Mutations In Non-coding Regions Research Articles

Precise correction of a spectrum of β-thalassemia mutations in coding and non-coding regions by base editors

Precise correction of a spectrum of β-thalassemia mutations in coding and non-coding regions by base editors

Assessing the reliability of point mutation as data augmentation for deep learning with genomic data

BackgroundDeep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation of deep neural networks, however, is their high demand for data during training. To overcome this challenge, other fields, such as computer vision, use various data augmentation techniques to artificially increase the available training data for DNNs. Unfortunately, most data augmentation techniques used in other domains do not transfer well to genomic data.ResultsMost genomic data possesses peculiar properties and data augmentations may significantly alter the intrinsic properties of the data. In this work, we propose a novel data augmentation technique for genomic data inspired by biology: point mutations. By employing point mutations as substitutes for codons, we demonstrate that our newly proposed data augmentation technique enhances the performance of DNNs across various genomic tasks that involve coding regions, such as translation initiation and splice site detection.ConclusionSilent and missense mutations are found to positively influence effectiveness, while nonsense mutations and random mutations in non-coding regions generally lead to degradation. Overall, point mutation-based augmentations in genomic datasets present valuable opportunities for improving the accuracy and reliability of predictive models for DNA sequences.

Al2O3/ZrO2 dual-dielectric Gr/CNT nanoribbon vertical tunnel FET based biosensor for genomic classification and S-protein detection in SARS-CoV-2

The ongoing genetic mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) possesses the capacity to inadvertently lead to an increase in both the rates of transmission and mortality. In this study, we showcase the use of an Al2O3/ZrO2 Dual-Dielectric Gr/CNT Nanoribbon vertical tunnel field-effect transistor biosensor for the purpose of detecting spike proteins of SARS-CoV-2 in clinical samples. The proteins mentioned above are situated within the protein capsids of the virus. The effectiveness of the suggested detector has been assessed through measurements of the alteration in current drain. The present study utilizes the dielectric coefficient analogue of viral proteins as a substitute for biomolecules that exhibit internal hybridization nanogaps. The high sensitivity of the suggested detector, as evaluated on a scale ranging from 0 to 115, suggests its potential as a high-quality sensing instrument. The purpose of this study is to examine the sensitivity of DNA charge density with the aim of identifying any alterations in the virus that may impact its ability to spread and infect humans. The chromosomal composition of SARS-CoV-2 has been determined. The CMC Research Centre, situated in Vellore, Tamil Nadu, India, conducted an examination of SARS-CoV-2 samples. The scientists possess the capability to do genome sequencing on these specimens, so facilitating the examination of mutation patterns and the dispersion of different clades. A total of 250 different mutations were found out of the 600 sequences that were evaluated. The sequencing data consists of a complete collection of 250 distinct variants, including 150 missense mutations, 80 synonymous mutations, 15 mutations in noncoding regions, and 5 deletions. The comprehension of genetic variety is significantly dependent on these mutations. The proposed detector is connected to a variety of previously documented biosensors based on field-effect transistors (FETs), which are employed for the examination of genetic modifications.

Abstract 2850: Noncoding regulatory mutations as driving event for the oncogenic core regulatory circuitries of neuroblastoma

