The stress specific impact of ALKBH1 on tRNA cleavage and tiRNA generation

tRNA modifications: greasing the wheels of translation and beyond

Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.

Queuosine tRNA Modification: Connecting the Microbiome to the Translatome

Transfer RNA (tRNA) modifications play an important role in regulating mRNA translation at the codon level. tRNA modifications can influence codon selection and optimality, thus shifting translation toward specific sets of mRNAs in a dynamic manner. Queuosine (Q) is a tRNA modification occurring at the wobble position. In eukaryotes, queuosine is synthesized by the tRNA-guanine trans-glycosylase (TGT) complex, which incorporates the nucleobase queuine (or Qbase) into guanine of the GUN anticodons. Queuine is sourced from gut bacteria and dietary intake. Q was recently shown to be critical for cellular responses to oxidative and mitochondrial stresses, as well as its potential role in neurodegenerative diseases and brain health. These unique features of Q provide an interesting insight into the regulation of mRNA translation by gut bacteria, and the potential health implications. In this review, Q biology is examined in the light of recent literature and nearly 4 decades of research. Q's role in neuropsychiatric diseases and cancer is highlighted and discussed. Given the recent interest in Q, and the new findings, more research is needed to fully comprehend its biological function and disease relevance, especially in neurobiology.

Decoding Codon Bias: The Role of tRNA Modifications in Tissue-Specific Translation

The tRNA epitranscriptome has been recognized as an important player in mRNA translation regulation. Our knowledge of the role of the tRNA epitranscriptome in fine-tuning translation via codon decoding at tissue or cell levels remains incomplete. We analyzed tRNA expression and modifications as well as codon optimality across seven mouse tissues. Our analysis revealed distinct enrichment patterns of tRNA modifications in different tissues. Queuosine (Q) tRNA modification was most enriched in the brain compared to other tissues, while mitochondrial tRNA modifications and tRNA expression were highest in the heart. Using this observation, we synthesized, and delivered in vivo, codon-mutated EGFP for Q-codons, where the C-ending Q-codons were replaced with U-ending codons. The protein levels of mutant EGFP were downregulated in liver, which is poor in Q, while in brain EGFP, levels did not change. These data show that understanding tRNA modification enrichments across tissues is not only essential for understanding codon decoding and bias but can also be utilized for optimizing gene and mRNA therapeutics to be more tissue-, cell-, or condition-specific.

tRNA-derived small RNAs: their role in the mechanisms, biomarkers, and therapeutic strategies of colorectal cancer

Colorectal cancer (CRC) is the third most prevalent malignancy and the second leading cause of cancer-related mortality worldwide, with an increasing shift towards younger age of onset. In recent years, there has been increasing recognition of the significance of tRNA-derived small RNAs (tsRNAs), encompassing tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs). Their involvement in regulating translation, gene expression, reverse transcription, and epigenetics has gradually come to light. Emerging research has revealed dysregulation of tsRNAs in CRC, implicating their role in CRC initiation and progression, and highlighting their potential in early diagnosis, prognosis, and therapeutic strategies. Although the clinical application of tsRNAs is still in its early stages, recent findings highlight a close relationship between the biogenesis and function of tsRNAs, tRNA chemical modifications, and the tumor immune microenvironment (TIME). Additionally, similar to other small RNAs, tsRNAs can be effectively delivered via nanoparticles (NPs). Consequently, future research should focus on elucidating the clinical significance of tsRNAs concerning base modifications, TIME regulation, cancer immunotherapy, and NPs delivery systems to facilitate their clinical translation.

ALKBH1: emerging biomarker and therapeutic target for cancer treatment

As neoplastic cells proliferate, disseminate, and infiltrate, they undergo substantial alterations in their epigenetic configuration. Among the pivotal enzymes implicated in this phenomenon is the AlkB family of demethylases, notably AlkB homolog 1 (ALKBH1), which demonstrates conspicuous upregulation across various malignancies. The heightened expression of ALKBH1 renders it a compelling candidate for the development of multifaceted anticancer modalities. Despite the commendable progress achieved by investigators in elucidating the perturbations associated with ALKBH1 in malignant tissues, a comprehensive mechanism remains elusive. The present study endeavors to address this lacuna by synthesizing recent advancements pertaining to ALKBH1's involvement in oncogenesis over the preceding decade. Therefore, this research not only furnishes novel insights but also establishes a foundation for prospective initiatives aimed at cancer prophylaxis and therapeutics that exploit epigenetic regulatory mechanisms.

Transfer RNAs and transfer RNA-derived small RNAs in cerebrovascular diseases

This article explores the important functions of transfer RNA and - transfer RNA derived small RNAs (tsRNAs) in cellular processes and disease pathogenesis, with a particular emphasis on their involvement in cerebrovascular disorders. It discusses the biogenesis and structure of tsRNAs, including types such as tRNA halves and tRNA-derived fragments, and their functional significance in gene regulation, stress response, and cell signaling pathways. The importance of tsRNAs in neurodegenerative diseases, cancer, and cardiovascular diseases has already been highlighted, while their role in cerebrovascular diseases is in early phase of exploration. This paper presents the latest advancements in the field of tsRNAs in cerebrovascular conditions, such as ischemic stroke, intracerebral hemorrhage, and moyamoya disease. Furthermore, revealing the aptitude of tsRNAs as biomarkers for the prediction of cerebrovascular diseases and as targets for therapeutic intervention. It provides insights into the role of tsRNAs in these conditions and proposes directions for future research.

tRNA-derived small RNAs (tsRNAs): establishing their dominance in the regulation of human cancer

The main function of transfer RNAs (tRNAs) is to carry amino acids into the ribosome and synthesize proteins under the guidance of messenger RNAs (mRNAs). In addition to this, it has been observed that tRNAs undergo precise cleavage at specific loci, giving rise to an extensive array of distinct small RNAs, termed tRNA-derived small RNAs (tsRNAs). Existing studies have shown that tsRNAs are widely present across various organisms and comprehensively regulate gene expression, aberrant expression of tsRNAs is inextricably linked to tumorigenesis and development, thus, a systematic understanding of tsRNAs is necessary. This review aims to comprehensively delineate the genesis and expression patterns of tsRNAs, elucidate their diverse functions and emphasize their prospective clinical application as biomarkers and targets for therapy. It is noteworthy that we innovatively address the roles played by tsRNAs in human cancers at the level of the hallmarks of tumorigenesis proposed by Hanahan in anticipation of a broad understanding of tsRNAs and to guide the treatment of tumors.

