Need For Cell Culture Research Articles

7007 Analytical & Clinical Performance of a Novel Sensitive Rapid Bioassay for Thyrotropin Receptor Antibodies

Abstract Disclosure: P.D. Olivo: Consulting Fee; Self; QuidelOrtho, CA USA. H. Kim: Employee; Self; QuidelOrtho. L. Miao: Employee; Self; QuidelOrtho. J. Houtz: Employee; Self; QuidelOrtho. M. Luffy: None. J. Wolf: None. G.J. Kahaly: Grant Recipient; Self; QuidelOrtho, USA. Background: The role of stimulatory anti-TSH-R-Ab in the pathogenesis of autoimmune hyperthyroidism is well established. A novel and rapid cell-based bioassay, referred to as Turbo TSITM, for measurement of thyroid-stimulating autoantibodies (TSAb) was recently developed. An assessment of the analytical & clinical performance of this bioassay is described herein. Methods: Turbo TSI greatly reduces the complexity and time required to measure TSAb. It avoids the need for cell culture, has no wash or lysis steps, and has a total turn-around-time of less than 90 minutes. Thawed cells from Turbo TSI kits were treated with different concentrations of a World Health Organization (WHO) international standard (IS) TSI or TSAb-positive serum. TSAb was measured as a function of luciferase activity measured as relative light units (RLU) and converted into international units per liter (IU/L). Two users at two sites performed analytical performance studies on numerous samples, over multiple days. Results: The limit of blank, limit of detection and limit of quantitation were determined to be 0.007 IU/L, 0.014 IU/L, and 0.021 IU/L, respectively. Receiver operator characteristics (ROC) analysis determined the cut-off to be 0.0241 IU/L with an area under the curve of 0.984. The linear range was shown to be from 0.015 to 11.958 IU/L. The intra-laboratory precision was ≤15 percent CV. The overall reproducibility of the assay was ≤20 percent CV for five concentrations (0.06 to 5.16 IU/L). Interference and cross reactivity studies with a variety of substances showed that the assay was robust. Turbo TSI demonstrated 95.2% (95% CI 83.3-98.1) sensitivity and 94.8% (95% CI 90.9-97.1) specificity when compared with an FDA-cleared bioassay (Thyretain® TSI) using serum from 295 patients with autoimmune thyroid disease (AITD). When testing 172 unselected, consecutive TSAb+ AITD patients, a US based, prospective, multicenter, blinded study showed a 98% concordance between Turbo TSI and Thyretain® TSI. When comparing Turbo TSI, Thyretain TSI and a TSH-R-Ab binding immunoassay (Cobas) in 670 unselected, consecutive, treated and untreated AITD subjects, sensitivity was 83%, 79% and 68%, respectively (Turbo vs. Cobas, P<0.001). Furthermore, testing 84 patients with naïve, untreated Graves’ hyperthyroidism, detection of TSH-R-Ab was 100%, 98% and 92%, respectively (Turbo TSI vs binding assay, P<0.01). Finally, 95% vs. 73% of 332 patients with Graves’ orbitopathy were TSH-R-Ab+ with Turbo TSI vs. binding assay (P<0.001). Conclusions: The Turbo TSI bioassay exhibits excellent analytical & clinical performance, a high level of reproducibility, and compares well with the FDA-cleared Thyretain® TSI. Presentation: 6/1/2024

Comparison of Wound Healing Effect of Skin Micrograft Impregnated into Two Kinds of Artificial Dermis in a Murine Wound Model.

Skin MG was prepared from the skin of C57BL/6JJcl mice using Rigeneracons and administered onto Pelnac Gplus and Integra sheets. The amount of MG suspension impregnated in Pelnac Gplus and Integra was evaluated. Pelnac Gplus and Integra sheets combined with MG were applied to murine defects, and wound area, neoepithelium length, granulation tissue formation, and newly formed capillaries were compared with the control groups on days 7 and 14. The weight percentage of the MG absorbed by Pelnac Gplus and Integra was 88.8% ± 3.5% and 28.2% ± 7.0%, respectively (P < 0.05). In the in vivo experiment, the area of newly formed granulation tissue and both the number and area of newly formed capillaries in the PelnacG + MG group were significantly larger than those in the control group at 14 days after implantation (P < 0.05). Skin MG was successfully impregnated into Pelnac Gplus by simple administration but not into Integra. Administration of skin MG into the Pelnac Gplus promoted granulation formation and angiogenesis. Pelnac Gplus was more suitable than Integra in the combination therapy.

