Uvarova, Aksinya N

Bogomolova E.A., Murashko M.M., Stasevich E.M., Uvarova A.N., Zheremyan E.A., Korneev K.V., Kuprash D.V., Demin D.E.

Abstract The MPC1 gene is involved in the transport of pyruvate into mitochondria, playing an important role in metabolic processes. Recently, it has been reported that higher MPC1 expression correlates with an increased number of immune cells in human cervical and lung cancers, indicating an enhanced antitumor immune response. Reduced MPC1 levels in gastric tumors are associated with a more severe disease course. Correlational analysis of the MPC1 gene in human lung, hippocampus and frontal cortex tissue samples based on data from the GTEx database revealed associations of this gene with schizophrenia, non-small cell lung cancer, and immune diseases. Our experiments showed that the mRNA level of the MPC1 gene in the non-small cell lung cancer cell line A549 increases 5-fold under the influence of the schizophrenia neuroleptic thioridazine. The observed elevation of MPC1 level may cause tumor infiltration by immune cells, complementing the previously reported data indicating the ability of thioridazine to slow cell growth, induce apoptosis and reduce the ability of cells to migrate.

Uvarova A.N., Zheremyan E.A., Ustiugova A.S., Murashko M.M., Bogomolova E.A., Demin D.E., Stasevich E.M., Kuprash D.V., Korneev K.V.

Interleukin 10 (IL10) is a major anti-inflammatory cytokine that acts as a master regulator of the immune response. A single nucleotide polymorphism rs3024505(C/T), located downstream of the IL10 gene, is associated with several aggressive inflammatory diseases, including systemic lupus erythematosus, Sjögren’s syndrome, Crohn’s disease, and ulcerative colitis. In such autoimmune pathologies, IL10-producing B cells play a protective role by decreasing the level of inflammation and restoring immune homeostasis. This study demonstrates that rs3024505 is located within an enhancer that augments the activity of the IL10 promoter in a reporter system based on a human B cell line. The common rs3024505(C) variant creates a functional binding site for the transcription factor STAT3, whereas the risk allele rs3024505(T) disrupts STAT3 binding, thereby reducing the IL10 promoter activity. Our findings indicate that B cells from individuals carrying the minor rs3024505(T) allele may produce less IL10 due to the disrupted STAT3 binding site, contributing to the progression of inflammatory pathologies.

Stasevich E.M., Simonova A.V., Bogomolova E.A., Murashko M.M., Uvarova A.N., Zheremyan E.A., Korneev K.V., Schwartz A.M., Kuprash D.V., Demin D.E.

A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases.

Stasevich E.M., Simonova A.V., Uvarova A.N., Zheremyan E.A., Korneev K.V., Bogomolova E.A., Demin D.E.

The transcription factor STAT3 serves as an immunoregulator by playing a crucial role in cytokine receptor signaling. However, in various cancer cell types, STAT3 is involved in the molecular mechanisms of oncogenesis. Specifically, in glioblastoma, the STAT3 immunoregulator has been linked to resistance to temozolomide, the most commonly used chemical agent for treating this type of cancer. Furthermore, literature suggests that activation of this oncogene in glioblastoma cells can significantly impact the tolerogenic tumor microenvironment, weakening the antitumor immune response and contributing to the aggressive course of the disease. Therefore, suppressing STAT3 may not only affect cell growth and resistance to chemotherapy but also enhance the immune response by improving the tumor microenvironment.The development of sequencing technologies has revealed that most of the transcribed material in the cell is noncoding. Long non-coding RNAs are gaining popularity in the study of oncogenesis due to their functional role in the development of various diseases, including oncology. A subtype of long non-coding RNAs transcribed from enhancer elements, known as enhancer RNAs, has garnered attention due to their high specificity in various cells and tissues. Gene co-expression analysis in glioblastoma tumors showed a correlation between STAT3 expression and the enhancer RNA LINC00910, which is located in the same chromosomal domain as the Stat3 gene. Previous literature has shown that LINC00910 is associated with both colorectal and gastric cancer. Additionally, data from the GeneHancer database suggests that the enhancer RNA LINC00910 may be involved in regulating the STAT3 immunoregulator. RNA interference was used to effectively knockdown the enhancer RNA LINC00910, resulting in an 8- to 10-fold reduction in its expression in glioblastoma cell lines. The reduction of LINC00910 expression did not significantly affect Stat3 gene expression in glioblastoma cell lines DBTRG-05MG and U251. This suggests that the correlation between LINC00910 RNA expression and STAT3 gene expression is not due to LINC00910’s direct involvement in STAT3 gene regulation in these cells. Further studies using the selected interfering RNA will help to clarify the role of the enhancer RNA LINC00910 in other signallingsignaling pathways, as well as its potential relationship with cancer development.

Uvarova A.N., Ustiugova A.S., Zheremyan E.A., Stasevich E.M., Korneev K.V., Kuprash D.V.

