Integrated single-cell RNA sequencing technologies reveal a high-resolution immune landscape of colorectal primary tumors and liver metastasis, identifying major immune cell types and distinct cell functional states of T and B cells as well as predictions of complex cell-cell interactions.

Parkinson's disease (PD) is the second most common neurodegenerative disease, and mild cognitive impairment (MCI) is a well-established risk factor for the development of dementia in PD. A growing body of evidence suggests that low expression of glucocerebrosidase (GBA) promotes the transmission of α-synuclein (α-Syn) interpolymers and the progression of PD. However, how GBA mutations affect the pathogenesis of PD via abnormal aggregation of α-Syn is unclear, and no clinically valid PD-MCI genetic markers have been identified. Here, we first located a GBA eQTL, rs12411216, by analysing DHS, eQTL SNP, and transcription factor binding site data using the UCSC database. Subsequently, we found that rs12411216 was significantly associated with PD-MCI (P < 0.05) in 306 PD patients by genotyping. In exploring the relationship between rs12411216 and GBA expression, the SNP was found to be associated with GBA expression in 50 PD patients through qPCR verification. In a further CRISPR/Cas9-mediated genome editing module, the SNP was identified to cause a decrease in GBA expression, weaken enzymatic activity and enhance the abnormal aggregation of α-Syn in SH-SY5Y cells. Additionally, using an electrophoretic mobility shift assay, we confirmed that the binding efficiency of transcription factor E2F4 was affected by the rs12411216 SNP. In conclusion, our results showed that rs12411216 regulated GBA expression, supporting its potential role as a PD-MCI genetic biomarker and highlighting novel mechanisms underlying Parkinson's disease.

Viral selection pressure has acted on restriction factors that play an important role in the innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To improve our understanding of the molecular evolution mechanism of antiviral differences between species, we leveraged 14 130 DHSs derived from 145 cell types to characterize the regulatory landscape of the TRIM region. Subsequently, we compared the alignments of the DHSs across six primates and found 375 DHSs that are conserved in non-human primates but exhibit significantly accelerated rates of evolution in the human lineage (haDHSs). Furthermore, we discovered 31 human-specific potential transcription factor motifs within haDHSs, including the KROX and SP1, that both interact with HIV-1. Importantly, the corresponding haDHS was correlated with antiviral factor TRIM23. Thus, our results suggested that some viruses may contribute, through regulatory DNA differences, to organismal evolution by mediating TRIM gene expression to escape immune surveillance.

18It has been challenged to determine the disease-causing variant(s) for most major 19 histocompatibility complex (MHC) associated diseases. However, it is becoming increasingly 20 clear that regulatory variation is pervasive and a fundamentally important mechanism 21 governing phenotypic diversity and disease susceptibility. We leveraged DNase I data from 22 136 human cells to characterize the regulatory landscape of the MHC region, including 4867 23 DNase I hypersensitive sites (DHSs). We identified thousands of regulatory elements that 24 have been gained or lost in the human or chimpanzee genomes since their evolutionary 25 divergence. We compared alignments of the DHS across six primates and found 149 DHSs 26 with convincing evidence of positive and/or purifying selection. Of these DHSs, compared to 27 neutral sequences, 24 evolved rapidly in the human lineage. We identified 15 instances of 28 transcription factor binding motif gains, such as USF, MYC, MAX, MAFK, STAT1 and PBX3 29 etc., and observed 16 GWAS SNPs associated with diseases within these 24 DHSs using 30 FIMO and UCSC ChIP-seq data. Combining eQTL and Hi-C data, our result indicated that 31 there were five SNPs located in human gains motifs affecting on the corresponding genes 32 expression, two of which closely matched DHS target genes. In addition, a significant SNP 33 rs7756521 at genome-wide significant level likely affects DDR expression and represents a 34 causal genetic variant for HIV-1 control. These results indicated that species-specific motif 35 gains or losses of rapidly evolving DHSs in the primate genomes might play a role during 36 adaptation evolution and provided some new evidences for a potentially causal role for these 37 GWAS SNPs. 38