Clinician's Guide to Epitranscriptomics: An Example of N1-Methyladenosine (m1A) RNA Modification and Cancer

Epitranscriptomics is the study of modifications of RNA molecules by small molecular residues, such as the methyl (-CH3) group. These modifications are inheritable and reversible. A specific group of enzymes called "writers" introduces the change to the RNA; "erasers" delete it, while "readers" stimulate a downstream effect. Epitranscriptomic changes are present in every type of organism from single-celled ones to plants and animals and are a key to normal development as well as pathologic processes. Oncology is a fast-paced field, where a better understanding of tumor biology and (epi)genetics is necessary to provide new therapeutic targets and better clinical outcomes. Recently, changes to the epitranscriptome have been shown to be drivers of tumorigenesis, biomarkers, and means of predicting outcomes, as well as potential therapeutic targets. In this review, we aimed to give a concise overview of epitranscriptomics in the context of neoplastic disease with a focus on N1-methyladenosine (m1A) modification, in layman's terms, to bring closer this omics to clinicians and their future clinical practice.

tRNA modifications and tRNA-derived small RNAs: new insights of tRNA in human disease

tRNAs are codon decoders that convert the transcriptome into the proteome. The field of tRNA research is excited by the increasing discovery of specific tRNA modifications that are installed at specific, evolutionarily conserved positions by a set of specialized tRNA-modifying enzymes and the biogenesis of tRNA-derived regulatory fragments (tsRNAs) which exhibit copious activities through multiple mechanisms. Dysregulation of tRNA modification usually has pathological consequences, a phenomenon referred to as "tRNA modopathy". Current evidence suggests that certain tRNA-modifying enzymes and tsRNAs may serve as promising diagnostic biomarkers and therapeutic targets, particularly for chemoresistant cancers. In this review, we discuss the latest discoveries that elucidate the molecular mechanisms underlying the functions of clinically relevant tRNA modifications and tsRNAs, with a focus on malignancies. We also discuss the therapeutic potential of tRNA/tsRNA-based therapies, aiming to provide insights for the development of innovative therapeutic strategies. Further efforts to unravel the complexities inherent in tRNA biology hold the promise of yielding better biomarkers for the diagnosis and prognosis of diseases, thereby advancing the development of precision medicine for health improvement.

tsRNA modifications: An emerging layer of biological regulation in disease

BACKGROUND

Transfer RNA (tRNA)-derived small RNA (tsRNA) represents an important and increasingly valued type of small non-coding RNA (sncRNA). The investigation of tRNA and tsRNA modification crosswalks has not only provided novel insights into the information and functions of tsRNA, but has also expanded the diversity and complexity of the tsRNA biological regulation network.

AIM OF REVIEW

Comparing with other sncRNAs, tsRNA biogenesis show obvious correlation with RNA modifications from mature tRNA and harbor various tRNA modifications. In this review, we aim to present the current aspect of tsRNA modifications and that modified tsRNA shape different regulatory mechanisms in physiological and pathological processes.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Strategies for studying tsRNA mechanisms include its specific generation and functional effects induced by sequence/RNA modification/secondary structure. tsRNAs could harbor more than one tRNA modifications such as 5-methylcytosine (m5C), N1-methyladenosine (m1A), pseudouridine (Ψ) and N7-methylguanosine (m7G). This review consolidates the current knowledge of tRNA modification regulating tsRNA biogenesis, outlines the functional roles of various modified tsRNA and highlights their specific contributions in various disease pathogenesis. Therefore, the improvement of tsRNA modification detection technology and the introduction of experimental methods of tsRNA modification are conducive to further broadening the understanding of tsRNA function at the level of RNA modification.

Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets

High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.

A Novel tsRNA, m7G-3' tiRNA LysTTT, Promotes Bladder Cancer Malignancy Via Regulating ANXA2 Phosphorylation

Emerging evidence indicates that transfer RNA (tRNA)-derived small RNAs (tsRNAs), originated from tRNA with high abundance RNA modifications, play an important role in many complex physiological and pathological processes. However, the biological functions and regulatory mechanisms of modified tsRNAs in cancer remain poorly understood. Here, it is screened for and confirmed the presence of a novel m7G-modified tsRNA, m7G-3'-tiRNA LysTTT (mtiRL), in a variety of chemical carcinogenesis models by combining small RNA sequencing with an m7G small RNA-modified chip. Moreover, it is found that mtiRL, catalyzed by the tRNA m7G-modifying enzyme mettl1, promotes bladder cancer (BC) malignancy in vitro and in vivo. Mechanistically, mtiRL is found to specifically bind the oncoprotein Annexin A2 (ANXA2) to promote its Tyr24 phosphorylation by enhancing the interactions between ANXA2 and Yes proto-oncogene 1 (Yes1), leading to ANXA2 activation and increased p-ANXA2-Y24 nuclear localization in BC cells. Together, these findings define a critical role for mtiRL and suggest that targeting this novel m7G-modified tsRNA can be an efficient way for to treat BC.

Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies

tRNA is the RNA type that undergoes the most modifications among known RNA, and in recent years, tRNA methylation has emerged as a crucial process in regulating gene translation. Dysregulation of tRNA abundance occurs in cancer cells, along with increased expression and activity of tRNA methyltransferases to raise the level of tRNA modification and stability. This leads to hijacking of translation and synthesis of multiple proteins associated with tumor proliferation, metastasis, invasion, autophagy, chemotherapy resistance, and metabolic reprogramming. In this review, we provide an overview of current research on tRNA methylation in cancer to clarify its involvement in human malignancies and establish a theoretical framework for future therapeutic interventions targeting tRNA methylation processes.