Diagnostic Utility of a New Assay for Thyroid Stimulating Immunoglobulins in Graves' Disease and Thyroid Eye Disease.

Background: The syndrome of thyrotoxicosis typically relies on radioactive iodine scans for establishing its etiology. Alternatively, the determination of thyrotropin (TSH) receptor antibodies (TRAbs) helps to distinguish Graves' disease (GD) from thyrotoxic thyroiditis. Current assays are impacted by limitations in sensitivity and/or turnaround time. Therefore, we decided to test a new assay for the detection of TSH receptor stimulating antibodies (TSAbs) and compare it with the clinically available assays. Methods: We enrolled 110 individuals in 5 cohorts: patients with incident or recurrent GD (cohort 1); patients with thyroiditis, painless or subacute (cohort 2); patients with Graves' orbitopathy/thyroid eye disease (TED) in cohort 3; patients with Hashimoto's thyroiditis (cohort 4), and a control group of normal volunteers (cohort 5). The patients were tested with the two clinically available assays: Roche Elecsys anti-TSHR assay (ROC-TBII) from Roche Diagnostics and Thyretain™ TSI Reporter BioAssay Kit (QUI-TSI) from Quidel. In addition, the samples were tested with the aequorin TSAb assay (OTS-TSI) provided by Otsuka Pharmaceutical Co., Ltd. (Tokyo, Japan). The data were collected in a cross-sectional manner before initiation of therapy. Results: We had 36 cases of GD, 17 cases of thyroiditis, 27 cases of TED, 10 cases of Hashimoto's thyroiditis, and 20 normal volunteers. OTS-TSI had 100% sensitivity and specificity in distinguishing GD from thyroiditis, identical with QUI-TSI but superior to ROC-TBII (sensitivity 86% and specificity 94.1%). OTS-TSI had 93% sensitivity and 100% specificity for the diagnosis of TED, compared with normal controls. QUI-TSI and ROC-TBII performed similarly in this analysis, demonstrating 82% sensitivity and 100% specificity. The range of detectable values for OTS-TSI was 20-29,000 mIU/L and the turnaround time was ≤6 hours, without the need for cell culture equipment. Conclusions: OTS-TSI performed excellently, though similarly to QUI-TSI, for the differential diagnosis of GD vs. thyroiditis, while being superior in that respect to ROC-TBII. Furthermore, OTS-TSI has superior sensitivity to QUI-TSI and ROC-TBII for TED diagnosis, while retaining high specificity. It has a short turnaround time and avoids the need for cell culture and sterility. Larger studies in U.S. populations are needed for its validation.

Noncultured Minimally Processed Adipose-Derived Stem Cells Improve Radiated Fracture Healing.

Adipose-derived stem cells mitigate deleterious effects of radiation on bone and enhance radiated fracture healing by replacing damaged cells and stimulating angiogenesis. However, adipose-derived stem cell harvest and delivery techniques must be refined to comply with the US Food and Drug Administration restrictions on implantation of cultured cells into human subjects prior to clinical translation. The purpose of this study is to demonstrate the preservation of efficacy of adipose-derived stem cells to remediate the injurious effects of radiation on fracture healing utilizing a novel harvest and delivery technique that avoids the need for cell culture. Forty-four Lewis rats were divided into 4 groups: fracture control (Fx), radiated fracture control (XFx), radiated fracture treated with cultured adipose-derived stem cells (ASC), and radiated fracture treated with noncultured minimally processed adipose-derived stem cells (MP-ASC). Excluding the Fx group, all rats received a fractionated human-equivalent dose of radiation. All groups underwent mandibular osteotomy with external fixation. Following sacrifice on postoperative day 40, union rate, mineralization, and biomechanical strength were compared between groups at P < 0.05 significance. Compared with Fx controls, the XFx group demonstrated decreased union rate (100% vs 20%), bone volume fraction (P = 0.003), and ultimate load (P < 0.001). Compared with XFx controls, the MP-ASC group tripled the union rate (20% vs 60%) and demonstrated statistically significant increases in both bone volume fraction (P = 0.005) and ultimate load (P = 0.025). Compared with the MP-ASC group, the ASC group showed increased union rate (60% vs 100%) and no significant difference in bone volume fraction (P = 0.936) and ultimate load (P = 0.202). Noncultured minimally processed adipose-derived stem cells demonstrate the capacity to improve irradiated fracture healing without the need for cell proliferation in culture. Further refinement of the cell harvest and delivery techniques demonstrated in this report will enhance the ability of noncultured minimally processed adipose-derived stem cells to improve union rate and bone quality, thereby optimizing clinical translation.

