Aberrant survival of uterine natural killer subsets in uterus transplant recipients

Uterine natural killer cells (uNKs) are critical mediators of pregnancy success, but how aberrancies in uNK survival or differentiation underpin pregnancy complications is unknown. To improve our understanding of normal and abnormal uNK biology, we studied 1) uNKs in uterus transplant (UTx) recipients at high risk for pregnancy complications and 2) uNK survival after exposure to pharmacologic immunosuppression in vitro. To address the first question, we analyzed uNKs isolated from endometrial biopsies of healthy controls (n=3) or UTx recipients (n=5) using scRNA-seq. In healthy controls, CD103-expressing uNK3 cells were the dominant uNK subset (30% of all uNK cells). In contrast, uNK1 cells were the most frequent (30%) in the majority of UTx recipients. This dominance of uNK1 cells in UTx recipients did not appear to arise only from loss of uNK3 cells, as the uNK1 transcriptional signature was abnormally upregulated in immature proliferating uNKs. Next, we used multiparameter flow cytometry to study single-cell suspensions of whole endometrium from deceased organ donors (n=4) that were cultured for one week with or without the calcineurin inhibitor FK506. Although FK506 significantly impaired the survival of CD103+ uNK3 cells in vitro, there was no evidence of uNK1 enhancement. Instead, FK506 appeared to selectively deplete CD39+ cells – a marker currently used to identify human decidual NK1 cells. Altogether, these results demonstrate that the distribution of uNK subsets is often altered in UTx recipients, and that FK506 can impact the survival of specific uNK subsets. Identification of the additional factors which impact uNK differentiation and survival will be necessary to understand the genesis of pregnancy complications.

Supported by NIH/NIAID (R01 AI 145905) University of Pennsylvania Institute for Immunology

Proteogenomic immune signatures delineate the landscape of pediatric acquired demyelinating syndromes

Approximately 20–30% of children presenting with acquired inflammatory demyelinating syndromes (ADS) have multiple sclerosis (MS). Another 30% harbor serum antibodies against myelin oligodendrocyte glycoprotein and are referred to as having MOG-associated disease (MOGAD). While MS and MOGAD can have similar features, differences in response to immune therapies point to distinct underlying immune mechanisms.

To assess potentially distinct immune mechanisms underlying MS and MOGAD, we applied proteogenomics to high quality cryopreserved peripheral blood mononuclear cells collected from patients with ADS prior to institution of immune therapy, as well as from healthy controls. CITE-Seq profiling was applied to a total of 92,716 single cells with equal contribution from 24 children (6 healthy donors; 6 with ADS but neither MS or MOGAD; 6 with MOGAD; and 6 with MS, ascertained with long-term follow-up).

Analysis revealed a pan-ADS enrichment of atypical (CD11c+) B cells compared to healthy controls. Children with MS were distinguished from children with MOGAD by MS-specific enrichments of checkpoint-molecule (TIGIT and CD137)-expressing CD8 memory T cells, STAT4+ Th1 CD4 memory T cells and CD56dim/CD16+ NK cells.

Overall, our study identifies distinct features of circulating cellular immune profiles that may serve to distinguish children with MS and MOGAD, and provides novel insights into early immune mechanisms that may be involved in each of these conditions.

Genetic Analysis for Type 1 Diabetes Genes in Juvenile Dermatomyositis Unveils Genetic Disease Overlap

OBJECTIVES

Juvenile dermatomyositis (JDM) is a serious autoimmune and complex genetic disease. Another autoimmune genetic disease, type 1 diabetes (T1D), has been observed for significantly increased prevalence in families with JDM, while increased JDM risk has also been observed in T1D cases. This study aimed to study whether these two autoimmune diseases, JDM and T1D, share common genetic susceptibility.

METHODS

From 169 JDM families, 121 unrelated cases with European ancestry (EA) were identified by genome-wide genotyping, principal component analysis (PCA), and identical-by-descent (IBD) analysis. T1D genetic risk score (GRS) were calculated in these cases, and were compared with 361 EA T1D cases and 1943 non-diabetes EA controls. 113 cases of the 121 unrelated European cases were sequenced by whole exome sequencing (WES).

