Insights for disease modeling from single-cell transcriptomics of iPSC-derived Ngn2-induced neurons and astrocytes across differentiation time and co-culture

BACKGROUND

Trans-differentiation of human-induced pluripotent stem cells into neurons via Ngn2-induction (hiPSC-N) has become an efficient system to quickly generate neurons a likely significant advance for disease modeling and in vitro assay development. Recent single-cell interrogation of Ngn2-induced neurons, however, has revealed some similarities to unexpected neuronal lineages. Similarly, a straightforward method to generate hiPSC-derived astrocytes (hiPSC-A) for the study of neuropsychiatric disorders has also been described.

RESULTS

Here, we examine the homogeneity and similarity of hiPSC-N and hiPSC-A to their in vivo counterparts, the impact of different lengths of time post Ngn2 induction on hiPSC-N (15 or 21 days), and the impact of hiPSC-N/hiPSC-A co-culture. Leveraging the wealth of existing public single-cell RNA-seq (scRNA-seq) data in Ngn2-induced neurons and in vivo data from the developing brain, we provide perspectives on the lineage origins and maturation of hiPSC-N and hiPSC-A. While induction protocols in different labs produce consistent cell type profiles, both hiPSC-N and hiPSC-A show significant heterogeneity and similarity to multiple in vivo cell fates, and both more precisely approximate their in vivo counterparts when co-cultured. Gene expression data from the hiPSC-N show enrichment of genes linked to schizophrenia (SZ) and autism spectrum disorders (ASD) as has been previously shown for neural stem cells and neurons. These overrepresentations of disease genes are strongest in our system at early times (day 15) in Ngn2-induction/maturation of neurons, when we also observe the greatest similarity to early in vivo excitatory neurons. We have assembled this new scRNA-seq data along with the public data explored here as an integrated biologist-friendly web-resource for researchers seeking to understand this system more deeply: https://nemoanalytics.org/p?l=DasEtAlNGN2&g=NES .

CONCLUSIONS

While overall we support the use of the investigated cellular models for the study of neuropsychiatric disease, we also identify important limitations. We hope that this work will contribute to understanding and optimizing cellular modeling for complex brain disorders.

Diabetes UK evidence-based nutrition guidelines for the prevention and management of diabetes

A summary of the latest evidence-based nutrition guidelines for the prevention and management of diabetes is presented. These guidelines are based on existing recommendations last published in 2011, and were formulated by an expert panel of specialist dietitians after a literature review of recent evidence. Recommendations have been made in terms of foods rather than nutrients wherever possible. Guidelines for education and care delivery, prevention of Type 2 diabetes, glycaemic control for Type 1 and Type 2 diabetes, cardiovascular disease risk management, management of diabetes-related complications, other considerations including comorbidities, nutrition support, pregnancy and lactation, eating disorders, micronutrients, food supplements, functional foods, commercial diabetic foods and nutritive and non-nutritive sweeteners are included. The sections on pregnancy and prevention of Type 2 diabetes have been enlarged and the weight management section modified to include considerations of remission of Type 2 diabetes. A section evaluating detailed considerations in ethnic minorities has been included as a new topic. The guidelines were graded using adapted 'GRADE' methodology and, where strong evidence was lacking, grading was not allocated. These 2018 guidelines emphasize a flexible, individualized approach to diabetes management and weight loss and highlight the emerging evidence for remission of Type 2 diabetes. The full guideline document is available at www.diabetes.org.uk/nutrition-guidelines.

Changes in Protein C and Free Protein S during Pregnancy and following Hysterectomy

Two longitudinal studies were undertaken to measure the naturally occurring coagulation inhibitors, protein C and protein S, in females who were either pregnant or who were undergoing hysterectomy. Functional and immunological protein C and free protein S were assayed. During pregnancy, protein C levels remained unchanged except for a small increase in protein C antigen at 28-32 weeks gestation. The free protein S fell significantly and progressively during pregnancy, although only in about one-third of patients did the level fall below the normal range. In the hysterectomy study, a significant fall in protein C occurred on days one and three after surgery but had returned to normal by the time of discharge (days 7-10). A small rise in free protein S was observed at time of discharge, but this factor was otherwise unchanged. We conclude that the changes observed may contribute to the hypercoagulable state which is associated with pregnancy or major surgery.

