NF-κB-induced R-loop accumulation and DNA damage select for nucleotide excision repair deficiencies in adult T cell leukemia

Causes and consequences of T cell DNA damage

Although DNA damage is a common cellular event, T cells experience significant genotoxic stresses because of rapid antigen-stimulated expansion and their presence in various nonlymphoid microenvironments. In addition to the well-established link between genomic instability and malignancy, recent genomic studies have uncovered a substantial mutational burden in nonmalignant T cells in both normal aging and disease contexts. Furthermore, genomic damage in T cells is accelerated in autoimmune diseases and in older individuals because of both intrinsic and extrinsic factors. This review highlights the different genotoxic stressors affecting T cells and the detrimental effects of persistent DNA damage and identifies the most critical knowledge gaps.

Viral oncogenesis in cancer: from mechanisms to therapeutics

The year 2024 marks the 60th anniversary of the discovery of the Epstein-Barr virus (EBV), the first virus confirmed to cause human cancer. Viral infections significantly contribute to the global cancer burden, with seven known Group 1 oncogenic viruses, including hepatitis B virus (HBV), human papillomavirus (HPV), EBV, Kaposi sarcoma-associated herpesvirus (KSHV), hepatitis C virus (HCV), human T-cell leukemia virus type 1 (HTLV-1), and human immunodeficiency virus (HIV). These oncogenic viruses induce cellular transformation and cancer development by altering various biological processes within host cells, particularly under immunosuppression or co-carcinogenic exposures. These viruses are primarily associated with hepatocellular carcinoma, gastric cancer, cervical cancer, nasopharyngeal carcinoma, Kaposi sarcoma, lymphoma, and adult T-cell leukemia/lymphoma. Understanding the mechanisms of viral oncogenesis is crucial for identifying and characterizing the early biological processes of virus-related cancers, providing new targets and strategies for treatment or prevention. This review first outlines the global epidemiology of virus-related tumors, milestone events in research, and the process by which oncogenic viruses infect target cells. It then focuses on the molecular mechanisms by which these viruses induce tumors directly or indirectly, including the regulation of oncogenes or tumor suppressor genes, induction of genomic instability, disruption of regular life cycle of cells, immune suppression, chronic inflammation, and inducing angiogenesis. Finally, current therapeutic strategies for virus-related tumors and recent advances in preclinical and clinical research are discussed.

Novel role of general transcript factor IIH subunit 2 (GTF2H2) in the development and sex disparity of hepatocellular carcinoma

Sex disparity is a hepatocellular carcinoma (HCC) hallmark, demonstrating aggressiveness and mortality more frequently in men than in women. However, the components of its basis remain largely unknown. It was identified in HCC frequent loss of heterozygosity of general transcript factor IIH subunit 2 (GTF2H2), a potential estrogen pathway gene. GTF2H2 functions in nucleotide excision repair (NER) and basal transcription, but the function of GTF2H2 in cancer has not been described in depth. Here, it was identified that GTF2H2 inhibited growth and invasive mobility and induced apoptosis of HCC cells, which was up-regulated by estrogen-dependent estrogen receptor alpha (ERα) signaling. Mechanistically, in vitro estrogen-treated HCC models with GTF2H2 knockdown and over-expression showed estrogen-regulated GTF2H2 promoted NER of HCC genomic DNA and inhibited cell cycle progression, and down-regulated PAM/NF-κB pathway. Xenografted HCC mice models showed higher tumor progression of HCC with low GTF2H2 expression in ovariectomized female mice or male mice, but could be rescued by GTF2H2 over-expression, which was also observed in spontaneous tumor mice models. Clinical association analysis of HCC cases showed GTF2H2 expression was higher in female HCC, with correlation positively with ERα expression. Taken together, the estrogen-regulated GTF2H2 may be involved in the development and sex disparity of HCC by maintaining NER-related genomic stability and affecting PAM/NF-κB signaling pathway.