Abstract Background and Aim: Neuroblastoma (NB) is the most aggressive solid tumor of infancy and arises from neural-crest-derived progenitor cells. It is composed by cell types reflecting developmental stages of the adrenergic lineage: mesenchymal (MES) and adrenergic (ADRN) cell types. These cell identities result from the activity of NB specific Core Regulatory Circuitries (CRCs), transcription factor (TF) sets that co-occupy regulatory regions together impacting the expression of their own genes and those of lineage-specific ones governing cell state transitions and cellular identities. Our hypothesis is that noncoding somatic single nucleotide variants (SNVs) located in NB CRCs TF binding sites (TFBSs) underlie NB CRCs activity, affecting cellular differentiation and promoting tumor onset. We aim to investigate such pattern of regulatory elements and identify putative driver SNVs, exploring their role and characterizing their action mechanism. Methods: Transcriptionally active TFBSs (aTFBSs) bound by ADRN CRC TFs (GATA3, HAND2, ISL1, TBX2, MYCN, PHOX2B, ASCL1 and LMO1) were identified integrating 27 ChIP-seq and 11 ATAC-seq experiments in 6 NB ADRN cell lines (SKNBE2C, Kelly, NGP, COGN415, LAN5 and NB1643). In particular, aTFBSs were defined as ChIP-seq peaks overlapping ATAC-seq signals in the same cell line. SNVs from 317 NB whole genomes were mapped on aTFBSs and the enrichment of mutations in core regions respect to flanking ones was tested using Fisher test. Observed mutation rate in aTFBSs was compared with background mutation rate due to local sequence context. SNVs in mutated aTFBSs were selected and their impact on TF binding affinity was evaluated with FABIAN-variant and motifbreakR tools. aTFBSs target-genes were identified through promoter capture HiC (CHiC) in ADRN NB cells (SKNBE2C and SHSY5Y). Results: We found a significant (FDR < 0.05) mutation enrichment in aTFBSs of ISL1, PHOX2B, TBX2, GATA3 and MYCN, suggesting a common somatic mutation burden for a subset of ADRN CRC TFBSs in ADRN NB cells. Starting from 839 SNVs falling in significantly mutated aTFBSs, we selected 269 mutations impacting the binding of ADRN CRC TFs. This mutations subset mapped in aTFBSs interacting with genes that significantly enriched pathways involved in neuronal development and migration (FDR < 0.05), thus suggesting their possible role in affecting cell identity definition. As an example, chr6:137753475:G>T mapped in aTFBSs interacting with the promoter of OLIG3, which takes part in neuronal differentiation. Interestingly, chr6:137753475:G>T was predicted to break the binding to ISL1 (FABIAN score: -0.24), a key regulator of ADRN CRC. Conclusions: These results demonstrate that somatic noncoding SNVs can act synergistically to promote NB onset, affecting CRCs activity and, in turn, the normal cell identity definition. Citation Format: Mario Capasso, Vincenzo Aievola, Vito Alessandro Lasorsa, Annalaura Montella, Ferdinando Bonfiglio, Marianna Avitabile, Teresa Maiorino, Matilde Tirelli, Giuseppe D'Alterio, Matthias Fischer, Frank Westermann, Achille Iolascon. Noncoding regulatory mutations as driving event for the oncogenic core regulatory circuitries of neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2850.

Abstract 7358: Role of noncoding genome architecture in esophageal cancer

Abstract Esophageal Cancer is a deadly disease with a tendency to be diagnosed at the later stages. Considered a rare disease, accounting for 1.1% of all cancers, EC comprises 2.6% of all cancer deaths. The survival rate for all stages is 21.7%. However, the survival rate decreases to 5.6 % for advanced-stage cancers. EC is more common in men and associated with older age and heavy alcohol and tobacco use. In the last 25 years, the death rate of EC has been decreasing slightly from 4.3 to 3.7. The death rates for lung, prostate, and colon cancers have decreased by half in the same time frame. Therefore, novel therapies and biomarkers are urgently needed to accelerate survival and reduce the death rates by at least half for patients with EC.We previously completed exome sequencing in a small sample size and observed that the mutations in the noncoding regions of the EC genome are highly affected. In this study, we perform exome sequencing in 110 paired esophageal tumors and normal tissues using an Agilent SSELXT HS Exon V8+UTR library enrichment kit. Twelve paired EC and normal tissues are sequenced using the PacBio Hifi system.In WES, we detected almost half of the noncoding region mutations in the 3UTR and 2kb downstream regions of the genome, significantly affecting 51 oncogenic or tumor suppressor genes. In addition, the involved genes are over-represented in critical signaling pathways and transcriptional regulation of pluripotent stem cells. The number of changes in the 5UTR and 2kb upstream are similar to the number of variations in the intronic regions. Apoptosis, stress response, and DNA double-strand break repair pathways are affected by 5UTR mutations. Mutations in the intronic regions frequently occurred in pro-tumorigenic immune regulation genes, such as IL-33 and IL-6, and oncogene-induced senescence.The combined effect of these genetic and coding region mutations on oncogenes, significant signaling pathways, cancer cell stemness, DNA damage repair pathways, and immune system regulation may significantly impact poor prognosis in EC patients. Further studies will verify the effectiveness of targeting these genes for developing candidate therapeutics. Citation Format: Hayriye Verda Erkizan, Robert Wadleigh. Role of noncoding genome architecture in esophageal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7358.