Abstract A071: Identification and characterization of long intergenic non-coding RNAs (lincRNAs) governing T cell development and function

Although a large portion of the human genome is actively transcribed, only a fraction of these RNAs are protein-coding genes. It is now well appreciated that these non-coding transcripts are not only highly diverse in size and structure, but are functional and can exert effects on a vast number of cellular processes. Long intergenic non-coding RNAs (lincRNA) have recently been shown to be key regulators of gene expression during development and oncogenesis. While the growth factors, signaling pathways, and microRNAs that govern lymphoid development and function have been extensively studied, the contribution of these long non-coding RNAs remains poorly characterized. To address this, we performed a genome-wide analysis of lincRNA expression throughout lymphoid and T-lineage development. Bone marrow lymphoid primed multipotent progenitors, DN1-4 and DP thymocytes, as well as mature naïve CD4+ T cells and differentiated helper T cells were sorted and subjected to RNAseq analysis; multiple unique lincRNAs were identified at each stage of development. Transgenic knockout mice were then generated for candidate lincRNAs and analyzed to characterize their function. Through this approach we have identified lincRNAs that regulate both early T lineage and lymphoid commitment as well as mature T cell differentiation and function. These findings offer novel insight into the regulation of lymphoid development and function and expand our understanding of the role non-coding transcripts play in hematopoiesis.

Citation Format: Will Bailis, Christian Harman, Jorge Henao-Mejia, Adam Williams, Loyall Goff, John Rinn, Richard Flavell. Identification and characterization of long intergenic non-coding RNAs (lincRNAs) governing T cell development and function [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A071.

The DPYSL2 gene connects mTOR and schizophrenia

We previously reported a schizophrenia-associated polymorphic CT di-nucleotide repeat (DNR) at the 5'-untranslated repeat (UTR) of DPYSL2, which responds to mammalian target of Rapamycin (mTOR) signaling with allelic differences in reporter assays. Now using microarray analysis, we show that the DNR alleles interact differentially with specific proteins, including the mTOR-related protein HuD/ELAVL4. We confirm the differential binding to HuD and other known mTOR effectors by electrophoretic mobility shift assays. We edit HEK293 cells by CRISPR/Cas9 to carry the schizophrenia risk variant (13DNR) and observe a significant reduction of the corresponding CRMP2 isoform. These edited cells confirm the response to mTOR inhibitors and show a twofold shortening of the cellular projections. Transcriptome analysis of these modified cells by RNA-seq shows changes in 12.7% of expressed transcripts at a false discovery rate of 0.05. These transcripts are enriched in immunity-related genes, overlap significantly with those modified by the schizophrenia-associated gene, ZNF804A, and have a reverse expression signature from that seen with antipsychotic drugs. Our results support the functional importance of the DPYSL2 DNR and a role for mTOR signaling in schizophrenia.

Plasma free fatty acids do not provide the link between obesity and insulin resistance or β-cell dysfunction: results of the Reading, Imperial, Surrey, Cambridge, Kings (RISCK) study

AIMS

To investigate the relationship between adiposity and plasma free fatty acid levels and the influence of total plasma free fatty acid level on insulin sensitivity and β-cell function.

METHODS

An insulin sensitivity index, acute insulin response to glucose and a disposition index, derived from i.v. glucose tolerance minimal model analysis and total fasting plasma free fatty acid levels were available for 533 participants in the Reading, Imperial, Surrey, Cambridge, Kings study. Bivariate correlations were made between insulin sensitivity index, acute insulin response to glucose and disposition index and both adiposity measures (BMI, waist circumference and body fat mass) and total plasma free fatty acid levels. Multivariate linear regression analysis was performed, controlling for age, sex, ethnicity and adiposity.

RESULTS

After adjustment, all adiposity measures were inversely associated with insulin sensitivity index (BMI: β = -0.357; waist circumference: β = -0.380; body fat mass: β = -0.375) and disposition index (BMI: β = -0.215; waist circumference: β = -0.248; body fat mass: β = -0.221) and positively associated with acute insulin response to glucose [BMI: β = 0.200; waist circumference: β = 0.195; body fat mass β = 0.209 (P values <0.001)]. Adiposity explained 13, 4 and 5% of the variation in insulin sensitivity index, acute insulin response to glucose and disposition index, respectively. After adjustment, no adiposity measure was associated with free fatty acid level, but total plasma free fatty acid level was inversely associated with insulin sensitivity index (β = -0.133), acute insulin response to glucose (β = -0.148) and disposition index [β = -0.218 (P values <0.01)]. Plasma free fatty acid concentration accounted for 1.5, 2 and 4% of the variation in insulin sensitivity index, acute insulin response to glucose and disposition index, respectively.