The biological function of demethylase ALKBH1 and its role in human diseases

AlkB homolog 1 (ALKBH1) is a member of the AlkB family of dioxygenases that are dependent on Fe(II) and α-ketoglutarate. Mounting evidence demonstrates that ALKBH1 exhibits enzymatic activity against various substrates, including N6-methyladenosine (m6A), N1-methyladenosine (m1A), N3-methylcytidine (m3C), 5-methylcytosine (m5C), N6-methyladenine (N6-mA, 6mA), and H2A, indicating its dual roles in different biological processes and involvement in human diseases. Up to the present, there is ongoing debate regarding ALKBH1's enzymatic activity. In this review, we present a comprehensive summary of recent research on ALKBH1, including its substrate diversity and pathological roles in a wide range of human disorders, the underlying mechanisms of its functions, and its dysregulation. We also explored the potential of ALKBH1 as a prognostic target.

Roles and regulation of tRNA-derived small RNAs in animals

A growing class of small RNAs, known as tRNA-derived RNAs (tdRs), tRNA-derived small RNAs or tRNA-derived fragments, have long been considered mere intermediates of tRNA degradation. These small RNAs have recently been implicated in an evolutionarily conserved repertoire of biological processes. In this Review, we discuss the biogenesis and molecular functions of tdRs in mammals, including tdR-mediated gene regulation in cell metabolism, immune responses, transgenerational inheritance, development and cancer. We also discuss the accumulation of tRNA-derived stress-induced RNAs as a distinct adaptive cellular response to pathophysiological conditions. Furthermore, we highlight new conceptual advances linking RNA modifications with tdR activities and discuss challenges in studying tdR biology in health and disease.

Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers

With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.

Translational response to mitochondrial stresses is orchestrated by tRNA modifications

Mitochondrial stress and dysfunction play important roles in many pathologies. However, how cells respond to mitochondrial stress is not fully understood. Here, we examined the translational response to electron transport chain (ETC) inhibition and arsenite induced mitochondrial stresses. Our analysis revealed that during mitochondrial stress, tRNA modifications (namely f5C, hm5C, queuosine and its derivatives, and mcm5U) dynamically change to fine tune codon decoding, usage, and optimality. These changes in codon optimality drive the translation of many pathways and gene sets, such as the ATF4 pathway and selenoproteins, involved in the cellular response to mitochondrial stress. We further examined several of these modifications using targeted approaches. ALKBH1 knockout (KO) abrogated f5C and hm5C levels and led to mitochondrial dysfunction, reduced proliferation, and impacted mRNA translation rates. Our analysis revealed that tRNA queuosine (tRNA-Q) is a master regulator of the mitochondrial stress response. KO of QTRT1 or QTRT2, the enzymes responsible for tRNA-Q synthesis, led to mitochondrial dysfunction, translational dysregulation, and metabolic alterations in mitochondria-related pathways, without altering cellular proliferation. In addition, our analysis revealed that tRNA-Q loss led to a domino effect on various tRNA modifications. Some of these changes could be explained by metabolic profiling. Our analysis also revealed that utilizing serum deprivation or alteration with Queuine supplementation to study tRNA-Q or stress response can introduce various confounding factors by altering many other tRNA modifications. In summary, our data show that tRNA modifications are master regulators of the mitochondrial stress response by driving changes in codon decoding.

tRNA-derived fragments: mechanism of gene regulation and clinical application in lung cancer

Lung cancer, being the most widespread and lethal form of cancer globally, has a high incidence and mortality rate primarily attributed to challenges associated with early detection, extensive metastasis, and frequent recurrence. In the context of lung cancer development, noncoding RNA molecules have a crucial role in governing gene expression and protein synthesis. Specifically, tRNA-derived fragments (tRFs), a subset of noncoding RNAs, exert significant biological influences on cancer progression, encompassing transcription and translation processes as well as epigenetic regulation. This article primarily examines the mechanisms by which tRFs modulate gene expression and contribute to tumorigenesis in lung cancer. Furthermore, we provide a comprehensive overview of the current bioinformatics analysis of tRFs in lung cancer, with the objective of offering a systematic and efficient approach for studying the expression profiling, functional enrichment, and molecular mechanisms of tRFs in this disease. Finally, we discuss the clinical significance and potential avenues for future research on tRFs in lung cancer. This paper presents a comprehensive systematic review of the existing research findings on tRFs in lung cancer, aiming to offer improved biomarkers and drug targets for clinical management of lung cancer.

ALKBH1 rs2267755 C>T polymorphism decreases neuroblastoma risk in Chinese children

Neuroblastoma is a highly malignant extracranial solid tumor in pediatrics. ALKBH1 as a recently discovered DNA N6-methyldeoxyadenosine (6mA) demethylase closely links to tumorigenesis. Whether the ALKBH1 polymorphism contributes to neuroblastoma risk remains unclear. In the present study, we genotyped the ALKBH1 single nucleotide polymorphisms (SNPs) in 402 neuroblastoma patients and 473 healthy controls by TaqMan assay. Odds ratios (ORs) and 95% confidence intervals (CIs) were also calculated to evaluate the strength of the association. Our result exhibited that the rs2267755 C>T (CT vs. CC, adjusted OR=0.69, 95% CI=0.50-0.94, P=0.019) is significantly associated with reduced neuroblastoma risk. And its protective effect is particularly significant in children with tumors originating from the retroperitoneal. Combined genotype analysis revealed that carriers with 1-2 protective genotypes are more susceptible to neuroblastoma than those with 3-4 protective genotypes (adjusted OR=0.71, 95% CI=0.53-0.97, P=0.028). Moreover, the rs2267755 C>T is significantly associated with messenger RNA (mRNA) expression of ALKBH1 and three of its surrounding genes, including SNWQ, ADCK1, and RPL21P10. These results suggest that the rs2267755 C>T may be a genetic variant to reduce neuroblastoma risk.

tRNA renovatio: Rebirth through fragmentation

tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.

tRNA-derived RNAs: Biogenesis and roles in translational control

Transfer RNA (tRNA)-derived RNAs (tDRs) are a class of small non-coding RNAs that play important roles in different aspects of gene expression. These ubiquitous and heterogenous RNAs, which vary across different species and cell types, are proposed to regulate various biological processes. In this review, we will discuss aspects of their biogenesis, and specifically, their contribution into translational control. We will summarize diverse roles of tDRs and the molecular mechanisms underlying their functions in the regulation of protein synthesis and their impact on related events such as stress-induced translational reprogramming. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.