Mutations in Coding and Non-Coding Regions in Varicella-Zoster Virus Causing Fatal Hemorrhagic Fever Without Rash in an Immunocompetent Patient: Case Report.

We report the case of a fatal hemorrhagic varicella primary infection in an immunocompetent man and whole-genome characterization of the virus for the investigation of biomarkers of virulence. A 38-year-old patient born in Nigeria presented to the emergency department with abdominal pain and subsequently developed fatal hemorrhagic disease without skin rash. Extensive laboratory tests including serology and PCR for arenaviruses, bunyaviruses and ebolaviruses were negative. Varicella-zoster virus (VZV) PCR of sera, liver and spleen tissue samples from autopsy revealed the presence of VZV DNA. Primary infection by varicella-zoster virus with hemorrhagic manifestations was diagnosed after virological testing. The VZV genome was sequenced using a mWGS approach. Bioinformatic analysis showed 53 mutations across the genome, 33 of them producing non-synonymous variants affecting up to 14 genes. Some of them, such as ORF11 and ORF 62, encoded for essential functions related to skin or neurotropism. To our knowledge, the mutations reported here have never been described in a VZV causing such a devastating outcome. In immunocompetent patients, viral factors should be considered in patients with uncommon symptoms or severe diseases. Some relevant mutations revealed by using whole genome sequencing (WGS) directly from clinical samples may be involved in this case and deserves further investigation. Differential diagnosis of varicella-zoster virus in immunocompetent adults should be considered among patients with suspected VHF, even if the expected vesicular rash is not present at admission and does not arise thereafter. Whole genome sequencing of strains causing uncommon symptoms and/or mortality is needed for epidemiological surveillance and further characterization of putative markers of virulence. Additionally, this report highlights the recommendation for a VZV vaccination policy in non-immunized migrants from developing countries.

Emerging concepts involving inhibitory and activating RNA functionalization towards the understanding of microcephaly phenotypes and brain diseases in humans.

Microcephaly is characterized as a small head circumference, and is often accompanied by developmental disorders. Several candidate risk genes for this disease have been described, and mutations in non-coding regions are occasionally found in patients with microcephaly. Various non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), SINEUPs, telomerase RNA component (TERC), and promoter-associated lncRNAs (pancRNAs) are now being characterized. These ncRNAs regulate gene expression, enzyme activity, telomere length, and chromatin structure through RNA binding proteins (RBPs)-RNA interaction. Elucidating the potential roles of ncRNA-protein coordination in microcephaly pathogenesis might contribute to its prevention or recovery. Here, we introduce several syndromes whose clinical features include microcephaly. In particular, we focus on syndromes for which ncRNAs or genes that interact with ncRNAs may play roles. We discuss the possibility that the huge ncRNA field will provide possible new therapeutic approaches for microcephaly and also reveal clues about the factors enabling the evolutionary acquisition of the human-specific "large brain."

CRISPR-Cas9 in hiPSCs: A new era in personalized treatment for Stargardt disease

CRISPR-Cas9 in hiPSCs: A new era in personalized treatment for Stargardt disease

Genomic architecture and evolutionary relationship of BA.2.75: A Centaurus subvariant of Omicron SARS-CoV-2.