Viral oncogenesis of δ-retroviruses, HTLV-1 and BLV, and recent advances in its diagnosis

The δ-retrovirus genus includes human T-cell leukemia viruses (HTLV-1, HTLV-2, HTLV-3), simian T-lymphotropic viruses (STLV), and bovine leukemia viruses (BLV), which establish lifelong, typically asymptomatic, infections. However, HTLV-1 and BLV can lead to leukemia or lymphoma in 2-5% of infected hosts after prolonged latency. HTLV-1, the first identified human oncogenic retrovirus, drives T-cell leukemia/lymphoma via cell-intrinsic mechanisms. Similarly, BLV induces B-cell lymphoma in cattle, sharing key genomic and disease progression features with HTLV-1. Retrovirus-induced leukemias/lymphomas arise through complex interactions of viral and host factors. This review explores current virological perspectives on δ-retroviral oncogenesis, focusing on proviral integration sites within the host genome. Additionally, we briefly compare HTLV-1 with the human immunodeficiency virus (HIV), highlighting that while HIV causes AIDS, it also induces clonal expansion of infected cells. Finally, we discuss the potential diagnostic and prognostic value of analyzing viral factors and integration sites.

Dysregulation of the tumor suppressor Menin and its target Bach2 in HTLV-1 infection

BACKGROUND

The tumor suppressor Menin, prone to mutations in both hereditary and sporadic endocrine tumors, along with its direct target Bach2, plays a crucial role in preventing autoimmunity by regulating CD4 + T cell senescence and maintaining cytokine homeostasis. Since human T-cell leukemia virus type 1 (HTLV-1) primarily infects CD4 + T cells, and its dysregulation contributes to both the hematological malignancy of adult T-cell leukemia/lymphoma (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), we examined the involvement of the Menin-Bach2 pathway in HTLV-1 infection.

METHODS

The mRNA expression of menin and bach2 in HTLV-1-infected and uninfected human T-cell lines, peripheral blood mononuclear cells (PBMCs) from patients with ATL, HAM/TSP, and asymptomatic carriers were analyzed. Additionally, interactions between Menin or Bach2 and the Tax or HBZ; the subcellular localization of these proteins; the effect of knockdown of menin, tax, and HBZ genes; and the effects of interaction inhibitors between menin and its cofactor, mixed lineage leukemia (MLL), on the proliferation of HTLV-1-infected T cells were evaluated.

RESULTS

The findings were as follows: (1) In all eight HTLV-1-infected T-cell lines tested, Menin protein was expressed, whereas Bach2 expression was absent in five of them; (2) the mRNA levels of both menin and bach2 significantly decreased in PBMCs from patients with HAM/TSP and ATL; (3) Tax and HBZ each physically interacted with both Menin and Bach2; (4) knockdown of tax, but not HBZ, downregulated Bach2, but not Menin expression in HTLV-1-transformed T-cell lines MT-2 and SLB-1; (5) knockdown of menin downregulated Bach2 expression in MT-2 but not in SLB-1; (6) A Menin-MLL interaction inhibitor suppressed cell growth of MT-2 but not in SLB-1; (7) HBZ and Menin exhibited different subcellular localization between MT-2 and SLB-1.

CONCLUSIONS

HTLV-1 infection alters the regulation of the Menin-Bach2 pathway, which controls cell proliferation. The Menin-MLL interaction inhibitor loses its effectiveness in suppressing cell proliferation when Menin loses control over Bach2 expression. Dysregulation of the Menin-Bach2 pathway may contribute to HTLV-1-associated disease pathogenesis.

Advancements and challenges of R-loops in cancers: Biological insights and future directions

R-loops involve in various biological processes under human normal physiological conditions. Disruption of R-loops can lead to disease onset and affect the progression of illnesses, particularly in cancers. Herein, we summarized and discussed the regulative networks, phenotypes and future directions of R-loops in cancers. In this review, we highlighted the following insights: (1) R-loops significantly influence cancer development, progression and treatment efficiency by regulating key genes, such as PARPs, BRCA1/2, sex hormone receptors, DHX9, and TOP1. (2) Currently, the ATM, ATR, cGAS/STING, and noncanonical pathways are the main pathways that involve in the regulatory network of R-loops in cancer. (3) Cancer biology can be modulated by R-loops-regulated phenotypes, including RNA methylation, DNA and histone methylation, oxidative stress, immune and inflammation regulation, and senescence. (4) Regulation of R-loops induces kinds of drug resistance in various cancers, suggesting that targeting R-loops maybe a promising way to overcome treatment resistance. (5) The role of R-loops in tumorigenesis remains controversial, and senescence may be a crucial research direction to unravel the mechanism of R-loop-induced tumorigenesis. Looking forward, further studies are needed to elucidate the specific mechanisms of R-loops in cancer, laying the groundwork for preclinical and clinical research.