Small RNAs: An expanding world with therapeutic promises

Small non-coding RNAs (sncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and transfer RNA (tRNA)-derived small RNAs (tsRNAs), play essential roles in regulating various cellular and developmental processes. Over the past three decades, researchers have identified novel sncRNA species from various organisms. These molecules demonstrate dynamic expression and diverse functions, and they are subject to intricate regulation through RNA modifications in both healthy and diseased states. Notably, certain sncRNAs in gametes, particularly sperm, respond to environmental stimuli and facilitate epigenetic inheritance. Collectively, the in-depth understanding of sncRNA functions and mechanisms has accelerated the development of small RNA-based therapeutics. In this review, we present the recent advances in the field, including new sncRNA species and the regulatory influences of RNA modifications. We also discuss the current limitations and challenges associated with using small RNAs as either biomarkers or therapeutic drugs.

RNA modifications in cancer

Currently, more than 170 modifications have been identified on RNA. Among these RNA modifications, various methylations account for two-thirds of total cases and exist on almost all RNAs. Roles of RNA modifications in cancer are garnering increasing interest. The research on m6A RNA methylation in cancer is in full swing at present. However, there are still many other popular RNA modifications involved in the regulation of gene expression post-transcriptionally besides m6A RNA methylation. In this review, we focus on several important RNA modifications including m1A, m5C, m7G, 2'-O-Me, Ψ and A-to-I editing in cancer, which will provide a new perspective on tumourigenesis by peeking into the complex regulatory network of epigenetic RNA modifications, transcript processing, and protein translation.

RNA methylation and cellular response to oxidative stress-promoting anticancer agents

Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.

The role and mechanism of action of tRNA-derived fragments in the diagnosis and treatment of malignant tumors

Cancer is a leading cause of morbidity and death worldwide. While various factors are established as causing malignant tumors, the mechanisms underlying cancer development remain poorly understood. Early diagnosis and the development of effective treatments for cancer are important research topics. Transfer RNA (tRNA), the most abundant class of RNA molecules in the human transcriptome, participates in both protein synthesis and cellular metabolic processes. tRNA-derived fragments (tRFs) are produced by specific cleavage of pre-tRNA and mature tRNA molecules, which are highly conserved and occur widely in various organisms. tRFs were initially thought to be random products with no physiological function, but have been redefined as novel functional small non-coding RNA molecules that help to regulate RNA stability, modulate translation, and influence target gene expression, as well as other biological processes. There is increasing evidence supporting roles for tRFs in tumorigenesis and cancer development, including the regulation of tumor cell proliferation, invasion, migration, and drug resistance. Understanding the regulatory mechanisms by which tRFs impact these processes has potential to inform malignant tumor diagnosis and treatment. Further, tRFs are expected to become new biological markers for early diagnosis and prognosis prediction in patients with tumors, as well as a targets for precision cancer therapies. Video abstract.

Paternal methotrexate exposure affects sperm small RNA content and causes craniofacial defects in the offspring

Folate is an essential vitamin for vertebrate embryo development. Methotrexate (MTX) is a folate antagonist that is widely prescribed for autoimmune diseases, blood and solid organ malignancies, and dermatologic diseases. Although it is highly contraindicated for pregnant women, because it is associated with an increased risk of multiple birth defects, the effect of paternal MTX exposure on their offspring has been largely unexplored. Here, we found MTX treatment of adult medaka male fish (Oryzias latipes) causes cranial cartilage defects in their offspring. Small non-coding RNA (sncRNAs) sequencing in the sperm of MTX treated males identify differential expression of a subset of tRNAs, with higher abundance for specific 5' tRNA halves. Sperm RNA methylation analysis on MTX treated males shows that m5C is the most abundant and differential modification found in RNAs ranging in size from 50 to 90 nucleotides, predominantly tRNAs, and that it correlates with greater testicular Dnmt2 methyltransferase expression. Injection of sperm small RNA fractions from MTX-treated males into normal fertilized eggs generated cranial cartilage defects in the offspring. Overall, our data suggest that paternal MTX exposure alters sperm sncRNAs expression and modifications that may contribute to developmental defects in their offspring.

Elucidation of transfer RNAs as stress regulating agents and the experimental strategies to conceive the functional role of tRNA-derived fragments in plants

In plants, the transfer RNAs (tRNAs) exhibit their profound influence in orchestrating diverse physiological activities like cell growth, development, and response to several surrounding stimuli. The tRNAs, which were known to restrict their function solely in deciphering the codons, are now emerging as frontline defenders in stress biology. The plants that are constantly confronted with a huge panoply of stresses rely on tRNA-mediated stress regulation by altering the tRNA abundance, curbing the transport of tRNAs, fragmenting the mature tRNAs during stress. Among them, the studies on the generation of transfer RNA-derived fragments (tRFs) and their biological implication in stress response have attained huge interest. In plants, the tRFs hold stable expression patterns and regulate biological functions under diverse environmental conditions. In this review, we discuss the fate of plant tRNAs upon stress and thereafter how the tRFs are metamorphosed into sharp ammunition to wrestle with stress. We also address the various methods developed to date for uncovering the role of tRFs and their function in plants.