Simple limbal epithelial transplantation: Current status and future perspectives.

Damage to limbal stem cells as a result of injury or disease can lead to limbal stem cell deficiency (LSCD). This disease is characterized by decreased vision that is often painful and may progress to blindness. Clinical features include inflammation, neovascularization, and persistent cornea epithelial defects. Successful strategies for treatment involve transplantation of grafts harvested from the limbus of the alternate healthy eye, called conjunctival‐limbal autograft (CLAU) and transplantation of limbal cell sheets cultured from limbal biopsies, termed cultured limbal epithelial transplantation (CLET). In 2012, Sangwan and colleagues presented simple limbal epithelial transplantation (SLET), a novel transplantation technique that combines the benefits of CLAU and CLET and avoids the challenges associated with both. In SLET a small biopsy from the limbus of the healthy eye is divided and distributed over human amniotic membrane, which is placed on the affected cornea. Outgrowth occurs from each small explant and a complete corneal epithelium is typically formed within 2 weeks. Advantages of SLET include reduced risk of iatrogenic LSCD occurring in the healthy cornea at harvest; direct transfer circumventing the need for cell culture; and the opportunity to perform biopsy harvest and transplantation in one operation. Success so far using SLET is comparable with CLAU and CLET. Of note, 336 of 404 (83%) operations using SLET resulted in restoration of the corneal epithelium, whereas visual acuity improved in 258 of the 373 (69%) reported cases. This review summarizes the results of 31 studies published on SLET since 2012. Progress, advantages, challenges, and suggestions for future studies are presented.

High-Resolution Next-Generation Whole Genome Optical Mapping As a Novel Molecular Diagnostic Tool for Comprehensive Assessment of Structural Chromosomal Variations in Myelodysplastic Syndromes