Dynamic Roles of RNA and RNA Epigenetics in HTLV-1 Biology

Since the discovery of RNA in the early 1900s, scientific understanding of RNA form and function has evolved beyond protein coding. Viruses, particularly retroviruses like human T-cell leukemia virus type 1 (HTLV-1), rely heavily on RNA and RNA post-transcriptional modifications to regulate the viral lifecycle, pathogenesis, and evasion of host immune responses. With the emergence of new sequencing technologies in the last decade, our ability to dissect the intricacies of RNA has flourished. The ability to study RNA epigenetic modifications and splice variants has become more feasible with the recent development of third-generation sequencing technologies, such as Oxford nanopore sequencing. This review will highlight the dynamic roles of known RNA and post-transcriptional RNA epigenetic modifications within HTLV-1 biology, including viral hbz, long noncoding RNAs, microRNAs (miRNAs), transfer RNAs (tRNAs), R-loops, N6-methyladenosine (m6A) modifications, and RNA-based therapeutics and vaccines.

Roles of chromatin and genome instability in cellular senescence and their relevance to ageing and related diseases

Ageing is a complex biological process in which a gradual decline in physiological fitness increases susceptibility to diseases such as neurodegenerative disorders and cancer. Cellular senescence, a state of irreversible cell-growth arrest accompanied by functional deterioration, has emerged as a pivotal driver of ageing. In this Review, we discuss how heterochromatin loss, telomere attrition and DNA damage contribute to cellular senescence, ageing and age-related diseases by eliciting genome instability, innate immunity and inflammation. We also discuss how emerging therapeutic strategies could restore heterochromatin stability, maintain telomere integrity and boost the DNA repair capacity, and thus counteract cellular senescence and ageing-associated pathologies. Finally, we outline current research challenges and future directions aimed at better comprehending and delaying ageing.

A Novel Tax-Responsive Reporter T-Cell Line to Analyze Infection of HTLV-1

Human T-cell leukemia virus type 1 (HTLV-1) infects CD4+ T-cells through close cell-cell contacts. The viral Tax-1 (Tax) protein regulates transcription by transactivating the HTLV-1 U3R promoter in the 5' long terminal repeat of the integrated provirus. Here, we generated a clonal Tax-responsive T-cell line to track HTLV-1 infection at the single-cell level using flow cytometry, bypassing intracellular viral protein staining. Jurkat T-cells stably transduced with the SMPU vector carrying green fluorescent protein (GFP) under control of 18 × 21 bp Tax-responsive element repeats of the U3R were evaluated. Among 40 clones analyzed for Tax responsiveness, the top two were characterized. Upon overexpression of Tax, over 40% of the cells showed GFP positivity, and approximately 90% of the Tax-positive cells were GFP-positive, indicating efficient reporter activity. However, with CREB-deficient Tax mutant M47, both total GFP-positive cell counts and those within the Tax-positive group significantly decreased. Co-culture with chronically HTLV-1-infected MT-2 or C91-PL cells led to an average of 0.9% or 2.4% GFP-positive cells, respectively, confirming the suitability to monitor HTLV-1 transmission and that HTLV-1 infection is very low. Thus, the novel Tax-responsive reporter T-cell line is a suitable tool to monitor infection of HTLV-1 on the single-cell level.