CONCLUSIONS

Plasma free fatty acid levels have a modest negative association with insulin sensitivity, β-cell secretion and disposition index but no association with adiposity measures. It is unlikely that plasma free fatty acids are the primary mediators of obesity-related insulin resistance or β-cell dysfunction.

Quantification of equine sacral and iliac motion during gait: a comparison between motion capture with skin-mounted and bone-fixated sensors

REASONS FOR PERFORMING STUDY

Information regarding movement at the ilium and sacrum in nonlame horses during normal gait may assist in understanding the biomechanics of the equine sacroiliac joint.

OBJECTIVES

To determine the amount and direction of motion at the ilium and sacrum using 3D orientation sensors during walk and trot in sound Thoroughbreds. To compare results from sensors fixed to the skin with results from sensors fixed to bone-implanted pins.

METHODS

Three 3D wireless orientation sensors were mounted to the skin over the tuber sacrale (TS) and sacrum of 6 horses and motion at the ilium and sacrum was recorded for lateral bending (LB) flexion-extension (F-E) and axial rotation (AR) during walk and trot. This process was repeated with the orientation sensors mounted to the same pelvic landmarks via Steinmann pins.

RESULTS

Mean walk values were greater than trot values using pin-mounted sensors for all planes of movement (P < 0.05). Walk had 1.64 ± 0.22° (mean ± s.e.) more LB than trot (pin-mounted) yet 0.68 ± 0.22° less than trot when skin-mounted; 3.45 ± 0.15° more F-E (pin- and skin-mounted), and 4.99 ± 0.4° more AR (pin-mounted), but trot had 3.4 ± 0.40° more AR than walk with skin mounting. Using pinned sensors for trot resulted in less LB (2.47 ± 0.22°), F-E (1.12 ± 0.15°) and AR (10.62 ± 0.40°); and for walk less F-E (1.12 ± 0.15°) and AR (2.15 ± 0.40°) compared to skin-mounted. Poor correlation existed between mean values for skin- and pin-mounted data for walk and trot, for all planes of motion.

CONCLUSIONS

Movements were smaller at trot with bone-fixated sensors compared to walk, suggesting increased muscular control of movement at the trot. The apparent increase in skin motion at the trot and no clear correlation between skin- and bone-mounted sensors indicates inaccuracies when measuring sacral and iliac movement with skin mounting.

Exploratory integration of peanut genetic and physical maps and possible contributions from Arabidopsis

Arachis hypogaea is a widely cultivated crop both as an oilseed and protein source. The genomic analysis of Arachis species hitherto has been limited to the construction of genetic maps; the most comprehensive one contains 370 loci over 2,210 cM in length. However, no attempt has been made to analyze the physical structure of the peanut genome. To investigate the practicality of physical mapping in peanut, we applied a total of 117 oligonucleotide-based probes ("overgos") derived from genetically mapped RFLP probes onto peanut BAC filters containing 182,784 peanut large-insert DNA clones in a multiplex experimental design; 91.5% of the overgos identified at least one BAC clone. In order to gain insights into the potential value of Arabidopsis genome sequence for studies in divergent species with complex genomes such as peanut, we employed 576 Arabidopsis-derived overgos selected on the basis of maximum homology to orthologous sequences in other plant taxa to screen the peanut BAC library. A total of 353 (61.3%) overgos detected at least one peanut BAC clone. This experiment represents the first steps toward the creation of a physical map in peanut and illustrates the potential value of leveraging information from distantly related species such as Arabidopsis for both practical applications such as comparative map-based cloning and shedding light on evolutionary relationships. We also evaluated the possible correlation between functional categories of Arabidopsis overgos and their success rates in hybridization to the peanut BAC library.

Mammalian fertilization, IVF, ICSI: physiological/molecular parameters, clinical application

Fertilization is associated with several phenomena: rearrangement of euplastic cytoskeleton, intra-cellular communication, cellular polarity, and the release of a variety of complex systems. Several criteria are used to score fertilization. On the day after fertilization, oocytes are cleaned of cumulus and examined for presence of 2 pronuclei and any possible cytological anomalies. Function tests to evaluate fertilization include SPA, ZBA, SCSA, AAA acrosome reaction and fluorescent probes. Fertilization failure, silent polyspermy, aster arrest, mitotic arrest, aster growth defect, or immuno-logical mechanisms cause infertility. Sperm-induced oocyte activation may be due to ligand-recep-tor-mediated interaction or a soluble sperm-derived factor that enters the oocyte at the time of fusion. Any abnormalities in transcription, translation, or any other significant molecular process responsible for producing the oocyte-activating ligand/effector molecule during spermatogenesis and/or spermatogenesis will ultimately cause fertilization failure. The centrosome is paternally derived. During the time course of fertilization the sperm centrosome is orchestrating producer mobilization, syngamy and, ultimately, early cleavage. Vesicle-associated membrane protein(VAMP) is typically lost at cell surface during sperm penetration. Understanding cytoskeletal motility during fertilization requires sophisticated digital imaging including conventional epifluorescence microscopy, laser scanning confocal microscopy and time lapse video microscopy. Clinical application of the recent finding is discussed with emphasis on timing of coitus or insemination, to coincide with time of monitored ovulation. Future research directions are outlined.