RESULTS

We observed increased T1D GRS in JDM cases (P=9.42E-05). Using whole exome sequencing (WES), we uncovered the T1D genes, phospholipase B1 (PLB1), cystic fibrosis transmembrane conductance regulator (CFTR), tyrosine hydroxylase (TH), CD6 molecule (CD6), perforin 1 (PRF1), and dynein axonemal heavy chain 2 (DNAH2), potentially associated with JDM by the burden test of rare functional coding variants.

CONCLUSION

Novel mechanisms of JDM related to these T1D genes are suggested by this study, which may imply novel therapeutic targets for JDM and warrant further study.

Isolation of myeloid cells from mouse brain tumors for single-cell RNA-seq analysis

Current single-cell RNA sequencing (scRNA-seq) protocols are limited by the number of cells that can be simultaneously sequenced, restricting the ability to resolve heterogeneity of rare cell types. We describe here a protocol for rapid isolation of myeloid cells from tumor-harboring mouse cerebellum without cell sorting to minimize cell damage for scRNA-seq. This protocol includes the procedures for further enrichment of myeloid cells using CD11b+ magnetic beads, followed by the generation of scRNA library and sequencing analysis. For complete details on the use and execution of this protocol, please refer to Dang et al. (2021).

Origin of human uterine natural killer cells

Uterine NK cells (uNK) are a distinct immune population which influence pregnancy outcome. While murine studies have suggested that tissue-resident uNKs predominate in virgin endometrium, the origin of uNKs in humans is unknown. To define subsets of uterine NKs in humans and determine their developmental origin, we performed single-cell RNA-sequencing on CD56+ uNKs sorted from endometrial biopsies of 4 healthy controls (HCs) (17,146 cells) and 5 uterus transplant (UTx) recipients (30,351 cells). SNP polymorphisms and HLA alleles were used to identify cells of donor (tissue-resident) or recipient (peripheral) origin in UTx recipients. Developmental trajectories were built with Monocle v.3.0. Ten major clusters were identified in HCs, with 48% of endometrial NK cells (eNKs) occupying 3 clusters (eNK1–3) that shared gene signatures with known human decidual NK cell subsets (dNK1–3). Pseudotime analysis revealed that the eNK1–3 clusters arose from proliferating subsets and were less mature than cytotoxic uNKs expressing ZEB2, TBX21, and FCGR3A (CD16). uNKs from UTx recipients were similarly distributed across the clusters, with a trend towards fewer cells in the FCGR3A-expressing mature subset. Notably, recipient-derived uNKs dominated all uNK subsets within four months post-transplant but became less frequent in UTx recipients >1 year after transplant (95% vs. 72%; early vs. late). The proportion of donor-derived to recipient-derived cells remained constant across subsets in all UTx recipients. In contrast to mouse models, our study suggests that human uNKs derive primarily from blood-borne peripheral immigrants and that environmental factors influence uNK differentiation more than genotype or developmental origin.

Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality

Tumor-associated macrophages (TAMs) play an important role in tumor immunity and comprise of subsets that have distinct phenotype, function, and ontology. Transcriptomic analyses of human medulloblastoma, the most common malignant pediatric brain cancer, showed that medulloblastomas (MBs) with activated sonic hedgehog signaling (SHH-MB) have significantly more TAMs than other MB subtypes. Therefore, we examined MB-associated TAMs by single-cell RNA sequencing of autochthonous murine SHH-MB at steady state and under two distinct treatment modalities: molecular-targeted inhibitor and radiation. Our analyses reveal significant TAM heterogeneity, identify markers of ontologically distinct TAM subsets, and show the impact of brain microenvironment on the differentiation of tumor-infiltrating monocytes. TAM composition undergoes dramatic changes with treatment and differs significantly between molecular-targeted and radiation therapy. We identify an immunosuppressive monocyte-derived TAM subset that emerges with radiation therapy and demonstrate its role in regulating T cell and neutrophil infiltration in MB.

scRNA-Seq Reveals New Enteric Nervous System Roles for GDNF, NRTN, and TBX3

BACKGROUND AND AIMS

Bowel function requires coordinated activity of diverse enteric neuron subtypes. Our aim was to define gene expression in these neuron subtypes to facilitate development of novel therapeutic approaches to treat devastating enteric neuropathies, and to learn more about enteric nervous system function.