Senataxin Attenuates DNA Damage Response Activation and Suppresses Senescence

Oxidative stress, driven by reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), induces DNA double-strand breaks (DSBs) that compromise genomic integrity. The DNA Damage Response (DDR), primarily mediated by ATM and ATR kinases, is crucial for recognizing and repairing DSBs. Senataxin (SETX), a DNA/RNA helicase, is critical in resolving R-loops, with mutations in SETX associated with neurodegenerative diseases. This study uncovers a novel function of senataxin in modulating DDR and its impact on cellular senescence. Senataxin is shown to be crucial not only for DSB repair but also for determining cell fate under oxidative stress. SETX knockout cells show impaired DSB repair and prolonged ATM/ATR signaling detected by Western blotting, leading to increased senescence, as indicated by elevated β-galactosidase activity following H2O2 exposure and I-PpoI-induced DSBs. Wild-type cells exhibit higher apoptosis levels compared to SETX knockout cells under H2O2 treatment, suggesting that senataxin promotes apoptosis over senescence in oxidative stress. This indicates that senataxin plays a protective role against the accumulation of senescent cells, potentially mitigating age-related cellular decline and neurodegenerative disease progression. These findings highlight senataxin as a critical mediator in DDR pathways and a potential therapeutic target for conditions where cellular senescence contributes to disease pathology.

DNA damage response defects in hematologic malignancies: mechanistic insights and therapeutic strategies

ABSTRACT

The DNA damage response (DDR) encompasses the detection and repair of DNA lesions and is fundamental to the maintenance of genome integrity. Germ line DDR alterations underlie hereditary chromosome instability syndromes by promoting the acquisition of pathogenic structural variants in hematopoietic cells, resulting in increased predisposition to hematologic malignancies. Also frequent in hematologic malignancies are somatic mutations of DDR genes, typically arising from replication stress triggered by oncogene activation or deregulated tumor proliferation that provides a selective pressure for DDR loss. These defects impair homology-directed DNA repair or replication stress response, leading to an excessive reliance on error-prone DNA repair mechanisms that results in genomic instability and tumor progression. In hematologic malignancies, loss-of-function DDR alterations confer clonal growth advantage and adverse prognostic impact but may also provide therapeutic opportunities. Selective targeting of functional dependencies arising from these defects could achieve synthetic lethality, a therapeutic concept exemplified by inhibition of poly-(adenosine 5'-diphosphate ribose) polymerase or the ataxia telangiectasia and Rad 3 related-CHK1-WEE1 axis in malignancies harboring the BRCAness phenotype or genetic defects that increase replication stress. Furthermore, the role of DDR defects as a source of tumor immunogenicity, as well as their impact on the cross talk between DDR, inflammation, and tumor immunity are increasingly recognized, thus providing rationale for combining DDR modulation with immune modulation. The nature of the DDR-immune interface and the cellular vulnerabilities conferred by DDR defects may nonetheless be disease-specific and remain incompletely understood in many hematologic malignancies. Their comprehensive elucidation will be critical for optimizing therapeutic strategies to target DDR defects in these diseases.

DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells

Epithelial barrier dysfunction and crypt destruction are hallmarks of inflammatory bowel disease (IBD). Intestinal stem cells (ISCs) residing in the crypts play a crucial role in the continuous self-renewal and rapid recovery of intestinal epithelial cells (IECs). However, how ISCs are dysregulated in IBD remains poorly understood. Here, we observe reduced DHX9 protein levels in IBD patients, and mice with conditional DHX9 depletion in the intestinal epithelium (Dhx9ΔIEC) exhibit an increased susceptibility to experimental colitis. Notably, Dhx9ΔIEC mice display a significant reduction in the numbers of ISCs and Paneth cells. Further investigation using ISC-specific or Paneth cell-specific Dhx9-deficient mice demonstrates the involvement of ISC-expressed DHX9 in maintaining epithelial homeostasis. Mechanistically, DHX9 deficiency leads to abnormal R-loop accumulation, resulting in genomic instability and the cGAS-STING-mediated inflammatory response, which together impair ISC function and contribute to the pathogenesis of IBD. Collectively, our findings highlight R-loop-mediated genomic instability in ISCs as a risk factor in IBD.

HTLV-1 Tax Tug-of-War: Cellular Senescence and Death or Cellular Transformation

Human T cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with a lymphoproliferative disease known as adult T cell leukemia/lymphoma (ATLL). HTLV-1 infection efficiently transforms human T cells in vivo and in vitro. The virus does not transduce a proto-oncogene, nor does it integrate into tumor-promoting genomic sites. Instead, HTLV-1 uses a random mutagenesis model, resulting in cellular transformation. Expression of the viral protein Tax is critical for the immortalization of infected cells by targeting specific cellular signaling pathways. However, Tax is highly immunogenic and represents the main target for the elimination of virally infected cells by host cytotoxic T cells (CTLs). In addition, Tax expression in naïve cells induces pro-apoptotic signals and has been associated with the induction of non-replicative cellular senescence. This review will explore these conundrums and discuss the mechanisms used by the Tax viral oncoprotein to influence life-and-death cellular decisions and affect HTLV-1 pathogenesis.