INTRODUCTION Structural variants (SV) include copy number aberrations (CNA) and balanced chromosomal rearrangements. Knowledge of SVs is important for diagnosis and prognosis of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), and can alter therapy in some cases. However, high-throughput identification for diagnostic use in a CLIA-certified laboratory is limited by the need for a combination of techniques to detect both CNA and balanced rearrangements. Karyotyping evaluates 20 metaphases from dividing cells. Fluorescence in situ hybridization (FISH) targets known SVs. Microarray is less sensitive and cannot detect balanced rearrangements. While exome sequencing has limited ability to detect medium-large SVs and those adjoining repetitive sequences. Next-generation optical mapping (OM) is a novel technique to identify SVs by de novo assembly of extremely long-read fluorescently labeled DNA sequences against a reference followed by serial imaging. We hypothesize that OM could potentially offer a single platform for identification of all SVs. METHODS High molecular weight DNA was isolated from fresh bone marrow mononuclear cells preserved in DMSO. Minimum number of cells required was 1 million. A minimum of 36 ng/dL was required based on initial validation studies using cell lines. Specific sequences across the entire genome were labeled using a direct labelling enzyme (DLE-1). The generated long chromosomal fragments underwent high-throughput high-resolution imaging of long chromosomal fragments resulting in &gt;100X genome coverage on Saphyr system (Bionano Genomics, San Diego). Algorithms to convert images to molecules was followed by de novo assembly of genome maps with reference [hg38]. Chromosomal aberrations were identified by comparing to a reference dataset that includes 200 healthy controls that facilitates detection of all structural abnormalities at a resolution of &gt; 500 bp. Only SVs not identified in the control sample database with recommended variant confidence scores and strong molecule support were considered. Insertions, deletions and duplications larger than 100 kbp were considered. Based on sensitivity studies performed using simulations, the level of detection (LOD) was ~95% for SVs with allele fraction of ~10%. The generated data was compared with results from karyotype, FISH and microarrays (results were blinded during analysis). RESULTS A total of 7 MDS samples with 17 previously known aberrations were selected: 4 with complex karyotype (CK) that included deletions, insertions and translocations [2-way such as t(9;11), 3-way: t(2;20;17)] leading to derivative chromosomes and 3 with normal karyotype (NK). All 7 samples successfully underwent DNA extraction with an average yield of 60 ng/dL. OM identified all SVs detected by karyotype/ array CGH. This included deletions, insertions and translocations. Sixteen of 17 SVs identified by karyotype alone were detected by OM. The only SV missed was der(7)add(7)(p13)add(7)(q32), noted in 3 of 20 (~15% cell fraction) metaphases. With this knowledge, upon re-review, SV was detectable in the raw data at an allele burden of 7.5%, which is below the assay's LOD. For the same reason, this SV was not identified by array CGH (assay detection level ~20%). OM identified multiple additional SVs not detected by conventional techniques. In 4 samples with CK, a total of 6 new SVs were noted. This included del(17p) [25% allele fraction] involving TP53 gene in one patient (pt) [Fig 1A]. Identification of TP53 loss in this MDS pt with concurrent TP53 mutation has important prognostic and therapeutic implications. A novel fusion t(1;12) FGGY-DUSP16 was identified in another pt [Fig 1B,C] along with 2.1 Mb chr(6) deletion and 114 Mb chr(16) duplication. In 3 samples with NK, OM detected additional deletion of chr(19) involving genes: TCF3, GNA11, MAP2K2, SH3GL1, MLLT1 in one pt. No additional SVs were found in remaining 2 NK samples. OM facilitated precise mapping of genomic co-ordinates of SVs, especially with complex rearrangements. The LOD from these samples was estimated at ~10% allele fraction. CONCLUSIONS High concordance between OM and conventional techniques provides proof-of-concept for potential use of OM technology as a single-platform for comprehensive assessment of all SVs (CNAs and balanced rearrangements) in MDS at a resolution comparable to standard-of-care assays without the need for cell culture. Figure 1 Disclosures Sasaki: Otsuka: Honoraria; Pfizer: Consultancy. Kantarjian:Cyclacel: Research Funding; AbbVie: Honoraria, Research Funding; Immunogen: Research Funding; Novartis: Research Funding; Ariad: Research Funding; Actinium: Honoraria, Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Research Funding; Amgen: Honoraria, Research Funding; Astex: Research Funding; Agios: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Jazz Pharma: Research Funding; BMS: Research Funding; Takeda: Honoraria. Bueso-Ramos:Incyte: Consultancy. Garcia-Manero:Amphivena: Consultancy, Research Funding; Helsinn: Research Funding; Novartis: Research Funding; AbbVie: Research Funding; Celgene: Consultancy, Research Funding; Astex: Consultancy, Research Funding; Onconova: Research Funding; H3 Biomedicine: Research Funding; Merck: Research Funding.

Rapid Prenatal Diagnosis of Chromosomal Aneuploidies Using Quantitative Fluorescence Polymerase Chain Reaction (QF-PCR)

Introduction: Prenatal diagnosis plays an important role in determining the health of fetus, which is why rapid diagnostic tests are so important. One of these quick diagnostic tests is quantitative fluorescent-polymerase chain (QF- PCR) technique. This technique employed to detect chromosomal aneuploidies (13, 18, 21, X and Y). In this method, there is no need for cell culturing. QF- PCR is rapid, suitable for automation, low cost and faster turnaround time. Material and Methods: In this study, 260 patients were studied, and analyzed by 26 short tandem repeat (STR) markers for detection of chromosomal abnormalities. The QF-PCR assay was performed by Devyser kit (Sweden). First DNA was extracted, and then PCR was performed, PCR products were run on capillary electrophoresis system, and finally analyzed by the Genemarker Software. Results: The results of QF-PCR were as follows: trisomy 21 (6 cases), 18 (3 cases), triploidy (1 case), klinefelter syndrome (1 case), without suspicion of any mosaicism. Conclusion: Prenatal diagnostic outcomes give early results, thus reducing parental anxiety and increasing clinical management of a high risk pregnancy.

