Summary Most disease variants lie within noncoding genomic regions, making their functional interpretation challenging. Because chromatin openness strongly influences transcriptional activity, we hypothesized that cell-type-specific open chromatin regions (OCRs) might highlight disease-relevant noncoding sequences. To investigate, we mapped global OCRs in neurons differentiating from hiPSCs, a cellular model for studying neurodevelopmental disorders such as schizophrenia (SZ). We found that the OCRs are highly dynamic and can stratify GWAS-implicated SZ risk variants. Of the more than 3,500 SZ-associated variants analyzed, we prioritized ∼100 putatively functional ones located in neuronal OCRs, including rs1198588, at a leading risk locus flanking MIR137. Excitatory neurons derived from hiPSCs with CRISPR/Cas9-edited rs1198588 or a rare proximally located SZ risk variant showed altered MIR137 expression, dendrite arborization, and synapse maturation. Our study shows that noncoding disease variants in OCRs can affect neurodevelopment, and that analysis of open chromatin regions can help prioritize functionally relevant noncoding variants identified by GWAS.

Schizophrenia (SZ) genome-wide association studies (GWASs) have identified common risk variants in >100 susceptibility loci; however, the contribution of rare variants at these loci remains largely unexplored. One of the strongly associated loci spans MIR137 (miR137) and MIR2682 (miR2682), two microRNA genes important for neuronal function. We sequenced ∼6.9 kb MIR137/MIR2682 and upstream regulatory sequences in 2,610 SZ cases and 2,611 controls of European ancestry. We identified 133 rare variants with minor allele frequency (MAF) <0.5%. The rare variant burden in promoters and enhancers, but not insulators, was associated with SZ (p = 0.021 for MAF < 0.5%, p = 0.003 for MAF < 0.1%). A rare enhancer SNP, 1:g.98515539A>T, presented exclusively in 11 SZ cases (nominal p = 4.8 × 10(-4)). We further identified its risk allele T in 2 of 2,434 additional SZ cases, 11 of 4,339 bipolar (BP) cases, and 3 of 3,572 SZ/BP study controls and 1,688 population controls; yielding combined p values of 0.0007, 0.0013, and 0.0001 for SZ, BP, and SZ/BP, respectively. The risk allele T of 1:g.98515539A>T reduced enhancer activity of its flanking sequence by >50% in human neuroblastoma cells, predicting lower expression of MIR137/MIR2682. Both empirical and computational analyses showed weaker transcription factor (YY1) binding by the risk allele. Chromatin conformation capture (3C) assay further indicated that 1:g.98515539A>T influenced MIR137/MIR2682, but not the nearby DPYD or LOC729987. Our results suggest that rare noncoding risk variants are associated with SZ and BP at MIR137/MIR2682 locus, with risk alleles decreasing MIR137/MIR2682 expression.

Background: Regulation of dopamine D2 receptor (DRD2) is pathophysiologically and pharmacologically important. Results: miR-9 and miR-326 target to the 3Ј-UTR of DRD2, and endogenously inhibit DRD2 expression. A functional single nucleotide polymorphism alters such regulation. Conclusion: DRD2 is post-transcriptionally regulated by miR-326 and miR-9. Significance: The study suggests a pathophysiological and pharmacological role of miR-9 and miR-326 in neuropsychiatric disorders.

Chromatin accessibility to transcription factors (TFs) strongly influences gene transcription and cell differentiation. However, a mechanistic understanding of the transcriptional control during the neuronal differentiation of human induced pluripotent stem cells (hiPSCs), a promising cellular model for mental disorders, remains elusive. Here, we carried out additional analyses on our recently published open chromatin regions (OCRs) profiling at different stages of hiPSC neuronal differentiation. We found that the dynamic changes of OCR during neuronal differentiation highlighted cell stage-specific gene networks, and the chromatin accessibility at the core promoter region of a gene correlates with the corresponding transcript abundance. Within the cell stage-specific OCRs, we identified the binding of cell stage-specific TFs and observed a lag of a neuronal TF binding behind the mRNA expression of the corresponding TF. Interestingly, binding footprints of NEUROD1 and NEUROG2, both of which induce high efficient conversion of hiPSCs to glutamatergic neurons, were among those most enriched in the relatively mature neurons. Furthermore, TF network analysis showed that both NEUROD1 and NEUROG2 were present in the same core TF network specific to more mature neurons, suggesting a pivotal mechanism of epigenetic control of neuronal differentiation and maturation. Our study provides novel insights into the epigenetic control of glutamatergic neurogenesis in the context of TF networks, which may be instrumental to improving hiPSC modeling of neuropsychiatric disorders.