METHODS

To identify subtype-specific genes, we performed single-nucleus RNA-seq on adult mouse and human colon myenteric plexus, and single-cell RNA-seq on E17.5 mouse ENS cells from whole bowel. We used immunohistochemistry, select mutant mice, and calcium imaging to validate and extend results.

RESULTS

RNA-seq on 635 adult mouse colon myenteric neurons and 707 E17.5 neurons from whole bowel defined seven adult neuron subtypes, eight E17.5 neuron subtypes and hundreds of differentially expressed genes. Manually dissected human colon myenteric plexus yielded RNA-seq data from 48 neurons, 3798 glia, 5568 smooth muscle, 377 interstitial cells of Cajal, and 2153 macrophages. Immunohistochemistry demonstrated differential expression for BNC2, PBX3, SATB1, RBFOX1, TBX2, and TBX3 in enteric neuron subtypes. Conditional Tbx3 loss reduced NOS1-expressing myenteric neurons. Differential Gfra1 and Gfra2 expression coupled with calcium imaging revealed that GDNF and neurturin acutely and differentially regulate activity of ∼50% of myenteric neurons with distinct effects on smooth muscle contractions.

CONCLUSION

Single cell analyses defined genes differentially expressed in myenteric neuron subtypes and new roles for TBX3, GDNF and NRTN. These data facilitate molecular diagnostic studies and novel therapeutics for bowel motility disorders.

A Transparent Approach to Calculate Detection Rate and Residual Risk for Carrier Screening

Carrier screening involves detection of carrier status for genes associated with recessive conditions. A negative carrier screening test result bears a nonzero residual risk (RR) for the individual to have an affected child. The RR depends on the prevalence of specific conditions and the detection rate (DR) of the test itself. Herein, we provide a detailed approach for calculating DR and RR. DR was calculated on the basis of the sum of disease allele frequencies (DAFs) of pathogenic variants found in published literature. As a proof of concept, DAF data for cystic fibrosis were compared with society guidelines. The DAF data calculated by this method were consistent with the published cystic fibrosis guideline. In addition, we compared DAF for four genes (ABCC8, ASPA, GAA, and MMUT) across three laboratories, and outlined the likely reasons for discrepancies between these laboratories. The utility of carrier screening is to support couples with information while making reproductive choices. Accurate development of DR and RR is therefore critical. The method described herein provides an unbiased and transparent process to collect, calculate, and report these data.

Variants in the Kisspeptin-GnRH Pathway Modulate the Hormonal Profile and Reproductive Outcomes

Kisspeptin has been identified as a key regulatory protein in the release of gonadotropin-releasing hormone (GnRH), which subsequently increases gonadotropin secretion during puberty to establish reproductive function and regulate the hypothalamic-pituitary-gonadal axis. The effects of variants in the KISS1, KISS1R, and GNRHR genes and their possible association with assisted reproduction outcomes remain to be elucidated. In this study, we used next-generation sequencing to investigate the associations of the genetic diversity at the candidate loci for KISS1, KISS1R, and GNRHR with the hormonal profiles and reproductive outcomes in 86 women who underwent in vitro fertilization treatments. Variants in the KISS1 and KISS1R genes were associated with luteinizing hormone (rs35431622:T>C), anti-Mullerian hormone (rs71745629delT), follicle-stimulating hormone (rs73507529:C>A), and estradiol (rs73507527:G>A, rs350130:A>G, and rs73507529:C>A) levels, as well as with reproductive outcomes such as the number of oocytes retrieved (s35431622:T>C), metaphasis II oocytes (rs35431622:T>C), and embryos (rs1132506:G>C). Additionally, variants in the GNRHR UTR3' (rs1038426:C>A, rs12508464:A>C, rs13150734:C>A, rs17635850:A>G, rs35683646:G>A, rs35610027:C>G, rs35845954:T>C, rs17635749:C>T, and rs7666201:C>T) were associated with low prolactin levels. A conjoint analysis of clinical, hormonal, and genetic variables using a generalized linear model identified two variants of the KISS1 gene (rs71745629delT and rs1132506:G>C) that were significantly associated with hormonal variations and reproductive outcomes. The findings suggest that variants in KISS1, KISS1R, and GNRHR genes can modulate hormone levels and reproductive outcomes.

