration of cyclophosphamide before vaccination

Enhanced Detection of Expanded Repeat mRNA Foci with Hybridization Chain Reaction

Transcribed nucleotide repeat expansions form detectable RNA foci in patient cells that contribute to disease pathogenesis. The most widely used method for detecting RNA foci, fluorescence in situ hybridization (FISH), is powerful but can suffer from issues related to signal above background. Here we developed a repeat-specific form of hybridization chain reaction (R-HCR) as an alternative method for detection of repeat RNA foci in two neurodegenerative disorders: C9orf72 associated ALS and frontotemporal dementia (C9 ALS/FTD) and Fragile X-associated tremor/ataxia syndrome. R-HCR to both G4C2 and CGG repeats exhibited comparable specificity but \u3e 40 × sensitivity compared to FISH, with better detection of both nuclear and cytoplasmic foci in human C9 ALS/FTD fibroblasts, patient iPSC derived neurons, and patient brain samples. Using R-HCR, we observed that integrated stress response (ISR) activation significantly increased the number of endogenous G4C2 repeat RNA foci and triggered their selective nuclear accumulation without evidence of stress granule co-localization in patient fibroblasts and patient derived neurons. These data suggest that R-HCR can be a useful tool for tracking the behavior of repeat expansion mRNA in C9 ALS/FTD and other repeat expansion disorders

South Dakota Fisheries: An Evaluation of a Chemical Immersion Marking Technique for Juvenile Yellow Perch and Application to a Stocking Assessment of Marsh-Reared Yellow Perch into Eastern South Dakota Lakes

Currently, yellow perch Perca flavescens stocking needs in South Dakota are met by intensive trap and transfer of juvenile and adult perch. The success of these stocking efforts is largely undocumented, primarily due to problems in distinguishing yellow perch produced within the recipient water body and stocked perch. We first developed a transfer-tank marking protocol to determine immersion duration and optimal concentration of oxytetracycline (OTC) hydrochloride needed to produce an effective mark. Then we validated the protocol for adult yellow perch and determined the persistence of OTC in edible muscle tissue. Marking results indicated that satisfactory OTC marks may be obtained in juvenile yellow perch using 600- to 700-ppm OTC for an immersion period of 6 to 8 h. OTC marks were evident in juvenile yellow perch otoliths and dorsal spines checked at 3 months post-immersion. Mark quality was observed to be slightly better in juvenile dorsal spines than otoliths. OTC marks in adult yellow perch were detectable at otolith margins at 9 d post-immersion. Adult muscle tissues were analyzed with high pressure liquid chromatography to quantify OTC residues. A nonlinear model (In epi-OTC [~g g-I] = 0.960 - 0.389*In time [h]; r\u27- = 0.99) describing the combined OTC base/epi residue relation to time indicated that no more than 0.5 ~g OTC g-I should be present at 73 h following immersion