A model for co-expression pattern analysis of genes implicated in angiogenesis and tumour cell invasion in cervical cancer

To date, numerous genes have been identified which are involved in both tumour neovascularisation (angiogenesis) and tumour cell invasion, and most of them are also expressed to some extent under normal physiological conditions. However, little is known about how these genes co-express in these settings. This study was undertaken to quantitate mRNA levels in normal and malignant cervical tissues of nine selected genes (VEGF(121), VEGF(165), VEGF(189), VEGF-C, eIF-4E, b-FGF, TSP-2, MMP-2 and MMP-9) implicated in the above processes using real-time quantitative RT-PCR. In addition, the Spearman's rank correlation was used to determine their co-expression patterns. The transcript levels for the different VEGF-A splice variants (VEGF(121), VEGF(165), VEGF(189)) were at least 10-fold higher in the cancer cases, with the highest levels in the primary tumours demonstrating lympho-vascular space involvement. The lymphangiogenic factor VEGF-C and MMP-9 were upregulated 130- and 80-fold respectively in cervical cancers. The highest levels of VEGF-C mRNA were found in the lymph-node positive group. The transcript levels for b-FGF were similar in normal cervical tissue and early-stage cervical cancer, however, higher levels were found in the cervical cancers with advanced stage disease. Comparing gene transcript levels between recurrent and non-recurrent cervical cancer patients revealed significant differences (P=0.038) in transcript levels for the angiogenesis inhibitor TSP-2, with the highest levels in non-recurrent cases. Co-expression pattern analysis in normal cervical tissue revealed highly significant co-expressions (P<0.0001) between TSP-2 and most other genes analysed (VEGF(121), VEGF(165), VEGF-C, b-FGF and MMP-2). In cervical cancer, TSP-2 appears only to be highly co-expressed with MMP-2 (P<0.0001). In contrast to normal cervical tissue, we found a highly significant co-expression (P<0.0001) between MMP-9 and VEGF(189) in cervical cancer. The combined application of real-time quantitative RT-PCR and Spearman's rank correlation identifies gene transcripts which are simultaneously co-expressed. Our results revealed a significant co-expression between the angiogenesis inhibitor TSP-2 and most other genes analysed in normal cervical tissue. In cervical cancer, we found a strong upregulation of VEGF-C and MMP-9 mRNA, with a highly significant co-expression between MMP-9 and VEGF(189).

Localisation of a novel region of recurrent amplification in follicular lymphoma to an approximately 6.8 Mb region of 13q32-33

Follicular lymphoma (FL) is characterised by the presence of the t(14;18)(q32;q21) and represents approximately 25% of new cases of non-Hodgkin's lymphoma. While the t(14;18) is a well-documented rearrangement, the role of secondary cytogenetic abnormalities in the development and progression of these tumours remains unclear. Comparative genomic hybridisation was used to characterise changes in DNA copy number in tumour DNA from patients with this malignancy. The mean numbers of deletion and amplification events found in each of the 45 samples studied were 1.8 and 2.3, respectively. Regions of recurrent (>10% tumour samples) gain involved chromosomes 2p13-16 (16%), 7 (20%), 12 (16%), 13q21-33 (18%), 18 (27%), and X (36%) and frequent losses localised to 6q (29%) and 17p (20%). Amplification of chromosome 13 represents a novel finding in FL. The minimal amplified region was refined to a 6.8-Mb interval of 13q32-33 between the BAC clones 88K16 and 44H20 by fluorescence in situ hybridisation studies using metaphase chromosomes derived from tumour material. There are a number of reports in the literature suggesting that amplification of chromosome 13 also occurs in other human cancers. The location of the putative oncogene on 13q described here in follicular and transformed lymphoma may also be important in the evolution of many other malignancies.