Drug-resistant epilepsy classified by a phenotyping algorithm associates with NTRK2

OBJECTIVE

Up to 40% of patients with epilepsy become drug resistant (DRE). Genetic factors are likely to play a role. While efforts have focused on the transporter and target hypotheses, neither of them fully explains the pan-pharmacoresistance seen in DRE.

MATERIALS AND METHODS

In this study, we developed and used a phenotyping algorithm for the identification of DRE, responders, and epilepsy-free controls that were sequenced using a gene panel developed by the Pharmacogenomics Research Network (PGRN), which includes 82 genes involved in drug response. We tested the transporter hypothesis of DRE, the association between drug resistance and variants in the ATP-binding cassette family of genes previously associated with DRE, and also investigated potential new genetic factors.

RESULTS

In the analysis of DRE vs controls, NTRK2 was significantly associated with DRE (rs76950094; P = 1.19 × 10^-7 and gene-based P-value = 1.67 × 10^-4 ). NTRK2 encodes TrkB, which is involved in the development and maturation of the central nervous system, and increased activation of TrkB signaling is suggested to promote epilepsy.

CONCLUSION

Although the role of NTRK2 in DRE needs to be elucidated, these results support alternative mechanisms underlying DRE, complementary to the existing hypotheses, that should be evaluated.

Abstract 5353: High-throughput automation of the 10x Genomics® Chromium™ workflow for linked-read whole exome sequencing and a targeted lynch syndrome panel

Traditional 2nd generation sequencing strategies have significantly reduced the cost of sequencing the human genome and provide flexibility to query specific gene panels, the whole exome, or the whole genome. However, these methodologies are based on short reads which limit their ability to phase/haplotype over long genomic distances, accurately map reads between highly homologous regions (e.g., genes vs. pseudogenes), and robustly detect particular types of structural variants (e.g., inversions and translocations).

Advances in microfluidics technology and precision reagent delivery allow long-range information to be rescued and preserved through the use of the 10x Genomics Chromium platform. Each input DNA fragment (~40-200kb) is partitioned into a gel-bead in emulsion (GEM), and subsequent biochemistry generates mini-libraries of NGS-ready molecules tagged with a barcode unique for each GEM. Thus, long-range context is achieved by linking short reads sharing the same barcode, and contiguity is established because they were derived from the same input fragment. Importantly, the barcoded mini-libraries are compatible with short-read sequencers and can be implemented as an add-on to existing sequencing infrastructures.

Here we describe and demonstrate how the user-friendly and uniquely-tuned liquid handling capabilities of the PerkinElmer Sciclone® NGSx Workstation interface with the 10x Genomics chip to successfully automate the Chromium Genome workflow. We show the preservation of intact genomic DNA during automated library preparation and demonstrate that these libraries have comparable quality to those generated by manual preparation. Following Chromium partitioning, mini-library generation, and pooling of all the GEM mini-libraries, samples were processed again on the Sciclone using a previously established automated workflow for exome/panel target capture using Agilent SureSelectTM baits. This end-to-end automated workflow was used to generate Linked-Read whole exome data on samples with unresolved structural rearrangements and targeted Linked Reads in a Lynch syndrome gene, PMS2. Linked Reads enable us to 1) fine-map structural rearrangements detected by karyotyping and 2) resolve variants in PMS2 versus those in its homologous pseudogene, PMS2CL, without invoking non-NGS methods such as MLPA or long-range PCR.

The benefits of automation are essential to the scale-up of high-throughput projects by removing manual variability and increasing efficiency. This partnership offers a unique workflow solution that enables exome and panel-based Linked-Read sequencing at scale.

For Research Use Only. Not for use in diagnostic procedures.