In this study, we explored the genomic architecture and phylogenomic relationship of BA.2.75, a subvariant of Omicron SARS-CoV-2. A set of 1468 whole-genome sequences of BA.2.75, submitted by 28 countries worldwide were retrieved from GISAID and used for finding genomic mutations. Moreover, the phylogenetic analysis of BA.2.75 was performed by using 2948 whole-genome sequences of all sub-variants of Omicron along with the Delta variant of SAS-CoV-2. We detected 1885 mutations, which were further grouped into 1025 missense mutations, 740 silent mutations, 72 mutations in non-coding regions, 16 in-frame deletions, 02 in-frame insertions, 8 frameshift deletions, 8 frameshift insertions and 14 stop-gained variants. Additionally, we also found 11 characteristic mutations having a prevalence of 81-99% and were not observed in any of the previously reported variant of SARS-CoV-2. Out of these mutations K147E, W152R, F157L, E210V, V213G, G339H were found in the NTD, and G446S & N460K in the RBD region of the Spike protein, whereas S403L and T11A were present in the NSP3, and E protein respectively. The phylogenetic relationship of this variant revealed that BA.2.75 is descended from the Omicron sub-variant BA.5. This evolutionary relationship suggests that the surge of BA.5 infections can reduce the severity of the infections accredited to BA.2.75. These findings would also improve our knowledge and understanding that how genetic similarities in different variants of SARS-CoV-2 can prime the immune system to fight off the infection caused by one subvariant, after defeating the other.

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan.

In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675-3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.

On- and Off-Target Analyses of CRISPR-Cas12b Genome Editing Systems in Rice.

The CRISPR-associated Cas12b system is the third most efficient CRISPR tool for targeted genome editing in plants after Cas9 and Cas12a. Although the genome editing ability of AaCas12b has been previously investigated in rice, its off-target effects in plants are largely not known. In this study, we first engineered single-guide RNA (sgRNA) complexes with various RNA scaffolds to enhance editing frequency. We targeted EPIDERMAL PATTERNING FACTOR LIKE 9 (OsEPFL9) and GRAIN SIZE 3 (OsGS3) genes with GTTG and ATTC protospacer adjacent motifs, respectively. The use of two Alicyclobacillus acidoterrestris scaffolds (Aac and Aa1.2) significantly increased the frequency of targeted mutagenesis. Next, we performed whole-genome sequencing (WGS) of stably transformed T0 rice plants to assess off-target mutations. WGS analysis revealed background mutations in both coding and noncoding regions with no evidence of sgRNA-dependent off-target activity in edited genomes. We also showed Mendelian segregation of insertion and deletion (indel) mutations in T1 generation. In conclusion, both Aac and Aa1.2 scaffolds provided precise and heritable genome editing in rice.

68. Integrative analysis of genomic and transcriptomic data using RegTools to identify splice-altering mutations within bulk

The interpretation of variants in cancer is often focused on genomic alterations that have a known coding consequence. This analysis strategy excludes somatic mutations in non-coding regions of the genome and even exonic mutations that may have unidentified regulatory consequences. To address this issue, we created RegTools, a software suite that integrates analysis of variant calls from genomic data with evidence of expressed splice junctions from transcriptomic data to efficiently identify variants that may cause aberrant splicing in tumors. To date, we have applied RegTools to over 9,000 bulk RNA-Seq samples from TCGA and clinical cohorts from Washington University to identify somatic variants that are associated with alternative splicing patterns within these tumors. We discovered 235,778 splice-altering events across 158,200 unique variants and 131,212 unique junctions.Only 1.4 percent of these mutations were previously discovered by similar attempts, while 98.6 percent are novel findings. We also applied RegTools to single cell RNA-Seq (scRNA) data from MC6BC, a transplantable organoid model of urothelial carcinoma with features of human basal-squamous urothelial carcinoma, and identified tumor-specific somatic variants leading to novel splice junctions at single-cell resolution. To our knowledge, this is the first analysis that identifies splice-altering variants within scRNA data. Future work will include utilizing RegTools to predict the novel proteins resulting from splice-altering variants and their neoantigenicity. RegTools is freely available and open-source (www.regtools.org) and all analysis scripts are provided within the project's GitHub repo (https://github.com/griffithlab/regtools).

Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator

The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.