'From R-lupus to cancer': Reviewing the role of R-loops in innate immune responses

Cells possess an inherent and evolutionarily conserved ability to detect and respond to the presence of foreign and pathological 'self' nucleic acids. The result is the stimulation of innate immune responses, signalling to the host immune system that defence mechanisms are necessary to protect the organism. To date, there is a vast body of literature describing innate immune responses to various nucleic acid species, including dsDNA, ssDNA and ssRNA etc., however, there is limited information available on responses to R-loops. R-loops are 3-stranded nucleic acid structures that form during transcription, upon DNA damage and in various other settings. Emerging evidence suggests that innate immune responses may also exist for the detection of R-loop related nucleic acid structures, implicating R-loops as drivers of inflammatory states. In this review, we aim to summarise the evidence indicating that R-loops are immunogenic species that can trigger innate immune responses in physiological and pathological settings and discuss the implications of this in the study of various diseases and therapeutic development.

Simulating Space Conditions Evokes Different DNA Damage Responses in Immature and Mature Cells of the Human Hematopoietic System

The impact of space radiation and microgravity on DNA damage responses has been discussed controversially, largely due to the variety of model systems engaged. Here, we performed side-by-side analyses of human hematopoietic stem/progenitor cells (HSPC) and peripheral blood lymphocytes (PBL) cultivated in a 2D clinostat to simulate microgravity before, during and after photon and particle irradiation. We demonstrate that simulated microgravity (SMG) accelerates the early phase of non-homologous end joining (NHEJ)-mediated repair of simple, X-ray-induced DNA double-strand breaks (DSBs) in PBL, while repair kinetics in HSPC remained unaltered. Repair acceleration was lost with increasing LET of ion exposures, which increases the complexity of DSBs, precluding NHEJ and requiring end resection for successful repair. Such cell-type specific effect of SMG on DSB repair was dependent on the NF-кB pathway pre-activated in PBL but not HSPC. Already under unperturbed growth conditions HSPC and PBL suffered from SMG-induced replication stress associated with accumulation of single-stranded DNA and DSBs, respectively. We conclude that in PBL, SMG-induced DSBs promote repair of radiation-induced damage in an adaptive-like response. HSPC feature SMG-induced single-stranded DNA and FANCD2 foci, i.e., markers of persistent replication stress and senescence that may contribute to a premature decline of the immune system in space.

DTSEA: A network-based drug target set enrichment analysis method for drug repurposing against COVID-19

The Coronavirus Disease 2019 (COVID-19) pandemic is still wreaking havoc worldwide. Therefore, the urgent need for efficient treatments pushes researchers and clinicians into screening effective drugs. Drug repurposing may be a promising and time-saving strategy to identify potential drugs against this disease. Here, we developed a novel computational approach, named Drug Target Set Enrichment Analysis (DTSEA), to identify potent drugs against COVID-19. DTSEA first mapped the disease-related genes into a gene functional interaction network, and then it used a network propagation algorithm to rank all genes in the network by calculating the network proximity of genes to disease-related genes. Finally, an enrichment analysis was performed on drug target sets to prioritize disease-candidate drugs. It was shown that the top three drugs predicted by DTSEA, including Ataluren, Carfilzomib, and Aripiprazole, were significantly enriched in the immune response pathways indicating the potential for use as promising COVID-19 inhibitors. In addition to these drugs, DTSEA also identified several drugs (such as Remdesivir and Olumiant), which have obtained emergency use authorization (EUA) for COVID-19. These results indicated that DTSEA could effectively identify the candidate drugs for COVID-19, which will help to accelerate the development of drugs for COVID-19. We then performed several validations to ensure the reliability and validity of DTSEA, including topological analysis, robustness analysis, and prediction consistency. Collectively, DTSEA successfully predicted candidate drugs against COVID-19 with high accuracy and reliability, thus making it a formidable tool to identify potential drugs for a specific disease and facilitate further investigation.