B cells play a crucial role in the pathogenesis of various diseases, such as autoimmune disorders, cancers, and infections. Unlike regulatory T cells, the anti-inflammatory capabilities of B cells have only recently garnered attention. Cytokines IL-10 and TGF-β are among the key secreted immunosuppressive factors, therefore studying the characteristics of their transcriptional regulation in B cells appears to be a relevant task. This study focuses on characterizing the promoter regions of IL10 and TGFB1 genes in immortalized B cell lines representing different developmental stages – Reh and Raji. To achieve this, we identified potential promoter regions guided by the epigenetic features of functional regulatory regions determined by bioinformatics methods of ChIP-Seq data analysis of chromatin marks in CD19+ lymphocytes. We examined the activity of selected promoters using reporter analysis in B cells. Additionally, we studied the impact of a single nucleotide polymorphism rs1800469 in the TGFB1 promoter, which is associated with the development of colorectal cancer, chronic obstructive pulmonary disease, and the risk of radiation fibrosis. Our results showed increased promoter activity of IL10 and TGFB1 in the Reh pro-B cells compared to the Raji mature B cells upon stimulation. Interestingly, the presence of the minor allele of rs1800469 led to enhanced TGFB1 promoter activity in the Reh cells. Higher activity of IL10 and TGFB1 promoters in acute lymphoblastic leukemia Reh cells may be associated with the increased immunosuppression, which is characteristic of this pathology. It is also possible that activation of pro-B cells Reh induces their differentiation into monocyte-like cells, which can be polarized into alternatively activated (M2) macrophages by autocrine TGF-β and IL-10. M2 macrophages can function as tumor-associated macrophages and contribute to the development of colorectal cancer. Moreover, increased levels of TGF-β in tissues increase the risks of fibrosis and decrease inflammation levels in chronic obstructive pulmonary disease.

Uvarova A.N., Tkachenko E.A., Stasevich E.M., Zheremyan E.A., Korneev K.V., Kuprash D.V.

Abstract Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through the Genome-Wide Association Studies. Majority of the clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain influence of the non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating molecular mechanisms underlying dependence of the disease pathogenesis on specific genetic variants within the non-coding sequences. A particular focus is on the methods for identification of transcription factors with binding efficiency dependent on polymorphic variations. Despite remarkable progress in bioinformatic resources enabling prediction of the impact of polymorphisms on the disease pathogenesis, there is still the need for experimental approaches to investigate this issue.

Uvarova A.N., Tkachenko E.A., Stasevich E.M., Bogomolova E.A., Zheremyan E.A., Kuprash D.V., Korneev K.V.

Abstract The complement inhibitor CD55/DAF is expressed on many cell types. Dysregulation of CD55 expression is associated with increased disease severity in influenza A infection and vascular complications in pathologies that involve excessive activation of the complement system. A luciferase reporter system was used to functionally analyze the single nucleotide polymorphism rs2564978 in the U937 human promonocytic cell line. The polymorphism is in the promoter of the CD55 gene, and its minor allele T is associated with a severe course of influenza A(H1N1)pdm09. A decreased activity of the CD55 promoter carrying the minor rs2564978(T) allele was observed in activated U937 cells, which provide a cell model of human macrophages. Using bioinformatics resources, PU.1 was identified as a potential transcription factor that may bind to the CD55 promoter at the rs2564978 site in an allele-specific manner. The involvement of PU.1 in modulating CD55 promoter activity was verified by a PU.1 genetic knockdown with small interfering RNAs under specific monocyte activation conditions.

Zheremyan E.A., Ustiugova A.S., Karamushka N.M., Uvarova A.N., Stasevich E.M., Bogolyubova A.V., Kuprash D.V., Korneev K.V.

Wound healing is a complex process involving a coordinated series of events aimed at restoring tissue integrity and function. Regulatory B cells (Bregs) are a subset of B lymphocytes that play an essential role in fine-tuning immune responses and maintaining immune homeostasis. Recent studies have suggested that Bregs are important players in cutaneous immunity. This review summarizes the current understanding of the role of Bregs in skin immunity in health and pathology, such as diabetes, psoriasis, systemic sclerosis, cutaneous lupus erythematosus, cutaneous hypersensitivity, pemphigus, and dermatomyositis. We discuss the mechanisms by which Bregs maintain tissue homeostasis in the wound microenvironment through the promotion of angiogenesis, suppression of effector cells, and induction of regulatory immune cells. We also mention the potential clinical applications of Bregs in promoting wound healing, such as the use of adoptive Breg transfer.

Uvarova A.N., Stasevich E.M., Ustiugova A.S., Mitkin N.A., Zheremyan E.A., Sheetikov S.A., Zornikova K.V., Bogolyubova A.V., Rubtsov M.A., Kulakovskiy I.V., Kuprash D.V., Korneev K.V., Schwartz A.M.