Development of a bacterial-based negative selection system for rapid screening of active single guide RNAs.

To develop an in vitro method for rapid evaluation of the capability of a designed single guide RNAs (sgRNAs) to guide Cas9 nucleases to cleave target loci in mammalian cells. We constructed a Cas9/sgRNA plasmid with two SP6 promoters to simultaneously express Cas9 nuclease and the sgRNA and a negative selection plasmid harbouring a target site of the sgRNA. After co-transforming chemically competent E. coli DH5α cells with the two plasmids, the transformants were plated at a low density on two LB plates: one containing only ampicillin and the other containing both ampicillin and chloramphenicol. The colony-count on the ampicillin+chloramphenicol plate was compared with that on the ampicillin-only plate to calculate the survival percentage. The survival % was negatively correlated with the genome editing efficiency of the sgRNA in mammalian cells evaluated by a T7 endonuclease 1 (T7E1) assay (r ranged from -0.8 to -0.92). This system eliminates the need for cell culture, transfection, FACS sorting, PCR and T7E1 nuclease treatment, and significantly reduces the cost of screening for active sgRNAs, especially in the case of large-scale screening. We have developed a bacterial-based negative selection system for rapid screening of active sgRNAs in mammalian cells at a very low cost.

A Systems Biology Interpretation of Array Comparative Genomic Hybridization (aCGH) Data through Phylogenetics.

Array Comparative Genomic Hybridization (aCGH) is a rapid screening technique to detect gene deletions and duplications, providing an overview of chromosomal aberrations throughout the entire genome of a tumor, without the need for cell culturing. However, the heterogeneity of aCGH data obfuscates existing methods of data analysis. Analysis of aCGH data from a systems biology perspective or in the context of total aberrations is largely absent in the published literature. We present here a novel alternative to the functional analysis of aCGH data using the phylogenetic paradigm that is well-suited to high dimensional datasets of heterogeneous nature, but has not been widely adapted to aCGH data. Maximum parsimony phylogenetic analysis sorts out genetic data through the simplest presentation of the data on a cladogram, a graphical evolutionary tree, thus providing a powerful and efficient method for aCGH data analysis. For example, the cladogram models the multiphasic changes in the cancer genome and identifies shared early mutations in the disease progression, providing a simple yet powerful means of aCGH data interpretation. As such, applying maximum parsimony phylogenetic analysis to aCGH results allows for the differentiation between drivers and passenger genes aberrations in cancer specimens. In addition to offering a novel methodology to analyze aCGH results, we present here a crucial software suite that we wrote to carry out the analysis. In a broader context, we wish to underscore that phylogenetic analysis of aCGH data is a non-parametric method that circumvents the pitfalls and frustrations of standard analytical techniques that rely on parametric statistics. Organizing the data in a cladogram as explained in this research article provides insights into the disease common aberrations, as well as the disease subtypes and their shared aberrations (the synapomorphies) of each subtype. Hence, we report the method and make the software suite publicly and freely available at http://software.phylomcs.com so that researchers can test alternative and innovative approaches to the analysis of aCGH data.

Primary chondrocytes and bone marrow cells on a 3D co-polymer scaffold: 2-year results of a prospective, multicenter, single-arm clinical trial in patients with cartilage defects of the knee

Introduction The potency of the combination of primary chondrocytes with multipotent cells to support cartilage tissue regeneration, without the need for cell culture, was first evidenced in 2001. INSTRUCT (CellCoTec B.V., Netherlands) is a patented technology that combines freshly isolated autologous chondrocytes and mono-nucleated cells from bone marrow with a porous scaffold in a single surgical procedure. Objectives The objective of the INSTRUCT study was to assess the safety and efficacy of a cell mixture of non-expanded chondrocytes and bone marrow cells seeded on a co-polymer scaffold for the treatment of symptomatic cartilage defects of the knee. Methods Forty patients were enrolled at 6 European sites in a prospective, open-label, single-arm clinical trial. Patients were to be aged 18–55 years, with a Modified Outerbridge grade III or IV focal cartilage defect on the femoral condyle. Mal-alignment, ligament laxity and osteoarthritis (KL grade III or IV) were exclusion criteria. Safety and efficacy endpoints (clinical improvement: KOOS, IKDC, Pain VAS and structural repair: MRIs and histology) were evaluated at baseline, 3, 6, 12, 18 and 24 months. A macroscopic evaluation of the repair tissue was performed during the second-look arthroscopy using the ICRS cartilage repair assessment score. Results A total of 40 patients were enrolled and treated. Ninety percent of patients (36/40) completed the 2-year follow-up. Patients were predominantly male patients (72%), the mean age was 35 years, the mean BMI was 26. Lesions were mostly Modified Outerbridge grade IV (70%) lesions of traumatic origin (60%) with a mean size of 2.1 cm 2 . The results showed a clinically and statistically significant ( P P P Conclusions The results from the INSTRUCT study show that the treatment of cartilage lesions with a combination of primary chondrocytes and bone marrow cells results in articular cartilage tissue repair associated with a sustained and significant clinical improvement and a safety profile in line with existing treatment options. This first clinical experience suggests that this single-surgery solution is a viable treatment option for patients with full-thickness cartilage defects of the knee.