We searched a gene expression dataset comprised of 634 schizophrenia (SZ) cases and 713 controls for expression outliers (i.e., extreme tails of the distribution of transcript expression values) with SZ cases overrepresented compared with controls. These outlier genes were enriched for brain expression and for genes known to be associated with neurodevelopmental disorders. SZ cases showed higher outlier burden (i.e., total outlier events per subject) than controls for genes within copy number variants (CNVs) associated with SZ or neurodevelopmental disorders. Outlier genes were enriched for CNVs and for rare putative regulatory variants, but this only explained a small proportion of the outlier subjects, highlighting the underlying presence of additional genetic and potentially, epigenetic mechanisms.

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Introduction: As T cell receptor (TCR) therapy emerges as a powerful therapy in cancer treatment, the field is still limited by a relatively small number of targets that are expressed widely in tumor cells but not expressed healthy normal tissues. Kita-Kyushu lung cancer antigen 1 (KK-LC-1) is a cancer-testis antigen that is expressed only in the testis of normal adult tissues. KK-LC-1 is widely expressed across a large percentage of solid tumors. Transcriptional profiling reveals expression in triple-negative breast (TNBC, 53% of tumors), non-small cell lung (NSCLC, 40%), gastric (81%), and cervical cancers (40%). T-Cure is developing a TCR targeting KK-LC-1 (820TCR) that is restricted to HLA-A*01, which is expressed in approximately 25-30% of the U.S. population. The 820TCR was identified to be specific for KK-LC-152-60 peptide NTDNNLAVY from a responder cervical carcinoma patient. Methods: KK-LC-1 gene expression was measured by qPCR in donor total RNA. Jurkat cells and PBMCs from 5 healthy donors were transduced with a retroviral construct containing the 820TCR, and transduction efficiency was measured by flow staining of the mouse TCR-B constant region. Cell-free binding assays were performed using A*01 tetramers loaded with KK-LC-152-60 peptide labeled with fluorescent markers assayed by flow. TCR specificity was measured by co-culture of transduced Jurkat and T cells with peptide pulsed APCs and on/off-target tumor cell panels. Off-target reactivity was assayed by co-culture of transduced T cells with a panel of normal primary cells across multiple organ systems. All co-cultures measured cytokine release by ELISA and multi-cytokine Luminex panels. Results: Gene expression analysis of RNA from a panel of normal primary donor tissues shows that KK-LC-1 expression is restricted to testis. Cell lines derived from affected histologies also maintain high KK-LC-1 expression in vitro. 820TCR transduced Jurkat and donor T cells showed over 85% of transduced T cells exhibited A*01-KK-LC-152-60 tetramer binding. 820TCR-transduced donor T cells displayed high specificity in co-culture with a panel of cell lines of mixed A*01 and KK-CL-1 status. Reactivity was observed in all naturally expressing KK-LC-1 lines that are A*01+. Reactivity was observed across a wide range of expression levels, and high expression was not required for tumor reactivity. No reactivity was observed in any non-A*01 HLA type or in A*01+/KK-LC-1- tumors. Reactivity could be induced in these cells by exogenous expression of A*01 in non-A*01/KK-LC1+ cells and KK-LC-1 in A*01/KK-LC-1- cells. Off target analysis revealed no reactivity of 820TCR with any normal primary cells. Conclusion: KK-LC-1 is a promising target for adoptive TCR cell therapy, and the 820TCR targeting KK-LC-1 is a highly potent and specific TCR with no observed off-target effects. A phase I clinical trial with 820TCR is being planned for patients with cervical, NSCLC, TNBC, and gastric cancers. Citation Format: Nicholas S. Davis, Catherine Leites, Helicia Paz, Leslie Ryan, Nathaniel Magilnick, Christian Hinrichs, Gang Zeng, Erika von Euw. KK-LC-1 targeting T cell receptor for adoptive T cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1496.