Single-nucleotide polymorphism rs71327024 located in the human 3p21.31 locus has been associated with an elevated risk of hospitalization upon SARS-CoV-2 infection. The 3p21.31 locus contains several genes encoding chemokine receptors potentially relevant to severe COVID-19. In particular, CXCR6, which is prominently expressed in T lymphocytes, NK, and NKT cells, has been shown to be involved in the recruitment of immune cells to non-lymphoid organs in chronic inflammatory and respiratory diseases. In COVID-19, CXCR6 expression is reduced in lung resident memory T cells from patients with severe disease as compared to the control cohort with moderate symptoms. We demonstrate here that rs71327024 is located within an active enhancer that augments the activity of the CXCR6 promoter in human CD4+ T lymphocytes. The common rs71327024(G) variant makes a functional binding site for the c-Myb transcription factor, while the risk rs71327024(T) variant disrupts c-Myb binding and reduces the enhancer activity. Concordantly, c-Myb knockdown in PMA-treated Jurkat cells negates rs71327024’s allele-specific effect on CXCR6 promoter activity. We conclude that a disrupted c-Myb binding site may decrease CXCR6 expression in T helper cells of individuals carrying the minor rs71327024(T) allele and thus may promote the progression of severe COVID-19 and other inflammatory pathologies.

Zheremyan E.A., Ustiugova A.S., Uvarova A.N., Karamushka N.M., Stasevich E.M., Gogoleva V.S., Bogolyubova A.V., Mitkin N.A., Kuprash D.V., Korneev K.V.

Regulatory B lymphocytes (Bregs) are B cells with well-pronounced immunosuppressive properties, allowing them to suppress the activity of effector cells. A broad repertoire of immunosuppressive mechanisms makes Bregs an attractive tool for adoptive cell therapy for diseases associated with excessive activation of immune reactions. Such therapy implies Breg extraction from the patient’s peripheral blood, ex vivo activation and expansion, and further infusion into the patient. At the same time, the utility of Bregs for therapeutic approaches is limited by their small numbers and extremely low survival rate, which is typical for all primary B cell cultures. Therefore, extracting CD19+ cells from the patient’s peripheral blood and specifically activating them ex vivo to make B cells acquire a suppressive phenotype seems to be far more productive. It will allow a much larger number of B cells to be obtained initially, which may significantly increase the likelihood of successful immunosuppression after adoptive Breg transfer. This comparative study focuses on finding ways to efficiently manipulate B cells in vitro to differentiate them into Bregs. We used CD40L, CpG, IL4, IL21, PMA, and ionomycin in various combinations to generate immunosuppressive phenotype in B cells and performed functional assays to test their regulatory capacity. This work shows that treatment of primary B cells using CD40L + CpG + IL21 mix was most effective in terms of induction of functionally active regulatory B lymphocytes with high immunosuppressive capacity ex vivo.

Demin D.E., Murashko M.M., Uvarova A.N., Stasevich E.M., Shyrokova E.Y., Gorlachev G.E., Zaretsky A.R., Korneev K.V., Ustiugova A.S., Tkachenko E.A., Kostenko V.V., Tatosyan K.A., Sheetikov S.A., Spirin P.V., Kuprash D.V., et. al.

The flurry of publications devoted to the functions of long non-coding RNAs (lncRNAs) published in the last decade leaves no doubt about the exceptional importance of lncRNAs in various areas including tumor biology. Contribution of lncRNAs to the early stages of oncogenesis remains poorly understood. In this study we explored a new role for lncRNAs: stimulation of specific chromosomal rearrangements upon DNA damage. We demonstrated that lncRNA CASTL1 (ENSG00000269945) stimulates the formation of the CCDC6-RET inversion (RET/PTC1) in human thyroid cells subjected to radiation or chemical DNA damage. Facilitation of chromosomal rearrangement requires lncRNA to contain regions complementary to the introns of both CCDC6 and RET genes as deletion of these regions deprives CASTL1 of the ability to stimulate the gene fusion. We found that CASTL1 expression is elevated in tumors with CCDC6-RET fusion which is the most frequent rearrangement in papillary thyroid carcinoma. Our results open a new venue for the studies of early oncogenesis in various tumor types, especially those associated with physical or chemical DNA damage. This article is protected by copyright. All rights reserved.

Zheremyan E.A., Ustiugova A.S., Radko A.I., Stasevich E.M., Uvarova A.N., Mitkin N.A., Kuprash D.V., Korneev K.V.

Demin D.E., Stasevich E.M., Murashko M.M., Tkachenko E.A., Uvarova A.N., Schwartz A.M.

Human securin (PTTG1) is a protooncogene whose expression is elevated in many types of malignant cells. We previously discovered a minor short isoform of securin lacking exons 3 and 4. The missing exons encode the main recognition site (D-box) of the anaphase-promoting complex (APC/C). We show that these two PTTG1 isoforms have different effects on transcription. Here, we have studied the effects of overexpression and selective knockdown of the short and complete securin isoforms on cell proliferation using the xCELLigence system. Notably, selective knockdown of the short isoform mRNA led to a dramatic decrease in cell growth, while overexpression of both isoforms accelerated cell growth. To search for genes with alternative isoforms similar to securin, we analyzed the GENCODE database and found that 54 of 128 genes with a PTTG1-like set of APC/C recognition sites have known isoforms without the D-box. Overall, the data obtained indicate the existence of a new class of alternative isoforms and reinstates the importance of minor isoforms.