Abstract 5440: Novel PD-1 blockade bioassay to assess therapeutic antibodies in PD-1 and PD-L1 immunotherapy programs

Abstract Programmed death receptor-1 (PD-1) and its ligand (PD-L1) are among the few important immunotherapy targets for cancer. Current PD1 assays measure cell proliferation or cytokine production in primary T cells which are tedious, have high assay variation and small assay window. To enable quantitative potency measurement for key anti-PD-1 drugs in the market or in clinical trials such as pembrolizumab and nivolumab, as well as anti-PD-L1 drugs in clinical trials such as MPDL3280A and BMS-936559, here we report the development of a robust bioluminescent cell-based PD1 blockade bioassay. For this, we built a PD-1 effector cells in Jurkat cells which stably express human PD-1 and a NFAT-RE-luciferase reporter, and a PD-L1 positive artificial Antigen Presenting Cells (PD-L1+ aAPC) in CHO-K1 cells which stably express PD-L1 and an engineered TCR activator. Once these two cell types were co-cultivated, transcriptional activation of NFAT pathway in PD-1 effector cells, mediated by binding of TCR complex with TCR activator in PD-L1+ aAPC, is significantly suppressed by PD-1/PD-L1 engagement. This inhibition can then be specifically reversed by co-incubation of PD-1 or PD-L1 blocking antibodies in dose-dependent manner, but not by the antibody for other immune checkpoint receptors such as anti-CTLA4 ipilimumab. We further developed both PD-1 effector cells and PD-L1+ aAPC in Thaw-and-Use format so the cells can be plated for assay without the need of cell culture. The resultant PD-1 assay using Thaw-and-Use cells brings the benefit of convenience, low day-to-day variation, and easy lab-to-lab assay transfer. We demonstrate the assay is able to measure relative potency for antibody biologics, and also can detect potency changes for stressed antibody samples. In summary, the reporter-based PD-1 blockade assay provides a valuable tool for both drug screening and characterization in early drug discovery, and lot release and stability study in drug manufacture for therapeutic antibody drug candidates in PD-1 and PD-L1 immunotherapy programs. Citation Format: Zhi-Jie Jey Cheng, Natasha Karassina, Jamison Grailer, Jim Hartnett, Frank Fan, Mei Cong. Novel PD-1 blockade bioassay to assess therapeutic antibodies in PD-1 and PD-L1 immunotherapy programs. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5440. doi:10.1158/1538-7445.AM2015-5440

Live fibroblast harvest reveals surface marker shift in vitro.

Current methods for the isolation of fibroblasts require extended ex vivo manipulation in cell culture. As a consequence, prior studies investigating fibroblast biology may fail to adequately represent cellular phenotypes in vivo. To overcome this problem, we describe a detailed protocol for the isolation of fibroblasts from the dorsal dermis of adult mice that bypasses the need for cell culture, thereby preserving the physiological, transcriptional, and proteomic profiles of each cell. Using the described protocol we characterized the transcriptional programs and the surface expression of 176 CD markers in cultured versus uncultured fibroblasts. The differential expression patterns we observed highlight the importance of a live harvest for investigations of fibroblast biology.