Immunohistochemical loss of enhancer of Zeste Homolog 2 (EZH2) protein expression correlates with EZH2 alterations and portends a worse outcome in myelodysplastic syndromes

AbstractEZH2 coding mutation (EZH2MUT), resulting in loss-of-function, is an independent predictor of overall survival in MDS. EZH2 function can be altered by other mechanisms including copy number changes, and mutations in other genes and non-coding regions of EZH2. Assessment of EZH2 protein can identify alterations of EZH2 function missed by mutation assessment alone. Precise evaluation of EZH2 function and gene-protein correlation in clinical MDS cohorts is important in the context of upcoming targeted therapies aimed to restore EZH2 function. In this study, we evaluated the clinicopathologic characteristics of newly diagnosed MDS patients with EZH2MUT and correlated the findings with protein expression using immunohistochemistry. There were 40 (~6%) EZH2MUT MDS [33 men, seven women; median age 74 years (range, 55–90)]. EZH2 mutations spanned the entire coding region. Majority had dominant EZH2 clone [median VAF, 30% (1–92)], frequently co-occurring with co-dominant TET2 (38%) and sub-clonal ASXL1 (55%) and RUNX1 (43%) mutations. EZH2MUT MDS showed frequent loss-of-expression compared to EZH2WT (69% vs. 27%, p = 0.001). Interestingly, NINE (23%) EZH2WT MDS also showed loss-of-expression. EZH2MUT and loss-of-expression significantly associated with male predominance and chr(7) loss. Further, only EZH2 loss-of-expression patients showed significantly lower platelet counts, a trend for higher BM blast% and R-IPSS scores. Over a 14-month median follow-up, both EZH2MUT (p = 0.027) and loss-of-expression (p = 0.0063) correlated with poor survival, independent of R-IPSS, age and gender. When analyzed together, loss-of-expression showed a stronger correlation than mutation (p = 0.061 vs. p = 0.43). In conclusion, immunohistochemical assessment of EZH2 protein, alongside mutation, is important for prognostic workup of MDS.

Highlights from Recent Cancer Literature

Breaking Insights| August 16 2022 Highlights from Recent Cancer Literature Author & Article Information Online ISSN: 1538-7445 Print ISSN: 0008-5472 ©2022 American Association for Cancer Research2022American Association for Cancer Research Cancer Res (2022) 82 (16): 2809–2810. https://doi.org/10.1158/0008-5472.CAN-82-16-BI Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record August 16 2022 Citation Highlights from Recent Cancer Literature. Cancer Res 15 August 2022; 82 (16): 2809–2810. https://doi.org/10.1158/0008-5472.CAN-82-16-BI Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search Although recurrent genetic alterations in coding regions have been well characterized in diffuse large B-cell lymphoma (DLBCL), these alterations alone appear to be insufficient to drive lymphomagenesis. Bal and colleagues have now uncovered recurrent mutations in noncoding regions in super-enhancers, leading to loss of transcriptional repression of oncogenes, resulting in tumorigenesis. These recurrent mutations share an activation-induced cytidine deaminase signature implicating activation-induced cytidine deaminase as the mutational driver. CRISPR–Cas9-mediated reversion of these mutations led to a significant decrease in oncogene expression and prevented proliferation and survival of DLBCL cell lines. Expert Commentary: This study has uncovered a previously unrecognized role for activation-induced cytidine deaminase-mediated hypermutation of super-enhancers in lymphomagenesis and suggests potential new drug targets in DLBCL. Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, et al. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature; Published online July 6, 2022; doi: 10.1038/s41586-022-04906-8. Clear... You do not currently have access to this content.

Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions.

Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies have suggested that the lack of homology in noncoding regions could be due to increased sequence divergence. We compared 30 kb of coding and 200 kb of noncoding DNA from 13 sequenced Fragaria mitogenomes, followed by analysis of the rate of sequence divergence, microinversion events and structural variations. Substitution rates in synonymous sites and nongenic sites are nearly identical, suggesting that the genome-wide point mutation rate is generally consistent. A surprisingly high number of large multinucleotide substitutions were detected in Fragaria mitogenomes, which may have resulted from microinversion events and could affect phylogenetic signal and local rate estimates. Fragaria mitogenomes preferentially accumulate deletions relative to insertions and substantial genomic arrangements, whereas mutation rates could positively associate with these sequence and structural changes among species. Together, these observations suggest that plant mitogenomes exhibit low point mutations genome-wide but exceptionally high structural variations, and our results favour a gain-and-loss model for the rapid loss of homology among plant mitogenomes.