Mikhailovna S.E., Vladimirovna S.A., Valeryevna P.A., Andreevna B.E., Nikolaevna U.A., Alekseevna Z.E., Viktorovich K.K., Markovich S.A., Vladimirovich K.D., Eriksonovich D.D.

Sabeti Akbar-Abad M., Majidpour M., Sargazi S., Ghasemi M., Saravani R.

Stathopoulou C., Zhao M., Jiang Q., Hong J., Bian J., Zhang J., Ho M., Hassan R.

AbstractStudies on the dynamic changes occurring in the tumor microenvironment (TME) following CAR-T cell therapy have been confounded by host lymphodepletion, multiple dosing and immunodeficient models. Here, a nanobody-based, mouse mesothelin-targeting CAR-T cell (A101) was developed, achieving effective primary tumor suppression, metastasis reduction, and improved survival after a single dose in immunocompetent, syngeneic mouse models without lymphodepletion. Temporal tumor profiling using RNA sequencing revealed initial downregulation of cell proliferation genes followed by upregulation of inflammation, epithelial-to-mesenchymal-transition (EMT) and extracellular matrix (ECM) modification genes in the CAR-T-treated tumors relative to mock-T-treated controls. This phenotype was reversed at a later timepoint which coincided with downregulation of immunosuppressiveCd274+Lcn2+neutrophils and upregulation of anti-tumorP2rx1+Nrf2-neutrophils. At the same time, upregulation ofCcl2+in fibroblasts and a more immunomodulatory macrophage phenotype was observed in CAR-T-treated tumors, indicating a tumor adaptation mechanism. This study demonstrates complex dynamic changes in the TME, and highlights time-dependent responses of solid tumors to CAR-T cell therapy. It further highlightsLcn2+neutrophils andCcl2+fibroblasts as potential therapeutic targets for improving CAR-T cell anti-tumor efficacy.Abstract FigureGraphical abstract.Tumor responses to A101 CAR-T cell treatment.

Hoffmann M., Vaz T., Chhatrala S., Hennighausen L.

Abstract Background Millions of single nucleotide polymorphisms (SNPs) have been identified in humans, but the functionality of almost all SNPs remains unclear. While current research focuses primarily on SNPs altering one amino acid to another one, the majority of SNPs are located in intergenic spaces. Some of these SNPs can be found in candidate cis-regulatory elements (CREs) such as promoters and enhancers, potentially destroying or creating DNA-binding motifs for transcription factors (TFs) and, hence, deregulating the expression of nearby genes. These aspects are understudied due to the sheer number of SNPs and TF binding motifs, making it challenging to identify SNPs that yield phenotypic changes or altered gene expression. Results We developed a data-driven computational protocol to prioritize high-potential SNPs informed from former knowledge for experimental validation. We evaluated the protocol by investigating SNPs in CREs in the Janus kinase (JAK) – Signal Transducer and Activator of Transcription (-STAT) signaling pathway, which is activated by a plethora of cytokines and crucial in controlling immune responses and has been implicated in diseases like cancer, autoimmune disorders, and responses to viral infections. The protocol involves scanning the entire human genome (hg38) to pinpoint DNA sequences that deviate by only one nucleotide from the canonical binding sites (TTCnnnGAA) for STAT TFs. We narrowed down from an initial pool of 3,301,512 SNPs across 17,039,967 nearly complete STAT motifs and identified six potential gain-of-function SNPs in regions likely to influence regulation within the JAK-STAT pathway. This selection was guided by publicly available open chromatin and gene expression data and further refined by filtering for proximity to immune response genes and conservation between the mouse and human genomes. Conclusion Our findings highlight the value of combining genomic, epigenomic, and cross-species conservation data to effectively narrow down millions of SNPs to a smaller number with a high potential to induce interferon regulation of nearby genes. These SNPs can finally be reviewed manually, laying the groundwork for a more focused and efficient exploration of regulatory SNPs in an experimental setting.

Buyan A., Meshcheryakov G., Safronov V., Abramov S., Boytsov A., Nozdrin V., Baulin E.F., Kolmykov S., Vierstra J., Kolpakov F., Makeev V.J., Kulakovskiy I.V.

Kazan H.H., Acınan İ.S., Kandemir B., Karahan C.P., Kayhan G., İşeri Ö.D.

Bogomolova E.A., Murashko M.M., Stasevich E.M., Uvarova A.N., Zheremyan E.A., Korneev K.V., Kuprash D.V., Demin D.E.