HTLV-1 persistence and the oncogenesis of adult T-cell leukemia/lymphoma

Human T-cell leukemia virus type 1 (HTLV-1), also known as human T-lymphotropic virus type 1, causes the aggressive malignancy known as adult T-cell leukemia/lymphoma (ATL) in 5% of infected people and a chronic progressive inflammatory disease of the central nervous system, HTLV-1-associated myelopathy, in ∼0.3% to 4% of them, varying between regions where it is endemic. Reliable treatments are lacking for both conditions, although there have been promising recent advances in the prevention and treatment of ATL. Because ATL typically develops after several decades of infection, it is necessary to understand how the virus persists in the host despite a strong immune response, and how this persistence results in oncogenesis.

Clinical and Mechanistic Implications of R-Loops in Human Leukemias

Genetic mutations or environmental agents are major contributors to leukemia and are associated with genomic instability. R-loops are three-stranded nucleic acid structures consisting of an RNA-DNA hybrid and a non-template single-stranded DNA. These structures regulate various cellular processes, including transcription, replication, and DSB repair. However, unregulated R-loop formation can cause DNA damage and genomic instability, which are potential drivers of cancer including leukemia. In this review, we discuss the current understanding of aberrant R-loop formation and how it influences genomic instability and leukemia development. We also consider the possibility of R-loops as therapeutic targets for cancer treatment.

Interactomics: Dozens of Viruses, Co-evolving With Humans, Including the Influenza A Virus, may Actively Distort Human Aging

Some viruses (e.g., human immunodeficiency virus 1 and severe acute respiratory syndrome coronavirus 2) have been experimentally proposed to accelerate features of human aging and of cellular senescence. These observations, along with evolutionary considerations on viral fitness, raised the more general puzzling hypothesis that, beyond documented sources in human genetics, aging in our species may also depend on virally encoded interactions distorting our aging to the benefits of diverse viruses. Accordingly, we designed systematic network-based analyses of the human and viral protein interactomes, which unraveled dozens of viruses encoding proteins experimentally demonstrated to interact with proteins from pathways associated with human aging, including cellular senescence. We further corroborated our predictions that specific viruses interfere with human aging using published experimental evidence and transcriptomic data; identifying influenza A virus (subtype H1N1) as a major candidate age distorter, notably through manipulation of cellular senescence. By providing original evidence that viruses may convergently contribute to the evolution of numerous age-associated pathways through co-evolution, our network-based and bipartite network-based methodologies support an ecosystemic study of aging, also searching for genetic causes of aging outside a focal aging species. Our findings, predicting age distorters and targets for anti-aging therapies among human viruses, could have fundamental and practical implications for evolutionary biology, aging study, virology, medicine, and demography.

R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response

R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.

DNA damage to bone marrow stromal cells by antileukemia drugs induces chemoresistance in acute myeloid leukemia via paracrine FGF10-FGFR2 signaling

Chemoresistance remains a major challenge in the current treatment of acute myeloid leukemia (AML). The bone marrow microenvironment (BMM) plays a complex role in protecting leukemia cells from chemotherapeutics, and the mechanisms involved are not fully understood. Antileukemia drugs kill AML cells directly but also damage the BMM. Here, we determined antileukemia drugs induce DNA damage in bone marrow stromal cells (BMSCs), resulting in resistance of AML cell lines to adriamycin and idarubicin killing. Damaged BMSCs induced an inflammatory microenvironment through NF-κB; suppressing NF-κB with small molecule inhibitor Bay11-7082 attenuated the prosurvival effects of BMSCs on AML cell lines. Furthermore, we used an ex vivo functional screen of 507 chemokines and cytokines to identify 44 proteins secreted from damaged BMSCs. Fibroblast growth factor-10 (FGF10) was most strongly associated with chemoresistance in AML cell lines. Additionally, expression of FGF10 and its receptors, FGFR1 and FGFR2, was increased in AML patients after chemotherapy. FGFR1 and FGFR2 were also widely expressed by AML cell lines. FGF10-induced FGFR2 activation in AML cell lines operates by increasing P38 MAPK, AKT, ERK1/2, and STAT3 phosphorylation. FGFR2 inhibition with small molecules or gene silencing of FGFR2 inhibited proliferation and reverses drug resistance of AML cells by inhibiting P38 MAPK, AKT, and ERK1/2 signaling pathways. Finally, release of FGF10 was mediated by β-catenin signaling in damaged BMSCs. Our data indicate FGF10-FGFR2 signaling acts as an effector of damaged BMSC-mediated chemoresistance in AML cells, and FGFR2 inhibition can reverse stromal protection and AML cell chemoresistance in the BMM.