Recent advances in andrology research: physiopathology and clinical application to fertility and infertility

Sperm maturation depends on androgen and is mediated by several unidentified epididymal factors: glycoproteins and metabolites affecting acrosomal stability and fertilizing potential of capacitated sperm. Several genes encoding human epididymis-specific proteins have been described. One of the cloned epididymal cDNA encodes a polypeptide designated as HE4 with an estimated molecular mass of 10,000. Leydig cells are rich in lipid droplets and display epithelioid features. These cells have a cord-like arrangement; the cords are formed by one or two closely apposed cells. In between these cells, labyrinthine or canalicular-like spaces are opened in wide perivascular spaces that improve cell secretion of hormones and facilitate their transport into the blood, as well as the traffic of fluids and metabolites. Coagulation and liquefaction in human semen plays an important role in the capacitation of semen. The liquefaction of semen is retarded by the powerful synthetic inhibitors of 6-amidino-2-naphtyl-p-guanidinobenzoate dimethansulfonate.

Development of bovine and porcine embryonic teratomas in athymic mice

Inner cell masses (ICM) and embryonic discs from bovine and porcine blastocysts of various ages were transplanted under the kidney capsule of athymic (nude) mice to evaluate growth of teratocarcinomas containing both differentiated tissues and undifferentiated stem cells. Inner cell masses were isolated immunosurgically from Day 8, Day 9 and Day 10 porcine blastocysts and from Day 8, Day 10 and Day 12 bovine blastocysts. Embryonic discs were mechanically dissected from Day 11 and Day 12 porcine embryos and from Day 14 bovine embryos. Day 6 egg cylinders were dissected from BALB/C embryos and from hybrid embryos of a cross between BALB/C and an outbred strain of mouse. Two to four ICM, embryonic discs or egg cylinders were transplanted under the kidney capsule of each athymic host. After 8 weeks, graft hosts were killed and their tumors removed, fixed and prepared for histological and immunohistochemical examination. Embryonic teratomas developed at high frequency from murine egg cylinders and from Day 11 and Day 12 porcine and Day 14 bovine embryos. Tumors were observed only infrequently from younger bovine and porcine blastocysts. Murine embryonic tumors were composed of numerous differentiated cell types of ectodermal, mesodermal and endodermal origins, but representation of the three embryonic germ layers was somewhat more restricted in bovine and porcine embryonic tumors. No undifferentiated stem cells were detected in tumors of any of the three species. These results demonstrate that teratomas will develop from bovine and porcine embryos when grafted to an immunocompromised host, but the presence of undifferentiated teratocarcinoma stem cells from these species has yet to be achieved.

CD45 tyrosine phosphatase-activated p59fyn couples the T cell antigen receptor to pathways of diacylglycerol production, protein kinase C activation and calcium influx

The role of the CD45 phosphotyrosine phosphatase in coupling the T cell antigen receptor complex (TCR) to intracellular signals was investigated. CD45- HPB-ALL T cells were transfected with cDNA encoding the CD45RA+B+C- isoform. The tyrosine kinase activity of p59fyn was found to be 65% less in CD45- cells than in CD45+ cells, whereas p56lck kinase activity was comparable in both sub-clones. In CD45- cells the TCR was uncoupled from protein tyrosine phosphorylation, phospholipase C gamma 1 regulation, inositol phosphate production, calcium signals, diacylglycerol production and protein kinase C activation. Restoration of TCR coupling to all these pathways correlated with the increased p59fyn activity observed in CD45-transfected cells. Co-aggregation of CD4- or CD8-p56lck kinase with the TCR in CD45- cells restored TCR-induced protein tyrosine phosphorylation, phospholipase C gamma 1 regulation and calcium signals. Receptor-mediated calcium signals were largely due (60-90%) to Ca2+ influx, and only a minor component (10-40%) was caused by Ca2+ release from intracellular stores. Maximal CD3-mediated Ca2+ influx occurred at CD3 mAb concentrations at which inositol phosphate production was non-detectable. These results indicate that CD45-regulated p59fyn plays a critical role in coupling the TCR to specific intracellular signalling pathways and that CD4- or CD8-p56lck can only restore signal transduction coupling in CD45- cells when brought into close association with the TCR.

Unusual myeloid leukaemia in patient with Hodgkin's disease

An unusual case of leukaemia in a patient with Hodgkin's disease is described. The leukaemic blast cell population was typified by the presence of a substantial proportion of binucleate and multinucleate cells, many of which had the morphological features of Sternberg-Reed cells. The circulating and bone marrow blast cells were shown by immunophenotyping to be of myeloid origin.