Abstract The MPC1 gene is involved in the transport of pyruvate into mitochondria, playing an important role in metabolic processes. Recently, it has been reported that higher MPC1 expression correlates with an increased number of immune cells in human cervical and lung cancers, indicating an enhanced antitumor immune response. Reduced MPC1 levels in gastric tumors are associated with a more severe disease course. Correlational analysis of the MPC1 gene in human lung, hippocampus and frontal cortex tissue samples based on data from the GTEx database revealed associations of this gene with schizophrenia, non-small cell lung cancer, and immune diseases. Our experiments showed that the mRNA level of the MPC1 gene in the non-small cell lung cancer cell line A549 increases 5-fold under the influence of the schizophrenia neuroleptic thioridazine. The observed elevation of MPC1 level may cause tumor infiltration by immune cells, complementing the previously reported data indicating the ability of thioridazine to slow cell growth, induce apoptosis and reduce the ability of cells to migrate.

Zhang F., Fu Y., Jimenez-Cyrus D., Zhao T., Shen Y., Sun Y., Zhang Z., Wang Q., Kawaguchi R., Geschwind D.H., He C., Ming G., Song H.

Saeed Issa B., Adhab A.H., Salih Mahdi M., Kyada A., Ganesan S., Bhanot D., Naidu K.S., Kaur S., Mansoor A.S., Radi U.K., Saadoun Abd N., Kariem M.

Uvarova A.N., Tkachenko E.A., Stasevich E.M., Zheremyan E.A., Korneev K.V., Kuprash D.V.

Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through Genome-Wide Association Studies. The majority of clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain the influence of non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating the molecular mechanisms underlying the dependence of disease pathogenesis on specific genetic variants within non-coding sequences. A particular focus is on the methods to identify the transcription factors with binding efficiency contingent upon polymorphic variations. Despite remarkable progress in the bioinformatic resources enabling the prediction of the impact of polymorphisms on disease pathogenesis, the imperative for experimental approaches to this inquiry still persists.

Gilbert E., Megia-Palma R., Zagar A., Lopez-Darias M., Carretero M.A., Seren N., Sellers G.S., Beltran-Alvarez P., Wollenberg Valero K.C.

AbstractClimate adaptation is caused by multiple mechanisms, including evolution of regulatory promoter sequences under broad environmental pressures, however, little is known about these processes in response to climate pressures in animals. Here, we examined spatial and temporal evolution of climate-related gene promoters in an insular species, the Western-Canaries lizardGallotia galloti, across diverse environmental conditions over nine years. Outlier SNPs linked to elevation-sensitive environmental factors identified adaptively significant loci, including in aquaporin and Electron Transfer Flavoprotein Subunit Alpha (ETFA) gene promoters, demonstrating roles in local climate adaptation. Adaptive indexing mapped climate-driven genetic differentiation across the landscape, revealing local adaptation along an elevational gradient. Signatures of climate-related selection at the temporal scale showed specific promoters shaped by balancing selection supporting survival across environments, while others experienced positive selection, revealing a selective sweep of beneficial alleles. In addition, elevation-based ancestry groups of climate loci differed from the pattern observed in neutral loci, and temporal shifts in ancestry composition responded to preceding extreme weather events over the span of a single generation. Selection on specific promoter regions indicated adaptive evolution in transcription factor binding sites with the potential to enhance transcriptional flexibility, resulting in increased cellular stress tolerance. Our findings open new avenues into genomic mechanisms of resilience across spatially heterogeneous environments and how rapid evolution correlates with extreme weather events associated with climate change.

Zhao D., Huai G., Yuan Y., Cui Y., Yuan Y., Zhao G.

Su Q., Jiang Z., Song X., Zhang S.

Cao J., Yang Z.

Vorontsov I.E., Kozin I., Abramov S., Boytsov A., Jolma A., Albu M., Ambrosini G., Faltejskova K., Gralak A.J., Gryzunov N., Inukai S., Kolmykov S., Kravchenko P., Kribelbauer-Swietek J.F., Laverty K.U., et. al.

AbstractA DNA sequence pattern, or “motif”, is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and computational motif discovery algorithm. As a part of the Codebook/GRECO-BIT initiative, here we evaluated at large scale the cross-platform recognition performance of positional weight matrices (PWMs), which remain popular motif models in many practical applications. We applied ten different DNA motif discovery tools to generate PWMs from the “Codebook” data comprised of 4,237 experiments from five different platforms profiling the DNA-binding specificity of 394 human proteins, focusing on understudied transcription factors of different structural families. For many of the proteins, there was no prior knowledge of a genuine motif. By benchmarking-supported human curation, we constructed an approved subset of experiments comprising about 30% of all experiments and 50% of tested TFs which displayed consistent motifs across platforms and replicates. We present the Codebook Motif Explorer (https://mex.autosome.org), a detailed online catalog of DNA motifs, including the top-ranked PWMs, and the underlying source and benchmarking data. We demonstrate that in the case of high-quality experimental data, most of the popular motif discovery tools detect valid motifs and generate PWMs, which perform well both on genomic and synthetic data. Yet, for each of the algorithms, there were problematic combinations of proteins and platforms, and the basic motif properties such as nucleotide composition and information content offered little help in detecting such pitfalls. By combining multiple PMWs in decision trees, we demonstrate how our setup can be readily adapted to train and test binding specificity models more complex than PWMs. Overall, our study provides a rich motif catalog as a solid baseline for advanced models and highlights the power of the multi-platform multi-tool approach for reliable mapping of DNA binding specificities.Abstract FigureGraphical Abstract

Li M., Xu T., Yang R., Wang X., Zhang J., Wu S.