Transfer RNA-derived small RNAs in tumor microenvironment

Transfer RNAs (tRNAs) are a class of non-coding RNAs responsible for amino acid translocation during protein synthesis and are ubiquitously found in organisms. With certain modifications and under specific conditions, tRNAs can be sheared and fragmented into small non-coding RNAs, also known as tRNA-derived small RNAs (tDRs). With the development of high-throughput sequencing technologies and bioinformatic strategies, more and more tDRs have been identified and their functions in organisms have been characterized. tRNA and it derived tDRs, have been shown to be essential not only for transcription and translation, but also for regulating cell proliferation, apoptosis, metastasis, and immunity. Aberrant expression of tDRs is associated with a wide range of human diseases, especially with tumorigenesis and tumor progression. The tumor microenvironment (TME) is a complex ecosystem consisting of various cellular and cell-free components that are mutually compatible with the tumor. It has been shown that tDRs regulate the TME by regulating cancer stem cells, immunity, energy metabolism, epithelial mesenchymal transition, and extracellular matrix remodeling, playing a pro-tumor or tumor suppressor role. In this review, the biogenesis, classification, and function of tDRs, as well as their effects on the TME and the clinical application prospects will be summarized and discussed based on up to date available knowledge.

Emerging roles of tRNA-derived fragments in cancer

tRNA-derived fragments (tRFs) are an emerging category of small non-coding RNAs that are generated from cleavage of mature tRNAs or tRNA precursors. The advance in high-throughput sequencing has contributed to the identification of increasing number of tRFs with critical functions in distinct physiological and pathophysiological processes. tRFs can regulate cell viability, differentiation, and homeostasis through multiple mechanisms and are thus considered as critical regulators of human diseases including cancer. In addition, increasing evidence suggest the extracellular tRFs may be utilized as promising diagnostic and prognostic biomarkers for cancer liquid biopsy. In this review, we focus on the biogenesis, classification and modification of tRFs, and summarize the multifaceted functions of tRFs with an emphasis on the current research status and perspectives of tRFs in cancer.

Mammalian DNA N6-methyladenosine: Challenges and new insights

DNA N6-methyldeoxyadenosine (6mA) modification was first discovered in Bacterium coli in the 1950s. Over the next several decades, 6mA was recognized as a critical DNA modification in the genomes of prokaryotes and protists. While important in prokaryotes, less is known about the presence and functional roles of DNA 6mA in eukaryotes, particularly in mammals. Taking advantage of recent technology advances that made 6mA detection and sequencing possible, studies over the past several years have brought new insights into 6mA biology in mammals. In this perspective, we present recent progress, discuss challenges, and pose four questions for future research regarding mammalian DNA 6mA.

Occurrence of RNA post-transcriptional modifications in plant viruses and viroids and their correlation with structural and functional features

Post-transcriptional modifications of RNA bases are widespread across all the tree of life and have been linked to RNA maturation, stability, and molecular interactions. RNA modifications have been extensively described in endogenous eukaryotic mRNAs, however, little is known about the presence of RNA modifications in plant viral and subviral RNAs. Here, we used a computational approach to infer RNA modifications in plant-pathogenic viruses and viroids using high-throughput annotation of modified ribonucleotides (HAMR), a software that predicts modified ribonucleotides using high-throughput RNA sequencing data. We analyzed datasets from representative members of different plant viruses and viroids and compared them to plant-endogenous mRNAs. Our approach was able to predict potential RNA chemical modifications (RCMs) in all analyzed pathogens. We found that both DNA and RNA viruses presented a wide range of RCM proportions while viroids had lowest values. Furthermore, we found that for viruses with segmented genomes, some genomic RNAs had a higher proportion of RCM. Interestingly, nuclear-replicating viroids showed most of the predicted modifications located in the pathogenesis region, pointing towards a possible functional role of RCMs in their infectious cycle. Thus, our results strongly suggest that plant viral and subviral RNAs might contain a variety of previously unreported RNA modifications, thus opening a new perspective in the multifaceted process of plant-pathogen interactions.

ALKBH1-mediated m1 A demethylation of METTL3 mRNA promotes the metastasis of colorectal cancer by downregulating SMAD7 expression

Colorectal cancer (CRC) is one of the most common malignancies, and the main cause of death from CRC is tumor metastasis. m¹ A RNA modification plays critical role in many biological processes. However, the role of m¹ A modification in CRC remains unclear. Here, we find that the m¹ A demethylase alkB homolog 1, histone H2A dioxygenase (ALKBH1) is overexpressed in CRC and is associated with metastasis and poor prognosis. Upregulation of ALKBH1 expression promotes CRC metastasis in vitro and in vivo. Mechanistically, knockdown of ALKBH1 results in a decrease in methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit (METTL3) expression, probably due to m¹ A modification of METTL3 mRNA, followed by m⁶ A demethylation of SMAD family member 7 (SMAD7) mRNA. In addition, downregulation of SMAD7 establishes an aggressive phenotype. More importantly, the cell migration and invasion defects caused by ALKBH1 depletion or METTL3 depletion are significantly reversed by SMAD7 silencing. Considering these results collectively, we propose that ALKBH1 promotes CRC metastasis by destabilizing SMAD7 through METTL3.

Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines

Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m5C), 2'-O-ribose methylation (Nm), 3-methylcytidine (m3C), 7-methylguanosine (m7G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs.

N1-methyladenosine modification in cancer biology: current status and future perspectives

Post-transcriptional modifications in RNAs regulate their biological behaviors and functions. N¹-methyladenosine (m¹A), which is dynamically regulated by writers, erasers and readers, has been found as a reversible modification in tRNA, mRNA, rRNA and long non-coding RNA (lncRNA). m¹A modification has impacts on the RNA processing, structure and functions of targets. Increasing studies reveal the critical roles of m¹A modification and its regulators in tumorigenesis. Due to the positive relevance between m¹A and cancer development, targeting m¹A modification and m¹A-related regulators has been of attention. In this review, we summarized the current understanding of m¹A in RNAs, covering the modulation of m¹A modification in cancer biology, as well as the possibility of targeting m¹A modification as a potential target for cancer diagnosis and therapy.