Time-course of host cell transcription during the HTLV-1 transcriptional burst

The human T-cell leukemia virus type 1 (HTLV-1) transactivator protein Tax has pleiotropic functions in the host cell affecting cell-cycle regulation, DNA damage response pathways and apoptosis. These actions of Tax have been implicated in the persistence and pathogenesis of HTLV-1-infected cells. It is now known that tax expression occurs in transcriptional bursts of the proviral plus-strand, but the effects of the burst on host transcription are not fully understood. We carried out RNA sequencing of two naturally-infected T-cell clones transduced with a Tax-responsive Timer protein, which undergoes a time-dependent shift in fluorescence emission, to study transcriptional changes during successive phases of the HTLV-1 plus-strand burst. We found that the transcriptional regulation of genes involved in the NF-κB pathway, cell-cycle regulation, DNA damage response and apoptosis inhibition were immediate effects accompanying the plus-strand burst, and are limited to the duration of the burst. The results distinguish between the immediate and delayed effects of HTLV-1 reactivation on host transcription, and between clone-specific effects and those observed in both clones. The major transcriptional changes in the infected host T-cells observed here, including NF-κB, are transient, suggesting that these pathways are not persistently activated at high levels in HTLV-1-infected cells. The two clones diverged strongly in their expression of genes regulating the cell cycle. Up-regulation of senescence markers was a delayed effect of the proviral plus-strand burst and the up-regulation of some pro-apoptotic genes outlasted the burst. We found that activation of the aryl hydrocarbon receptor (AhR) pathway enhanced and prolonged the proviral burst, but did not increase the rate of reactivation. Our results also suggest that sustained plus-strand expression is detrimental to the survival of infected cells.

Walking a tightrope: The complex balancing act of R-loops in genome stability

Although transcription is an essential cellular process, it is paradoxically also a well-recognized cause of genomic instability. R-loops, non-B DNA structures formed when nascent RNA hybridizes to DNA to displace the non-template strand as single-stranded DNA (ssDNA), are partially responsible for this instability. Yet, recent work has begun to elucidate regulatory roles for R-loops in maintaining the genome. In this review, we discuss the cellular contexts in which R-loops contribute to genomic instability, particularly during DNA replication and double-strand break (DSB) repair. We also summarize the evidence that R-loops participate as an intermediate during repair and may influence pathway choice to preserve genomic integrity. Finally, we discuss the immunogenic potential of R-loops and highlight their links to disease should they become pathogenic.

NF-κB-Induced R-Loops and Genomic Instability in HTLV-1-Infected and Adult T-Cell Leukemia Cells

Human T-cell leukemia virus type 1 (HTLV-1) is a human delta retrovirus that causes adult T-cell leukemia/lymphoma (ATL) in 3–5% of the infected population after decades of clinical latency. HTLV-1 Tax is a potent activator of IKK/NF-κB and a clastogen. While NF-κB activities are associated with cell survival and proliferation, constitutive NF-κB activation (NF-κB hyperactivation) by Tax leads to senescence and oncogenesis. Until recently, the mechanisms underlying the DNA damage and senescence induced by Tax and NF-κB were unknown. Current data indicate that NF-κB hyperactivation by Tax causes the accumulation of a nucleic acid structure known as an R-loop. R-loop excision by the transcription-coupled nucleotide excision repair (TC-NER) endonucleases, Xeroderma pigmentosum F (XPF), and XPG, in turn, promotes DNA double-strand breaks (DSBs). NF-κB blockade prevents Tax-induced R-loop accumulation, DNA damage, and senescence. In the same vein, the silencing of XPF and XPG mitigates Tax senescence, while deficiency in either or both frequently occurs in ATL of all types. ATL cells maintain constitutively active NF-κB, accumulate R-loops, and resist Tax-induced senescence. These results suggest that ATL cells must have acquired adaptive changes to prevent senescence and benefit from the survival and proliferation advantages conferred by Tax and NF-κB. In this review, the roles of R-loops in Tax- and NF-κB-induced DNA DSBs, senescence, and ATL development, and the epigenetic and genetic alterations that arise in ATL to reduce R-loop-associated DNA damage and avert senescence will be discussed.