The increasing problems of drug and radiotherapy resistance in cervical cancer underscores the need for novel methods for its management. Reports indicate that the expression of MPC1 may be associated with the tumor microenvironment and the occurrence of ferroptosis in cervical cancer. The objective of this study was to visually illustrate the prognostic significance and immunological characterization of MPC1 in cervical cancer. The expression profile and prognostic significance of MPC1 were analyzed using various databases, including UALCAN, TIMER2, GEPIA2, and Kaplan–Meier Plotter. TISIDB, TIMER2, and immunohistochemical analysis were used to investigate the correlation between MPC1 expression and immune infiltration. GO enrichment analysis, KEGG analysis, Reactome analysis, ConsensusPathDB, and GeneMANIA were used to visualize the functional enrichment of MPC1 and signaling pathways related to MPC1. The correlation analysis was carried out to examine the relationship between MPC1 and Ferroptosis gene in TIMER 2.0, ncFO, GEPIA Database and Kaplan–Meier Plotter. We demonstrated that the expression levels of MPC1 in cervical cancer tissues were lower than those in normal cervical tissues. Kaplan–Meier survival curves showed shorter overall survival in cervical cancer patients with low levels of MPC1 expression. The expression of MPC1 was related to the infiltrating levels of tumor-infiltrating immune cells in cervical cancer. Moreover, MPC1 expression was associated with the iron-mediated cell death pathway, and several important ferroptosis genes were upregulated in cervical cancer cells. Furthermore, after knocking down MPC1 in HeLa cells, the expression of these genes decreased. These findings indicate that MPC1 functions as a prognostic indicator and plays a role in the regulation of the ferroptosis pathway in cervical cancer.

Li F., Huang C., Zhou M., Zhang W., Zhang D., Liu F., Zhou J.

Uvarova A.N., Ustiugova A.S., Zheremyan E.A., Stasevich E.M., Korneev K.V., Kuprash D.V.

B cells play a crucial role in the pathogenesis of various diseases, such as autoimmune disorders, cancers, and infections. Unlike regulatory T cells, the anti-inflammatory capabilities of B cells have only recently garnered attention. Cytokines IL-10 and TGF-β are among the key secreted immunosuppressive factors, therefore studying the characteristics of their transcriptional regulation in B cells appears to be a relevant task. This study focuses on characterizing the promoter regions of IL10 and TGFB1 genes in immortalized B cell lines representing different developmental stages – Reh and Raji. To achieve this, we identified potential promoter regions guided by the epigenetic features of functional regulatory regions determined by bioinformatics methods of ChIP-Seq data analysis of chromatin marks in CD19+ lymphocytes. We examined the activity of selected promoters using reporter analysis in B cells. Additionally, we studied the impact of a single nucleotide polymorphism rs1800469 in the TGFB1 promoter, which is associated with the development of colorectal cancer, chronic obstructive pulmonary disease, and the risk of radiation fibrosis. Our results showed increased promoter activity of IL10 and TGFB1 in the Reh pro-B cells compared to the Raji mature B cells upon stimulation. Interestingly, the presence of the minor allele of rs1800469 led to enhanced TGFB1 promoter activity in the Reh cells. Higher activity of IL10 and TGFB1 promoters in acute lymphoblastic leukemia Reh cells may be associated with the increased immunosuppression, which is characteristic of this pathology. It is also possible that activation of pro-B cells Reh induces their differentiation into monocyte-like cells, which can be polarized into alternatively activated (M2) macrophages by autocrine TGF-β and IL-10. M2 macrophages can function as tumor-associated macrophages and contribute to the development of colorectal cancer. Moreover, increased levels of TGF-β in tissues increase the risks of fibrosis and decrease inflammation levels in chronic obstructive pulmonary disease.

Uvarova A.N., Tkachenko E.A., Stasevich E.M., Zheremyan E.A., Korneev K.V., Kuprash D.V.

Abstract Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through the Genome-Wide Association Studies. Majority of the clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain influence of the non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating molecular mechanisms underlying dependence of the disease pathogenesis on specific genetic variants within the non-coding sequences. A particular focus is on the methods for identification of transcription factors with binding efficiency dependent on polymorphic variations. Despite remarkable progress in bioinformatic resources enabling prediction of the impact of polymorphisms on the disease pathogenesis, there is still the need for experimental approaches to investigate this issue.

Uvarova A.N., Tkachenko E.A., Stasevich E.M., Bogomolova E.A., Zheremyan E.A., Kuprash D.V., Korneev K.V.