Emerging functions of tRNA modifications in mRNA translation and diseases

tRNAs are essential modulators that recognize mRNA codons and bridge amino acids for mRNA translation. The tRNAs are heavily modified, which is essential for forming a complex secondary structure that facilitates codon recognition and mRNA translation. In recent years, studies have identified the regulatory roles of tRNA modifications in mRNA translation networks. Misregulation of tRNA modifications is closely related to the progression of developmental diseases and cancers. In this review, we summarize the tRNA biogenesis process and then discuss the effects and mechanisms of tRNA modifications on tRNA processing and mRNA translation. Finally, we provide a comprehensive overview of tRNA modifications' physiological and pathological functions, focusing on diseases including cancers.

tRNA-Derived Small RNAs: Novel Insights into the Pathogenesis and Treatment of Cardiovascular Diseases

tRNA-derived small RNAs (tsRNAs) are non-coding RNAs with diverse functions in various diseases. Although research on tsRNAs has focused on their roles in cancer, such as gene expression regulation to influence cancer progression and realize clinical effects, a growing number of studies are investigating the association of tsRNAs with cardiovascular diseases (CVDs), including atherosclerosis, myocardial infarction, and pulmonary hypertension. tsRNA expression varies across these diseases and could be regulated by epigenetics, tsRNA structure, and tRNA-binding proteins. tsRNAs play key roles in CVD progression, including the regulation of protein synthesis, and the different mechanisms underlying these functional roles of tsRNAs have been elucidated. Furthermore, tsRNAs are potential diagnostic biomarkers and therapeutic targets in CVDs. In this review, we summarize the biogenesis, classification, and regulation of tsRNAs and their potential application for CVD diagnosis and therapy. We also highlight the current challenges and provide perspectives for further investigation.

Codon Usage and mRNA Stability are Translational Determinants of Cellular Response to Canonical Ferroptosis Inducers

Ferroptosis is a non-apoptotic cell death mechanism characterized by the generation of lipid peroxides. While many effectors in the ferroptosis pathway have been mapped, its epitranscriptional regulation is not yet fully understood. Ferroptosis can be induced via system xCT inhibition (Class I) or GPX4 inhibition (Class II). Previous works have revealed important differences in cellular response to different ferroptosis inducers. Importantly, blocking mRNA transcription or translation appears to protect cells against Class I ferroptosis inducing agents but not Class II. In this work, we examined the impact of blocking transcription (via Actinomycin D) or translation (via Cycloheximide) on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. Blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. Cycloheximide led to increased levels of GSH alone or when co-treated with Erastin via the activation of the reverse transsulfuration pathway. RNA sequencing analysis revealed early activation of a strong alternative splice program before observed changes in transcription. mRNA stability analysis revealed divergent mRNA stability changes in cellular response to Erastin or RSL3. Importantly, codon optimality biases were drastically different in either condition. Our data also implicated translation repression and rate as an important determinant of the cellular response to ferroptosis inducers. Given that mRNA stability and codon usage can be influenced via the tRNA epitranscriptome, we evaluated the role of a tRNA modifying enzyme in ferroptosis stress response. Alkbh1, a tRNA demethylase, led to translation repression and increased the resistance to Erastin but made cells more sensitive to RSL3.

Transfer RNAs-derived small RNAs and their application potential in multiple diseases

The role of tRNAs is best known as adapter components of translational machinery. According to the central dogma of molecular biology, DNA is transcribed to RNA and in turn is translated into proteins, in which tRNA outstands by its role of the cellular courier. Recent studies have led to the revision of the canonical function of transfer RNAs (tRNAs), which indicates that tRNAs also serve as a source for short non-coding RNAs called tRNA-derived small RNAs (tsRNAs). tsRNAs play key roles in cellular processes by modulating complicated regulatory networks beyond translation and are widely involved in multiple diseases. Herein, the biogenesis and classification of tsRNAs were firstly clarified. tsRNAs are generated from pre-tRNAs or mature tRNAs and are classified into tRNA-derived fragments (tRFs) and tRNA halves (tiRNA). The tRFs include five types according to the incision loci: tRF-1, tRF-2, tRF-3, tRF-5 and i-tRF which contain 3′ tiRNA and 5′ tiRNA. The functions of tsRNAs and their regulation mechanisms involved in disease processes are systematically summarized as well. The mechanisms can elaborate on the specific regulation of tsRNAs. In conclusion, the current research suggests that tsRNAs are promising targets for modulating pathological processes, such as breast cancer, ischemic stroke, respiratory syncytial virus, osteoporosis and so on, and maintain vital clinical implications in diagnosis and therapeutics of various diseases.

Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases

Epitranscriptomic RNA modifications can regulate fundamental biological processes, but we lack approaches to map modification sites and probe writer enzymes. Here we present a chemoproteomic strategy to characterize RNA 5-methylcytidine (m⁵C) dioxygenase enzymes in their native context based upon metabolic labeling and activity-based crosslinking with 5-ethynylcytidine (5-EC). We profile m⁵C dioxygenases in human cells including ALKBH1 and TET2 and show that ALKBH1 is the major hm⁵C- and f⁵C-forming enzyme in RNA. Further, we map ALKBH1 modification sites transcriptome-wide using 5-EC-iCLIP and ARP-based sequencing to identify ALKBH1-dependent m⁵C oxidation in a variety of tRNAs and mRNAs and analyze ALKBH1 substrate specificity in vitro. We also apply targeted pyridine borane-mediated sequencing to measure f⁵C sites on select tRNA. Finally, we show that f⁵C at the wobble position of tRNA-Leu-CAA plays a role in decoding Leu codons under stress. Our work provides powerful chemical approaches for studying RNA m⁵C dioxygenases and mapping oxidative m⁵C modifications and reveals the existence of novel epitranscriptomic pathways for regulating RNA function.