Protein microarray generation by in situ protein expression from template DNA

Today, whole genomes are analyzed by Next‐Generation Sequencing systems, or displayed by DNA microarray in situ synthesis. However, genomic data are mainly static and do not exactly reveal the complexity of protein interaction networks of any organism or cell. To investigate protein interactions, the generation of protein microarrays, displaying whole proteomes is a prerequisite. But traditional protein microarray generation is time consuming, costly, and is restricted by a wide range of technical difficulties concerning cell culturing, protein purification, and transfer onto microarray. Some of these obstacles can be bypassed by application of cell‐free expression systems, enabling fast in situ synthesis of protein microarrays without need for cell culturing. This review provides a historical timeline of the different methods to generate protein microarrays by cell‐free expression, highlights differences and similarities, and reports the current state of the different approaches.

Development of a one-step approach for the reconstruction of full thickness skin defects using minced split thickness skin grafts and biodegradable synthetic scaffolds as a dermal substitute

IntroductionTissue engineering has progressed in delivering laboratory-expanded keratinocytes to the clinic; however the production of a suitable alternative to a skin graft, containing both epidermis and dermis still remains a challenge. AimTo develop a one-step approach to wound reconstruction using finely minced split thickness skin and a biodegradable synthetic dermal substitute. MethodsThis was explored in vitro using scalpel diced pieces of split thickness human skin combined with synthetic electrospun polylactide (PLA) scaffolds. To aid the spreading of tissue, 1% methylcellulose was used and platelet releasate was examined for its effect on cellular outgrowth from tissue explants. The outcome parameters included the metabolic activity of the migrating cells and their ability to produce collagen. Cell presence and migration on the scaffolds were assessed using fluorescence microscopy and SEM. Cells were identified as keratinocytes by immunostaining for pan-cytokeratin. Collagen deposition was quantified by using Sirius red. ResultsSkin cells migrated along the fibers of the scaffold and formed new collagen. 1% methylcellulose improved the tissue handling properties of the minced skin. Platelet releasate did not stimulate the migration of skin cells along scaffold fibers. Immunohistochemistry and SEM confirmed the presence of both epithelial and stromal cells in the new tissue. ConclusionWe describe the first key steps in the production of a skin substitute to be assembled in theatre eliminating the need for cell culture. Whilst further experiments are needed to develop this technique it can be a useful addition to armamentarium of the reconstructive surgeon.

Rapid prenatal diagnosis of common beta‐thalassemia mutations in Southeast Asia using pyrosequencing

Current methods of prenatal diagnosis to detect beta-thalassemia are Sanger sequencing and reverse dot blot. These methods are time-consuming and can prolong assay turnaround time. We aim to develop a sensitive and rapid method to detect 27 beta-thalassemia mutations using pyrosequencing. Pyrosequencing primer pairs and sequencing primers were designed to detect 27 most common beta-thalassemia mutations found in Singapore. Pyrosequencing was performed on 191 DNA samples with known beta-thalassemia mutations isolated from 143 peripheral blood and 48 prenatal samples (seven chorionic villus biopsies, 26 cultured amniocytes, 15 uncultured amniocytes). All mutations were validated with Sanger sequencing. Pyrosequencing identified 210 alleles with beta-thalassemia mutations and 82 alleles without mutations with 100% sensitivity (lower 95% confidence interval [CI], 97.8%) and 100% specificity (lower 95% CI, 94.4%). All pyrosequences were concordant with Sanger-based sequences. Pyrosequencing was able to detect DNA concentrations as low as 2 ng, obviating the need for cell culture in volume-restricted samples. Sample receipt-to-report assay turnaround times were 16 to 18 h (Sanger sequencing) and 4 to 6 h (pyrosequencing). Pyrosequencing is a rapid and sensitive method to detect common beta-thalassemia mutations without the need for cell culture, thus reducing the assay turnaround time.

Limitations and possibilities of low cell number ChIP-seq

BackgroundChromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers.ResultsWe present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells.ConclusionsThe optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance.