Abstract The complement inhibitor CD55/DAF is expressed on many cell types. Dysregulation of CD55 expression is associated with increased disease severity in influenza A infection and vascular complications in pathologies that involve excessive activation of the complement system. A luciferase reporter system was used to functionally analyze the single nucleotide polymorphism rs2564978 in the U937 human promonocytic cell line. The polymorphism is in the promoter of the CD55 gene, and its minor allele T is associated with a severe course of influenza A(H1N1)pdm09. A decreased activity of the CD55 promoter carrying the minor rs2564978(T) allele was observed in activated U937 cells, which provide a cell model of human macrophages. Using bioinformatics resources, PU.1 was identified as a potential transcription factor that may bind to the CD55 promoter at the rs2564978 site in an allele-specific manner. The involvement of PU.1 in modulating CD55 promoter activity was verified by a PU.1 genetic knockdown with small interfering RNAs under specific monocyte activation conditions.

Hardtke H.A., Zhang Y.J.

Hou S., Zhao Y., Chen J., Lin Y., Qi X.

AbstractMetastasis is the leading cause of high mortality in colorectal cancer (CRC), which is not only driven by changes occurring within the tumor cells, but is also influenced by the dynamic interaction between cancer cells and components in the tumor microenvironment (TME). Currently, the exploration of TME remodeling and its impact on CRC metastasis has attracted increasing attention owing to its potential to uncover novel therapeutic avenues. Noteworthy, emerging studies suggested that tumor-associated macrophages (TAMs) within the TME played important roles in CRC metastasis by secreting a variety of cytokines, chemokines, growth factors and proteases. Moreover, TAMs are often associated with poor prognosis and drug resistance, making them promising targets for CRC therapy. Given the prognostic and clinical value of TAMs, this review provides an updated overview on the origin, polarization and function of TAMs, and discusses the mechanisms by which TAMs promote the metastatic cascade of CRC. Potential TAM-targeting techniques for personalized theranostics of metastatic CRC are emphasized. Finally, future perspectives and challenges for translational applications of TAMs in CRC development and metastasis are proposed to help develop novel TAM-based strategies for CRC precision medicine and holistic healthcare.

Zheremyan E.A., Ustiugova A.S., Karamushka N.M., Uvarova A.N., Stasevich E.M., Bogolyubova A.V., Kuprash D.V., Korneev K.V.

Wound healing is a complex process involving a coordinated series of events aimed at restoring tissue integrity and function. Regulatory B cells (Bregs) are a subset of B lymphocytes that play an essential role in fine-tuning immune responses and maintaining immune homeostasis. Recent studies have suggested that Bregs are important players in cutaneous immunity. This review summarizes the current understanding of the role of Bregs in skin immunity in health and pathology, such as diabetes, psoriasis, systemic sclerosis, cutaneous lupus erythematosus, cutaneous hypersensitivity, pemphigus, and dermatomyositis. We discuss the mechanisms by which Bregs maintain tissue homeostasis in the wound microenvironment through the promotion of angiogenesis, suppression of effector cells, and induction of regulatory immune cells. We also mention the potential clinical applications of Bregs in promoting wound healing, such as the use of adoptive Breg transfer.

Zou H., Yin Y., Xiong K., Luo X., Sun Z., Mao B., Xie Q., Tan M., Kong R.

Background Abnormal mitochondrial pyruvate carrier 1 (MPC1) expression plays a key role in tumor metabolic reprogramming and progression. Understanding its significance in non-small cell lung cancer (NSCLC) is crucial for identifying therapeutic targets. Methods TIMER 2.0 was utilized to assess the expression of MPC1 in both normal and cancer tissues in pan-cancer. Overall survival (OS) differences between high and low MPC1 expression were analyzed in NSCLC using the Cancer Genome Atlas (TCGA) datasets. We also examined the expression of MPC1 in NSCLC cell lines using western blotting and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). In addition, the tissue samples and clinical information of 80 patients with NSCLC from our hospital were collected. Immunohistochemistry (IHC) was used to assess MPC1 expression, and OS was evaluated using Kaplan-Meier curves and the log-rank test. Univariate and multivariate Cox regression analyses were conducted to evaluate the prognostic values of the clinical characteristics and MPC1expression. Results Analysis of public databases suggested that MPC1 was downregulated in NSCLC compared to that in normal lung tissue and predicted poor prognosis. In addition, the expression of MPC1 in NSCLC cell lines was lower than that in human bronchial epithelial (HBE) cells at both protein and mRNA levels. Further clinical analysis suggested that MPC1 expression was correlated with age, tumor T stage, and TNM stage. Kaplan-Meier analysis revealed that NSCLC patients with high MPC1 expression had a better prognosis, particularly in lung adenocarcinoma (LUAD), whereas no survival benefit was observed in lung squamous cell carcinoma (LUSC). Univariate and multivariate analyses suggested that MPC1 was an independent prognostic factor for patients with NSCLC. Conclusions MPC1 is poorly expressed in NSCLC, particularly in LUAD, which predicts a poor prognosis and may serve as an independent prognostic factor. Further studies on MPC1 may reveal new targets for the treatment of NSCLC.