Kleiner and co-workers profile RNA 5-methylcytidine (m⁵C) dioxygenase enzymes using an activity-based metabolic probing strategy. They reveal ALKBH1 as the major 5-formylcytidine (f⁵C) writer and characterize modification sites across mRNA and tRNA.

Experimental paradigms revisited: oxidative stress-induced tRNA fragmentation does not correlate with stress granule formation but is associated with delayed cell death

tRNA fragmentation is an evolutionarily conserved molecular phenomenon. tRNA-derived small RNAs (tsRNAs) have been associated with many cellular processes, including improved survival during stress conditions. Here, we have revisited accepted experimental paradigms for modeling oxidative stress resulting in tRNA fragmentation. Various cell culture models were exposed to oxidative stressors followed by determining cell viability, the production of specific tsRNAs and stress granule formation. These experiments revealed that exposure to stress parameters commonly used to induce tRNA fragmentation negatively affected cell viability after stress removal. Quantification of specific tsRNA species in cells responding to experimental stress and in cells that were transfected with synthetic tsRNAs indicated that neither physiological nor non-physiological copy numbers of tsRNAs induced the formation of stress granules. Furthermore, the increased presence of tsRNA species in culture medium collected from stressed cells indicated that cells suffering from experimental stress exposure gave rise to stable extracellular tsRNAs. These findings suggest a need to modify current experimental stress paradigms in order to allow separating the function of tRNA fragmentation during the acute stress response from tRNA fragmentation as a consequence of ongoing cell death, which will have major implications for the current perception of the biological function of stress-induced tsRNAs.

A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation

Small RNAs include tRNA, snRNA, micro-RNA, tRNA fragments and others that constitute > 90% of RNA copy numbers in a human cell and perform many essential functions. Popular small RNA-seq strategies limit the insights into coordinated small RNA response to cellular stress. Small RNA-seq also lacks multiplexing capabilities. Here, we report a multiplex small RNA-seq library preparation method (MSR-seq) to investigate cellular small RNA and mRNA response to heat shock, hydrogen peroxide, and arsenite stress. Comparing stress-induced changes of total cellular RNA and polysome-associated RNA, we identify a coordinated tRNA response that involves polysome-specific tRNA abundance and synergistic N3-methylcytosine (m³C) tRNA modification. Combining tRNA and mRNA response to stress we reveal a mechanism of stress-induced down-regulation in translational elongation. We also find that native tRNA molecules lacking several modifications are biased reservoirs for the biogenesis of tRNA fragments. Our results demonstrate the importance of simultaneous investigation of small RNAs and their modifications in response to varying biological conditions.

tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes

tRNA is the most extensively modified RNA in cells. On average, a bacterial tRNA contains 8 modifications per molecule and a eukaryotic tRNA contains 13 modifications per molecule. Recent studies reveal that tRNA modifications are highly dynamic and respond extensively to environmental conditions. Functions of tRNA modification dynamics include enhanced, on-demand decoding of specific codons in response genes and regulation of tRNA fragment biogenesis. This review summarizes recent advances in the studies of tRNA modification dynamics in biological processes, tRNA modification erasers, and human-associated bacteria. Furthermore, we use the term "metaepitranscriptomics" to describe the potential and approach of tRNA modification studies in natural biological communities such as microbiomes. tRNA is highly modified in cells, and tRNA modifications respond extensively to environmental conditions to enhance translation of specific genes and produce tRNA fragments on demand. We review recent advances in tRNA sequencing methods, tRNA modification dynamics in biological processes, and tRNA modification studies in natural communities such as the microbiomes.

Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen

Epitranscriptomic marks, in the form of enzyme catalyzed RNA modifications, play important gene regulatory roles in response to environmental and physiological conditions. However, little is known with respect to how acute toxic doses of pharmaceuticals influence the epitranscriptome. Here we define how acetaminophen (APAP) induces epitranscriptomic reprogramming and how the writer Alkylation Repair Homolog 8 (Alkbh8) plays a key gene regulatory role in the response. Alkbh8 modifies tRNA selenocysteine (tRNA^Sec) to translationally regulate the production of glutathione peroxidases (Gpx’s) and other selenoproteins, with Gpx enzymes known to play protective roles during APAP toxicity. We demonstrate that APAP increases toxicity and markers of damage, and decreases selenoprotein levels in Alkbh8 deficient mouse livers, when compared to wildtype. APAP also promotes large scale reprogramming of many RNA marks comprising the liver tRNA epitranscriptome including: 5-methoxycarbonylmethyluridine (mcm⁵U), isopentenyladenosine (i⁶A), pseudouridine (Ψ), and 1-methyladenosine (m¹A) modifications linked to tRNA^Sec and many other tRNA’s. Alkbh8 deficiency also leads to wide-spread epitranscriptomic dysregulation in response to APAP, demonstrating that a single writer defect can promote downstream changes to a large spectrum of RNA modifications. Our study highlights the importance of RNA modifications and translational responses to APAP, identifies writers as key modulators of stress responses in vivo and supports the idea that the epitranscriptome may play important roles in responses to pharmaceuticals.

Deciphering the tRNA-derived small RNAs: origin, development, and future

Transfer RNA (tRNA)-derived small RNAs (tsRNAs), a novel category of small noncoding RNAs, are enzymatically cleaved from tRNAs. Previous reports have shed some light on the roles of tsRNAs in the development of human diseases. However, our knowledge about tsRNAs is still relatively lacking. In this paper, we review the biogenesis, classification, subcellular localization as well as action mechanism of tsRNAs, and discuss the association between chemical modifications of tRNAs and the production and functions of tsRNAs. Furthermore, using immunity, metabolism, and malignancy as examples, we summarize the molecular mechanisms of tsRNAs in diseases and evaluate the potential of tsRNAs as new biomarkers and therapeutic targets. At the same time, we compile and introduce several resource databases that are currently publicly available for analyzing tsRNAs. Finally, we discuss the challenges associated with research in this field and future directions.

