Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis

Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art ‘HPV integrated site capture’ (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a ‘looping’ mechanism by which flanking host regions become amplified. Furthermore, using our ‘HPV16-specific Region Capture Hi-C’ technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (<500 kbp) and long-range (>500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a ‘cancer-causing gene’ is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.

HOST GENOME INTERACTIONS IN COVID-19: DIFFICULTIES IN PATIENT MANAGEMENT AND HEALTHCARE POLICY MANAGEMENT

Mankind during current pandemic has displayed the best possible responses utilizing researched knowledge base, cutting edge biotechnology and most importantly the will to take down tis mammoth menace of our times. Though mixed sorrows and failures progress towards the “war on COVID-19” without doubt outshined against the challenger from the development of timely diagnostics and prognostics to novel therapeutics and vaccinations. The more we explore the delicate & detailed intricacies surrounding the ongoing pandemic, there remains questions still to be answered. Rather, a reply most of the time in itself opens up newer Pandora boxes and it seems like an ongoing unlimited brawl with few troughs in between. While targeting statistical exactness among Homo Sapien’s response to COVID-19 infection, we remain less educated to decide for nature's defined hostgenome variability about disease pathogenesis. While we all humans are the same genetically, but then weare not that same again genetically.

Three-Dimensional Genome Interactions Identify Potential Adipocyte Metabolism-Associated Gene STON1 and Immune-Correlated Gene FSHR at the rs13405728 Locus in Polycystic Ovary Syndrome

Backgroundrs13405728 was identified as one of the most prevalent susceptibility loci for polycystic ovary syndrome (PCOS) in Han Chinese and Caucasian women. However, the target genes and potential mechanisms of the rs13405728 locus remain to be determined.MethodsThree-dimensional (3D) genome interactions from the ovary tissue were characterized via high-through chromosome conformation capture (Hi-C) and Capture Hi-C technologies to identify putative targets at the rs13405728 locus. Combined analyses of eQTL, RNA-Seq, DNase-Seq, ChIP-Seq, and sing-cell sequencing were performed to explore the molecular roles of these target genes in PCOS. PCOS-like mice were applied to verify the expression patterns.ResultsGenerally, STON1 and FSHR were identified as potential targets of the rs13405728 locus in 3D genomic interactions with epigenomic regulatory peaks, with STON1 (P=0.0423) and FSHR (P=0.0013) being highly expressed in PCOS patients. STON1 co-expressed genes were associated with metabolic processes (P=0.0008) in adipocytes (P=0.0001), which was validated in the fat tissue (P&lt;0.0001) and ovary (P=0.0035) from fat-diet mice. The immune system process (GO:0002376) was enriched in FSHR co-expressed genes (P=0.0002) and PCOS patients (P=0.0002), with CD4 high expression in PCOS patients (P=0.0316) and PCOS-like models (P=0.0079). Meanwhile, FSHR expression was positively correlated with CD4 expression in PCOS patients (P=0.0252) and PCOS-like models (P=0.0178). Furthermore, androgen receptor (AR) was identified as the common transcription factor for STON1 and FSHR and positively correlated with the expression of STON1 (P=0.039) and FSHR (P=4e-06) in ovary tissues and PCOS-like mice.ConclusionOverall, we identified STON1 and FSHR as potential targets for the rs13405728 locus and their roles in the processes of adipocyte metabolism and CD4 immune expression in PCOS, which provides 3D genomic insight into the pathogenesis of PCOS.

Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells

Chromatin-associated RNA (caRNA) is a vital component of the interphase nucleus; yet its distribution and role in the 3D genome organization remain poorly understood. Here, we map caRNA's spatial distribution on the 3D genome in human embryonic stem cells, fibroblasts, and myelogenous leukemia cells. We find that the relative abundance of trans-acting caRNA on DNA reflects the 3D compartmentalization, and the caRNA's sequence is predictive of its spatial localization. We observe localized caRNA-genome interactions that span several hundred kilobases to several megabases. These caRNA domains correlate with chromatin loops and enhancer-promoter interactions. Global reduction of caRNA abundance increases the number of chromatin loops and strengths, which could be reversed by suppression of caRNA's electrostatic interactions. These results indicate that caRNA regulates chromatin looping, at least in part through RNA's electrostatic interactions.

Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale

The structural organization of the genome plays an important role in multiple aspects of genome function. Understanding how genomic sequence influences 3D organization can help elucidate their roles in various processes in healthy and disease states. However, the sequence determinants of genome structure across multiple spatial scales are still not well understood. To learn the complex sequence dependencies of multiscale genome architecture, here we developed a sequence-based deep learning approach, Orca, that predicts genome 3D architecture from kilobase to whole-chromosome scale, covering structures including chromatin compartments and topologically associating domains. Orca also makes both intrachromosomal and interchromosomal predictions and captures the sequence dependencies of diverse types of interactions, from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions. Orca enables the interpretation of the effects of any structural variant at any size on multiscale genome organization and provides an in silico model to help study the sequence-dependent mechanistic basis of genome architecture. We show that the models accurately recapitulate effects of experimentally studied structural variants at varying sizes (300bp-80Mb) using only sequence. Furthermore, these sequence models enable in silico virtual screen assays to probe the sequence-basis of genome 3D organization at different scales. At the submegabase scale, the models predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, based on virtual screens of sequence activities, we propose a new model for the sequence basis of chromatin compartments: sequences at active transcription start sites are primarily responsible for establishing the expression-active compartment A, while the inactive compartment B typically requires extended stretches of AT-rich sequences (at least 6-12kb) and can form 'passively' without depending on any particular sequence pattern. Orca thus effectively provides an 'in silico genome observatory' to predict variant effects on genome structure and probe the sequence-based mechanisms of genome organization.

Distortion Discovery: A Framework to Model, Spot and Explain Tumor Heterogeneity and Mitigate its Negative Impact on Cancer Risk Assessment

ABSTRACTIn a complex system of inter-genome interactions, false negatives remain an overwhelming problem when using omics data for disease risk prediction. This is especially clear when dealing with complex diseases like cancer in which the infiltration of stromal and immune cells into the tumor tissue can affect the degree of its tumor purity and hence its cancer signal. Previous work was done to estimate the degree of cancer purity in a tissue. In this work, we introduce a data and biomarker selection independent, information theoretic, approach to tackle this problem. We model distortion as a source of false negatives and introduce a mechanism to detect and remove its impact on the accuracy of disease risk prediction.

Genome-wide analysis of focal DNA hypermethylation in IDH-mutant AML samples

Altered DNA methylation is a common feature of acute myeloid leukemia (AML) and is thought to play a significant role in disease pathogenesis. Gain of function mutations in IDH1 or IDH2 result in widespread but highly focal regions of hypermethylation across the genome that occurs due to the production of 2-hydroxyglutarate that inhibits TET-mediated demethylation. We used whole-genome bisulfite sequencing to identify canonical regions of DNA hypermethylation that are associated specifically with IDH1 and IDH2 mutations in primary AML samples. Consistent with previous reports, IDH mutant (IDHmut) AMLs were the most hypermethylated among all mutationally-defined AML categories analyzed. We observed notable differences in the degree of hypermethylation associated with IDH mutation type, with IDH1mut AMLs having more profound hypermethylation at specific regions than IDH2mut samples. AMLs with biallelic inactivating mutations in TET2 displayed more modest DNA methylation changes compared to normal hematopoietic stem/progenitor cells, but methylation in these samples was increased in the IDHmut-specific regions, providing further support that these mutations act on the same TET-mediated demethylation pathway. Focal hypermethylated regions in IDHmut AML samples tended to occur in regions with low steady state methylation levels in normal stem/progenitor cells, which implies that both DNA methylation and demethylation pathways are active at these loci. Indeed, analysis of AML samples containing mutations in both IDH1 or IDH2 and DNMT3AR882 were less hypermethylated, providing evidence that focal IDHmut-associated hypermethylation is mediated by DNMT3A. IDHmut-specific regions of hypermethylation were largely distinct from CpG island hypermethylation, and showed a significant enrichment for putative enhancers. Analysis of three-dimensional genome interactions from primary hematopoietic cells showed that differentially methylated enhancers formed direct interactions with highly expressed genes, including MYC and ETV6. Taken together, these results suggest that focal hypermethylation in IDH-mutant AML cells occurs by disrupting the balance of DNA methylation and demethylation, which is highly active in genomic regions involved in gene regulation.

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture.

Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model

During the development of mouse embryonic stem cells (ESC) to neuronal committed cells (NCC), coordinated changes in the expression of 2851 genes take place, mediated by the nuclear form of FGFR1. In this paper, widespread differences are demonstrated in the ESC and NCC inter- and intra-chromosomal interactions, chromatin looping, the formation of CTCF- and nFGFR1-linked Topologically Associating Domains (TADs) on a genome-wide scale and in exemplary HoxA-D loci. The analysis centered on HoxA cluster shows that blocking FGFR1 disrupts the loop formation. FGFR1 binding and genome locales are predictive of the genome interactions; likewise, chromatin interactions along with nFGFR1 binding are predictive of the genome function and correlate with genome regulatory attributes and gene expression. This study advances a topologically integrated genome archipelago model that undergoes structural transformations through the formation of nFGFR1-associated TADs. The makeover of the TAD islands serves to recruit distinct ontogenic programs during the development of the ESC to NCC.