A rapid molecular strategy for early detection and characterization of Vietnamese foot-and-mouth disease virus serotypes O, A, and Asia 1

A one-step RT-PCR method using newly designed primers VN-VP1F/VN-VP1R targeting the full VP1 capsid protein-coding gene, combined with direct sequencing of its PCR product, has been developed successfully for universal detection and characterization of Vietnamese FMDV serotypes O, A, and Asia 1 directly from clinical samples. The one-step RT-PCR amplified 821-bp dsDNA products covering the entire VP1 gene of FMDV serotypes O, A, and Asia 1. The obtained dsDNA products were suitable for direct sequencing, cloning, and other molecular epidemiology studies of Vietnamese FMDV strains, which eliminated the need for cell culture and virus purification. This one-step RT-PCR system was applied to detect and characterize 55 field FMDV strains, including 34 serotype O, 17 serotype A, and 4 serotype Asia 1 isolates collected from endemic outbreaks in Vietnam from 2005 to 2010. Interestingly, the PCR products obtained from the present PCR method could be used as DNA templates for the second PCR typing method using serotypes O, A, and Asia 1-specific primers (Le et al., 2011). The use of the second PCR amplification increased markedly the sensitivity of the test for FMDV detection. The present RT-PCR method promises to be an effective tool for molecular epidemiological studies of FMD in Vietnam.

Whole genome scanning as a cytogenetic tool in hematologic malignancies

AbstractOver the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture. Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects. In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications. Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies. Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases.

Detection and initial characterization of synovial lining fragments in synovial fluid

Free fragments of synovium have occasionally been seen in synovial fluid but have not been studied systematically. We wished to establish a method for the reliable detection of these fragments in joint and bursa effusions and begin to characterize them by histochemical and immunohistochemical methods. Cell smears, wet drop preparations and cytospins were prepared from 39 consecutive joint and bursa effusions. Paraffin cell blocks were prepared from a subset. Analysis encompassed standard and polarized light microscopy, histochemistry, immunohistochemistry and transmission electron microscopy (EM). Synovial biopsy tissue from one different patient was examined for comparison. Tissue fragments were not seen in Wright-stained cell smears and only rarely in wet drop preparations. In contrast, variously sized fragments with the histological appearance of hyperplastic synovial lining were detected in ethanol-fixed, haematoxylin/eosin-stained cytospins from bursitis and all arthropathies studied [17/24 (71%) of non-inflammatory and 12/15 (80%) of inflammatory specimens]. Immunostaining revealed CD68 expression in a subset of cells in a pattern characteristic of hyperplastic synovial lining. Juxtaposed cells with morphological features of macrophage-like and fibroblast-like synoviocytes were seen by EM. Synovial lining fragments can be detected in effusions from diverse arthropathies and bursitis. They maintain important properties of the synovial lining and can be analysed by immunohistochemistry. They may afford the opportunity to study a relatively pure preparation of synovial lining cells without the need for cell culture, and to evaluate their possible role in augmenting or perpetuating synovitis or joint damage.

High-Resolution Identification of Chromosomal Abnormalities Using Oligonucleotide Arrays Containing 116,204 SNPs

Mutation of the human genome ranges from single base-pair changes to whole-chromosome aneuploidy. Karyotyping, fluorescence in situ hybridization, and comparative genome hybridization are currently used to detect chromosome abnormalities of clinical significance. These methods, although powerful, suffer from limitations in speed, ease of use, and resolution, and they do not detect copy-neutral chromosomal aberrations--for example, uniparental disomy (UPD). We have developed a high-throughput approach for assessment of DNA copy-number changes, through use of high-density synthetic oligonucleotide arrays containing 116,204 single-nucleotide polymorphisms, spaced at an average distance of 23.6 kb across the genome. Using this approach, we analyzed samples that failed conventional karyotypic analysis, and we detected amplifications and deletions across a wide range of sizes (1.3-145.9 Mb), identified chromosomes containing anonymous chromatin, and used genotype data to determine the molecular origin of two cases of UPD. Furthermore, our data provided independent confirmation for a case that had been misinterpreted by karyotype analysis. The high resolution of our approach provides more-precise breakpoint mapping, which allows subtle phenotypic heterogeneity to be distinguished at a molecular level. The accurate genotype information provided on these arrays enables the identification of copy-neutral loss-of-heterozygosity events, and the minimal requirement of DNA (250 ng per array) allows rapid analysis of samples without the need for cell culture. This technology overcomes many limitations currently encountered in routine clinical diagnostic laboratories tasked with accurate and rapid diagnosis of chromosomal abnormalities.