Abstract 6342: Pan-cancer analysis of promoter or promoter-proximal somatic mutations defines transcription-replication conflict mutational signature

Abstract Introduction: While the nature of somatic mutations in cancer exomes has been described, mutations in non-coding regions are less well-characterized. Compared to the rest of the genome, promoter or promoter-proximal (PPP) regions are more susceptible to mutagenesis and distinct mutational processes [e.g., transcription-replication conflicts (TRCs)]. We sought to investigate the nature of mutations in PPP regions across human cancer types and to define a novel TRC mutational signature. Methods: Whole genome and RNA sequencing data for untreated primary cancers were downloaded from the International Cancer Genome Consortium repository. PPP regions were defined as 1kb upstream of transcription start sites. We quantified the number of mutations in 1) PPP regions, 2) PPP regions of highly transcribed genes (HTGs; ≥75th percentile), and 3) common fragile sites (CFS). Results: A total of 835 patients across 12 tumor types were included in our analysis. Our data show significant variation in PPP mutations across cancer types with liver, pancreatic, and ovarian cancers demonstrating the highest burden of PPP mutations (Table 1). These same cancer types also possessed high numbers of PPP mutations specifically in HTGs. Since PPP mutations may be caused by TRCs, we proposed that liver, pancreatic, and ovarian cancers exhibited a strong TRC mutational signature. Therefore, we examined the correlation between the signature and CFS mutations—known to be caused by TRCs—to validate our results. The data show a positive correlation across tumor types; this correlation was strongest for cancer types where a TRC signature was more prevalent [correlation coefficient (R): liver: 0.985, pancreas: 0.991, ovary: 0.964]. Conclusions: Our analysis of PPP and CFS mutations suggests that transcription-dependent genome instability is more prevalent in liver, pancreatic, and ovarian cancers. Further, PPP in HTGs may be a novel TRC mutational signature. Medians and interquartile ranges of mutations by disease type. PPP: promoter or promoter-proximal Disease type Number of patients Mutations in PPP regions Mutations in PPP regions of highly transcribed genes (≥75%ile) Mutations in common fragile sites Bladder 23 4 (2-8) 2 (1-5) 12 (7-17) Bone 49 5 (2-12) 2 (0-3) 14 (7-43) Breast 89 1 (0-2) 0 (0-2) 5 (2-7) Cervix 20 1 (0-2) 1 (0-1) 3 (2-5) Colorectal 43 2 (1-14) 1 (0-5) 11 (6-81) Liver 227 54 (37-75) 13 (9-18) 264 (180-368) Lung 38 3 (1-6) 1 (0-2) 9 (4-24) Ovary 102 41 (3-68) 36 (16-52) 148 (7-213) Pancreas 140 31 (15-45) 25 (19-37) 113 (66-161) Prostate 19 0 (0-0) 0 (0-0) 1 (0-1) Stomach 34 2 (1-3) 1 (0-2) 8 (3-17) Uterus 51 1 (0-4) 1 (0-3) 6 (3-21) Citation Format: Marc A. Attiyeh, Fan Meng, Yilun Liu, Nicholas Banovich, Mustafa Raoof. Pan-cancer analysis of promoter or promoter-proximal somatic mutations defines transcription-replication conflict mutational signature [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6342.

Overview of Neural Tube Defects: Gene-Environment Interactions, Preventative Approaches and Future Perspectives.