Li Z., Wang D., Zhang W., Shi H., Zhu M.

The expression of long non-coding RNAs (LncRNAs) in peripheral blood mononuclear cell (PBMC) and its clinical relevance in colorectal cancer (CRC) remains largely uncharacterized. To address these gaps, we investigated the expression profiles of lncRNAs in PBMC from CRC and healthy controls (HC) by RNA sequencing. The expression level of differentially expressed lncRNAs (DElncRNAs) were evaluated by quantitative PCR in PBMC samples from CRC patients and HC. A total of 447 DElncRNAs were identified, with 178 elevated lncRNAs and 269 decreased lncRNAs in PBMC from CRC patients as compared with that from HC. RT-PCR results supported a significant elevation of NEAT1:11, lnc-PDZD8-1:5 and LINC00910:16 in 98 CRC patients and 82 HC. The clinical implication of NEAT1:11, lnc-PDZD8-1:5 and LINC00910:16 as CRC diagnostic biomarker were determined by receiver operating characteristic (ROC) curve, showing sensitivity 74.5% and specificity 84.5% for joint detection the three lncRNAs. Notably, NEAT1:11 was closely related with the size and extent of primary tumor, with higher relative expression of NEAT1:11 in higher T stage (P=0.0047). Moreover, NEAT1:11 was related with grade (P=0.012). Collectively, PBMC from patients with CRC show significantly variable expression profiles of lncRNAs, and detection of these differential expression lncRNAs may provide useful information for basic and clinical research.

Godbout K., Rousseau J., Tremblay J.P.

We report the first correction from prime editing a mutation in the RYR1 gene, paving the way to gene therapies for RYR1-related myopathies. The RYR1 gene codes for a calcium channel named Ryanodine receptor 1, which is expressed in skeletal muscle fibers. The failure of this channel causes muscle weakness in patients, which leads to motor disabilities. Currently, there are no effective treatments for these diseases, which are mainly caused by point mutations. Prime editing allows for the modification of precise nucleotides in the DNA. Our results showed a 59% correction rate of the T4709M mutation in the RYR1 gene in human myoblasts by RNA delivery of the prime editing components. It is to be noted that T4709M is recessive and, thus, persons having a heterozygous mutation are healthy. These results are the first demonstration that correcting mutations in the RYR1 gene is possible.

Ren X., Yang H., Nierenberg J.L., Sun Y., Chen J., Beaman C., Pham T., Nobuhara M., Takagi M.A., Narayan V., Li Y., Ziv E., Shen Y.

Summary Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.

Li Y., Zhang X., Liu Y., Lu A.

Abstract Background Allele-specific binding (ASB) events occur when transcription factors (TFs) bind more favorably to one of the two parental alleles at heterozygous single nucleotide polymorphisms (SNPs). Evidence suggests that ASB events could reveal the impact of sequence variations on TF binding and may have implications for the risk of diseases. Results Here we present ASB-analyzer, a software platform that enables the users to quickly and efficiently input raw sequencing data to generate individual reports containing the cytogenetic map of ASB SNPs and their associated phenotypes. This interactive tool thereby combines ASB SNP identification, biological annotation, motif analysis, phenotype associations and report summary in one pipeline. With this pipeline, we identified 3772 ASB SNPs from thirty GM12878 ChIP-seq datasets and demonstrated that the ASB SNPs were more likely to be enriched at important sites in TF-binding domains. Conclusions ASB-analyzer is a user-friendly tool that enables the detection, characterization and visualization of ASB SNPs. It is implemented in Python, R and bash shell and packaged in the Conda environment. It is available as an open-source tool on GitHub at https://github.com/Liying1996/ASBanalyzer.

Petrova I.O., Smirnikhina S.A.

Prime editing is a rapidly developing method of CRISPR/Cas-based genome editing. The increasing number of novel PE applications and improved versions demands constant analysis and evaluation. The present review covers the mechanism of prime editing, the optimization of the method and the possible next step in the evolution of CRISPR/Cas9-associated genome editing. The basic components of a prime editing system are a prime editor fusion protein, consisting of nickase and reverse transcriptase, and prime editing guide RNA, consisting of a protospacer, scaffold, primer binding site and reverse transcription template. Some prime editing systems include other parts, such as additional RNA molecules. All of these components were optimized to achieve better efficiency for different target organisms and/or compactization for viral delivery. Insights into prime editing mechanisms allowed us to increase the efficiency by recruiting mismatch repair inhibitors. However, the next step in prime editing evolution requires the incorporation of new mechanisms. Prime editors combined with integrases allow us to combine the precision of prime editing with the target insertion of large, several-kilobase-long DNA fragments.

Akatsu M., Ehara H., Kujirai T., Fujita R., Ito T., Osumi K., Ogasawara M., Takizawa Y., Sekine S., Kurumizaka H.

RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 (SHL(-5) and SHL(-1), respectively). In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.