XPG: a multitasking genome caretaker

The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.

Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma

Simple Summary

Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma.

Abstract

Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.

Molecular identification of an immunity- and Ferroptosis-related gene signature in non-small cell lung Cancer

Background

Lung cancer is one of the dominant causes of cancer-related deaths worldwide. Ferroptosis, an iron-dependent form of programmed cell death, plays a key role in cancer immunotherapy. However, the role of immunity- and ferroptosis-related gene signatures in non-small cell lung cancer (NSCLC) remain unclear.

Methods

RNA-seq data and clinical information pertaining to NSCLC were collected from The Cancer Genome Atlas dataset. Univariate and multivariate Cox regression analyses were performed to identify ferroptosis-related genes. A receiver operating characteristic (ROC) model was established for sensitivity and specificity evaluation. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to explore the function roles of differentially expressed genes.

Results

A signature composed of five ferroptosis-related genes was established to stratify patients into high- and low-risk subgroups. In comparison with patients in the low-risk group, those in the high-risk one showed significantly poor overall survival in the training and validation cohorts (P < 0.05). Multivariate Cox regression analysis indicated risk score to be an independent predictor of overall survival (P < 0.01). Further, the 1-, 2-, and 3-year ROCs were 0.623 vs. 0.792 vs. 0.635, 0.644 vs. 0.792 vs. 0.634, and 0.631 vs. 0.641 vs. 0.666 in one training and two validation cohorts, respectively. Functional analysis revealed that immune-related pathways were enriched and associated with abnormal activation of immune cells.

Conclusions

We identified five immunity- and ferroptosis-related genes that may be involved in NSCLC progression and prognosis. Targeting ferroptosis-related genes seems to be an alternative to clinical therapy for NSCLC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08541-w.

miRNA-31 increases radiosensitivity through targeting STK40 in colorectal cancer cells

Objective

To propose and verify that miRNA‐31 increases the radiosensitivity of colorectal cancer and explore its potential mechanism.

Method

A bioinformatics analysis was performed to confirm that the expression of miRNA‐31 was higher in colorectal cancer than in normal colorectal tissue. The expression of miRNA‐31 was detected to verify the change in its expression in a radiotherapy‐resistant cell line. Methylation was detected to explore the cause of the decrease in miRNA‐31 expression. Overexpression or inhibition of miRNA‐31 further confirmed the change in its expression in colorectal cancer cell lines. Bioinformatics methods were used to screen the downstream target genes and for experimental verification. A luciferase assay was performed to determine the miRNA‐31 binding site in STK40. Overexpression or inhibition of STK40 in colorectal cancer cell lines further confirmed the change in STK40 expression in vitro.

Results

The bioinformatics results showed higher expression of miRNA‐31 in tumors than in normal tissue, and miRNA‐31 mainly participated in the pathway related to cell replication. Next, we observed the same phenomenon: miRNA‐31 was expressed at higher levels in colorectal tumors than in normal colorectal tissue and its expression decreased in radiation‐resistant cell lines after radiation, implying that miRNA‐31 increased the radiosensitivity of colorectal cancer cell lines. No significant change in upstream methylation was observed. miRNA‐31 regulated the radiosensitivity of colorectal cancer cell lines by inhibiting STK40. Notably, miRNA‐31 played a role by binding to the 3′ untranslated region of SK40. STK40 negatively regulated the radiosensitivity of colorectal cancer cells.

Conclusions

miRNA‐31 increases the radiosensitivity of colorectal cancer cells by targeting STK40; miRNA‐31 and STK40 are expected to become potential biomarkers for increasing the sensitivity of tumor radiotherapy in clinical treatment.