Neural tube defects (NTDs) are the second most common congenital malformations of humans, characterized by impaired development of the central nervous system. Even though the etiology of most birth defects remains undetermined, genetic and environmental risk factors in the background of NTDs have been identified and extensively reported. On top of genetic and nutritional risks which include mutations in both coding and non-coding regions and maternal folate status, respectively, recent years have seen a rise in the identification of a variety of teratogens that could be implicated in NTD development. These include polycyclic aromatic hydrocarbons, arsenic, pesticides, maternal hyperthermia and antibiotics as well as pain and seizure medication. With an increase in understanding of teratogens leading to NTD formation, preventative and treatment approaches have witnessed great advances throughout the years. While the most common preventative approach includes folic acid food fortification as well as suggested inositol supplementation, treatment and management approaches differ greatly depending on the developmental stage and the site of the lesion and include prenatal surgery, stem cell transplantation and postnatal surgery. Because NTDs still represent a large health and financial burden for the patient and society as a whole, it is crucial to investigate potential risk factors and develop novel approaches in order to fully prevent this category of disorders.

JC Polyomavirus Whole Genome Sequencing at the Single-Molecule Level Reveals Emerging Neurotropic Populations in Progressive Multifocal Leukoencephalopathy.

JC polyomavirus (JCV) mostly causes asymptomatic persistent renal infections but may give rise in immunosuppressed patients to neurotropic variants that replicate in the brain, causing progressive multifocal leukoencephalopathy (PML). Rearrangements in the JCV genome regulator noncoding control region (NCCR) and missense mutations in the viral capsid VP1 gene differentiate neurotropic variants from virus excreted in urine. To investigate intrahost emergence of JCV neurotropic populations in PML, we deep sequenced JCV whole genome recovered from cerebrospinal fluid (CSF) and urine samples from 32 human immunodeficiency virus (HIV)-infected and non-HIV-infected PML patients at the single-molecule level. JCV strains distributed among 6 of 7 known genotypes. Common patterns of NCCR rearrangements included an initial deletion mostly located in a short 10-nucleotide sequence, followed by duplications/insertions. Multiple NCCR variants present in individual CSF samples shared at least 1 rearrangement, suggesting they stemmed from a unique viral population. NCCR variants independently acquired single or double PML-specific adaptive VP1 mutations. NCCR variants recovered from urine and CSF displayed opposite deletion or duplication patterns in binding sites for transcription factors. Long-read deep sequencing shed light on emergence of neurotropic JCV populations in PML.

Clinical, hormonal and molecular-genetic characteristics of monogenic diabetes mellitus associated with the mutations in the <i>INS</i> gene

Background:Currently more than 50 mutations of the INS gene are known to affect the various stages of insulin biosynthesis in the beta cells of the pancreas. However only individual cases of diabetes mellitus (DM) associated with heterozygous mutations in the coding region of the INS gene were reported in Russian Federation. We report a group of patients with a clinical manifestation of DM caused by mutations in both coding and non-coding regions of the INS gene. The patients with a mutation in the intron of the INS gene are reported for the first time in Russian FederationMaterials and methods: 60 patients with an isolated course of neonatal DM (NDM), 52 patients with a manifestation of DM at the age of 7–12 months and the absence of the main autoimmune markers of type 1 DM, 650 patients with the MODY phenotype were included in the study. NGS technology was used for molecular genetic research. Author’s panel of primers (Custom DNA Panel) was used for multiplex PCR and sequencing using Ion Ampliseq™ technology. The author’s panel “­Diabetes Mellitus” included 28 genes (13 candidate genes of MODY and other genes associated with DM).Results:13 heterozygous mutations were identified in 16 probands and 9 relatives. The majority of mutations were detected in patients with PNDM (18.75%) and in patients with an onset of DM at the age of 7–12 months (9.6%). Mutations in the INS gene were detected in 2 patients (0.3%) in the group with the MODY phenotype. Mutations in the INS gene were not detected in patients with transient NDM (TNDM). Analysis of clinical data in patients with PND and onset of diabetes at the age of 7–12 months did not show significant differences in the course of the disease. The clinical characteristics of the cases of MODY10 and diabetes caused by a mutation in the intron of the INS gene are reported in details.Conclusion:The role of INS gene mutations in NDM, MODY, and DM with an onset at the age of 7–12 months was analyzed in a large group of patients. The clinical characteristics of DM due to a mutation in the intron of the INS gene are reported for the first time in the Russian Federation.