Circulating tRNA-Derived Small RNAs as Novel Radiation Biomarkers of Heavy Ion, Proton and X-ray Exposure

The effective and minimally invasive radiation biomarkers are valuable for exposure scenarios in nuclear accidents or space missions. Recent studies have opened the new sight of circulating small non-coding RNA (sncRNA) as radiation biomarkers. The tRNA-derived small RNA (tsRNA) is a new class of sncRNA. It is more abundant than other kinds of sncRNAs in extracellular vesicles or blood, presenting great potential as promising biomarkers. However, the circulating tsRNAs in response to ionizing radiation have not been reported. In this research, Kunming mice were total-body exposed to 0.05-2 Gy of carbon ions, protons, or X-rays, and the RNA sequencing was performed to profile the expression of sncRNAs in serum. After conditional screening and validation, we firstly identified 5 tsRNAs including 4 tRNA-related fragments (tRFs) and 1 tRNA half (tiRNA) which showed a significant level decrease after exposure to three kinds of radiations. Moreover, the radiation responses of these 5 serum tsRNAs were reproduced in other mouse strains, and the sequences of them could be detected in serum of humans. Furthermore, we developed multi-factor models based on tsRNA biomarkers to indicate the degree of radiation exposure with high sensitivity and specificity. These findings suggest that the circulating tsRNAs can serve as new minimally invasive biomarkers and can make a triage or dose assessment from blood sample collection within 4 h in exposure scenarios.

tRNA modifications and their potential roles in pancreatic cancer

Since the breakthrough discovery of N6-methyladenosine (m⁶A), the field of RNA epitranscriptomics has attracted increasing interest in the biological sciences. Transfer RNAs (tRNAs) are extensively modified, and various modifications play a crucial role in the formation and stability of tRNA, which is universally required for accurate and efficient functioning of tRNA. Abnormal tRNA modification can lead to tRNA degradation or specific cleavage of tRNA into fragmented derivatives, thus affecting the translation process and frequently accompanying a variety of human diseases. Increasing evidence suggests that tRNA modification pathways are also misregulated in human cancers. In this review, we summarize tRNA modifications and their biological functions, describe the type and frequency of tRNA modification alterations in cancer, and highlight variations in tRNA-modifying enzymes and the multiple functions that they regulate in different types of cancers. Furthermore, the current implications and the potential role of tRNA modifications in the progression of pancreatic cancer are discussed. Collectively, this review describes recent advances in tRNA modification in cancers and its potential significance in pancreatic cancer. Further study of the mechanism of tRNA modifications in pancreatic cancer may provide possibilities for therapies targeting enzymes responsible for regulating tRNA modifications in pancreatic cancer.

Research progress on the tsRNA classification, function, and application in gynecological malignant tumors

A large number of small non-coding RNAs derived from tRNAs, called tRNA-derived small RNA (tsRNAs), have been identified by high-throughput RNA sequencing of cell lines. Further research has revealed that they are not produced via random tRNA degradation, but through degradation by specific nuclease cleavages, such as Elac Ribonuclease Z 2 (ELAC2)/RNase Z, RNase L, Dicer, and angiogenin (ANG), the tsRNAs can be classified into the following types based on the location from which they have been derived from the parental tRNA: tRF-1s, tRF-3s, tRF-5s, tiRNA, and tRF-2s/i-tRFs. Moreover, tsRNAs are a type of small RNAs with diverse functions, including gene expression regulation, anti-apoptosis, translation inhibition, participation in epigenetic regulation, initial virus reverse transcription, promote virus replication and cell-to-cell communication. Certain types of tsRNAs are overexpressed in cancer tissues, but are underexpressed in normal tissues. Therefore, the relationship between tsRNAs and the occurrence and development of cancer has attracted significant research attention. Research advancements have contributed to further discoveries of the biological activities of tsRNAs, but the mechanisms of their biogenesis and functions have not been fully elucidated. This article reviews the classification and biological functions of tsRNAs, and introduces the research progress in gynecological malignancies.

The epitranscriptome of small non-coding RNAs

Small non-coding RNAs are short RNA molecules and involved in many biological processes, including cell proliferation and differentiation, immune response, cell death, epigenetic regulation, metabolic control. A diversity of RNA modifications have been identified in these small non-coding RNAs, including transfer RNAs (tRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNA (snRNA), small nucleolar RNAs (snoRNAs), and tRNA-derived small RNAs (tsRNAs). These post-transcriptional modifications are involved in the biogenesis and function of these small non-coding RNAs. In this review, we will summarize the existence of RNA modifications in the small non-coding RNAs and the emerging roles of these epitranscriptomic marks.

tRNA Metabolism and Lung Cancer: Beyond Translation

Lung cancer, one of the most malignant tumors, has extremely high morbidity and mortality, posing a serious threat to global health. It is an urgent need to fully understand the pathogenesis of lung cancer and provide new ideas for its treatment. Interestingly, accumulating evidence has identified that transfer RNAs (tRNAs) and tRNA metabolism–associated enzymes not only participate in the protein translation but also play an important role in the occurrence and development of lung cancer. In this review, we summarize the different aspects of tRNA metabolism in lung cancer, such as tRNA transcription and mutation, tRNA molecules and derivatives, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (ARSs), aiming at a better understanding of the pathogenesis of lung cancer and providing new therapeutic strategies for it.

Origins and evolving functionalities of tRNA-derived small RNAs

Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, which are rooted in tsRNA sequence conservation, RNA modifications, and protein-binding abilities. We summarize the mechanisms of tsRNA biogenesis and the impact of RNA modifications, and propose how thinking of tsRNA functionality from an evolutionary perspective urges the expansion of tsRNA research into a wider spectrum, including cross-tissue/cross-species regulation and harnessing of the 'tsRNA code' for precision medicine.