Citation Format: Renata Pellegrino, Michael Benway, Paulina Kocjan, Andrew Price, Charlly Kao, Brian A. Gerwe, Adrian Fehr, Fernanda Mafra, James Garifallou, Hakon Hakonarson. High-throughput automation of the 10x Genomics® Chromium™ workflow for linked-read whole exome sequencing and a targeted lynch syndrome panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5353. doi:10.1158/1538-7445.AM2017-5353

Copy number variation analysis reveals additional variants contributing to endometriosis development

PURPOSE

Endometriosis is a gynecological disease influenced by multiple genetic and environmental factors. The aim of the current study was to use SNP-array technology to identify genomic aberrations that may possibly contribute to the development of endometriosis.

METHODS

We performed an SNP-array genotyping of pooled DNA samples from both patients (n = 100) and controls (n = 50). Copy number variation (CNV) calling and association analyses were performed using PennCNV software. MLPA and TaqMan Copy-Number assays were used for validation of CNVs discovered.

RESULTS

We detected 49 CNV loci that were present in patients with endometriosis and absent in the control group. After validation procedures, we confirmed six CNV loci in the subtelomeric regions, including 1p36.33, 16p13.3, 19p13.3, and 20p13, representing gains, while 17q25.3 and 20q13.33 showed losses. Among the intrachromosomal regions, our results revealed duplication at 19q13.1 within the FCGBP gene (p = 0.007).

CONCLUSIONS

We identified CNVs previously associated with endometriosis, together with six suggestive novel loci possibly involved in this disease. The intergenic locus on chromosome 19q13.1 shows strong association with endometriosis and is under further functional investigation.

Association of WNT4 polymorphisms with endometriosis in infertile patients

PURPOSE

Recently, several genome-wide association studies have demonstrated an association between endometriosis and markers located in or near to WNT4 gene. In order to assess the validity of the findings, we conducted a replication case-control study in a Brazilian population.

METHODS

Genetic association study comprising 400 infertile women with endometriosis and 400 fertile women as controls. TaqMan allelic discrimination technique was used to investigate the relationship between endometriosis and four single-nucleotide polymorphisms (rs16826658, rs3820282, rs2235529, and rs7521902) in WNT4 gene. Genotype distribution, allele frequency, and haplotype analysis of the WNT4 polymorphisms were performed. A p value <0.05 was considered significant.

RESULTS

The results revealed a significant association of rs16826658 (p = 7e-04) and rs3820282 (p = 0.048) single-nucleotide polymorphisms (SNPs) on WNT4 gene with endometriosis-related infertility, while rs2235529 and rs7521902 SNPs showed no difference between cases and controls.

CONCLUSIONS

Our results suggested that rs16826658 and rs3820282 polymorphisms on WNT4 gene might be involved in the pathogenesis of endometriosis in the infertile women studied. Analysis of WNT4 genetic variants might help to identify patients at high risk for disease development.

CYP2C19 polymorphism increases the risk of endometriosis

PURPOSE

Estrogen metabolizing gene mutations can be associated with defective hormonal signaling leading to disease processes. Endometriosis is an estrogen dependent that can be influenced by defective signaling in the estrogen pathway.

OBJECTIVES

To evaluate the association of A/G 85952 CYP2C19 and A/G 937 HSD17B1 gene polymorphisms with endometriosis through the investigation of a large Brazilian sample of women with endometriosis and a fertile control group.

METHODS

Five hundred women with endometriosis and 500 women without endometriosis were tested for CYP2C19 and HSD17B1 polymorphisms, by TaqMan Real Time PCR. The results were statistically analyzed by chi-square, logistic regression and tested for Hardy-Weinberg equilibrium.

RESULTS

The comparison of genotype and allelic frequency of CYP2C19 polymorphism (rs11592737) in patients with endometriosis and control group showed a statistically significant difference (p = 0.0203) and for the HSD17B1 polymorphism (rs605059) differences were not significant (p = 0.0687). Comparing the stages I/II and III/IV endometriosis with the control group for the CYP2C19 we observed p = 0.0133 and p = 0.0564, respectively, and for HSD17B1 the values for p = 0.4319 and p = 0.0667.

CONCLUSION

We observed that CYP2C19 polymorphism is associated with endometrisis in Brazilian women and can be considered a potential biomarker of the disease.