Role of tRNA-derived small RNAs(tsRNAs) in the diagnosis and treatment of malignant tumours

Clinical Significance of the Serum 3'tRF-AlaAGC, Neutrophil to High-Density Lipoprotein Ratio, and Lymphocyte-to-Monocyte Ratio in Breast Cancer with Lymph Node Metastasis

Objective

Breast cancer (BC) is a common malignant tumor among women, the local recurrence, lymph node metastasis (LNM), and distant metastasis are the key factors affecting the prognosis of patients. tRNA-derived small RNAs (tDRs) are non-coding small RNA fragments [16-40 nucleotides (nt) in length] that play an important role in carcinogenesis and can serve as novel biological markers for the diagnosis and prognosis of various tumors. Accumulating evidence suggests that blood-based inflammatory indicators are linked with the pathogenesis of BC. However, the clinical significance of the combination of tDRs and inflammatory indicators in BC patients with LNM is still unclear.

Methods

The serum samples were collected from 175 patients with BC admitted to our hospital during June 2021 and May 2024, and 94 age-matched healthy women, and the clinical data of the research subjects were recorded. Serum 3'tRF-AlaAGC levels were measured using quantitative real-time PCR (qRT-PCR) and the blood-based inflammatory indicators were calculated from peripheral blood samples. Lasso-cox regression and multiple logistic regression were employed for variable selection. Receiver operating characteristic (ROC) was used to calculate the cut-off value of variables. Spearman correlation test was used to examine the correlation between 3'tRF-AlaAGC levels and neutrophil to HDL-C ratio (NHR), lymphocyte-to-monocyte ratio (LMR). A nomogram model for risk assessment of LNM in BC was established by using the rms package of R software.

Results

Serum 3'tRF-AlaAGC levels in BC patients with LNM were significantly higher than that in without LNM [5.17 (1.79, 16.55) vs 11.68 (2.64, 58.74), P=0.009]. The variables screened by Lasso-cox regression including 3'tRF-AlaAGC, NHR and LMR, with optimal cut-off values of 18.78, 2.94 and 5.41, respectively. NHR levels were significantly negatively associated with LMR in low 3'tRF-AlaAGC expression groups (r=-0.209, P=0.021). Multivariate logistic regression analysis confirmed that 3'tRF-AlaAGC (OR: 3.242, 95% CI: 1.583-6.641, P=0.001), NHR (OR: 3.305, 95% CI: 1.543-7.079, P=0.002), and LMR (OR: 0.329, 95% CI: 0.150-0.723, P=0.006) were independent risk factors of BC with LNM. The C-statistic of the nomograms model was 0.704, with a sensitivity of 57.14% and a specificity of 77.14%.

Conclusion

3'tRF-AlaAGC >18.78, NHR > 2.94, and LMR ≤ 5.41 were the independent risk factors of BC with LNM. The nomogram model incorporating 3'tRF-AlaAGC, NHR and LMR can effectively predict the risk of LNM of BC patients.

A novel tRNA-Derived fragment, tRF-20-M0NK5Y93 inhibits the malignant progression of non-small cell lung cancer by mediating PLOD1

OBJECTIVE

Non-small cell lung cancer (NSCLC) constitutes a common malignant tumor characterized by substantial mortality rates. Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have been implicated in the progression of various cancers, including NSCLC. However, to date, only a limited number of tsRNAs have been reported to be involved in the development of NSCLC. Hence, the present study aimed to investigate the potential roles of tsRNAs in the progression of NSCLC.

MATERIALS AND METHODS

A total of forty-six patients with NSCLC who underwent surgical resection were enrolled in this study. The expression patterns of tRNA-derived fragments (tRFs) in tumor and normal tissues of 6 NSCLC cases were investigated using RNA-sequencing assay. Cell viability, proliferation capacity, and migratory ability were measured utilizing the CCK-8, colony formation, and Transwell assays, respectively. Furthermore, cell apoptosis was evaluated by applying flow cytometry. The xenograft tumor model was constructed to observe tumor growth. The relationship between tRF-20-M0NK5Y93 and PLOD1 was clarified using the luciferase and RIP assays.

RESULTS

The RNA-sequencing assay revealed a significant decrease in the expression of tRF-20-M0NK5Y93 in tumor tissues. In line with this finding, qRT-PCR analysis further confirmed a meaningful downregulation of tRF-20-M0NK5Y93 in 46 patient samples with NSCLC. Importantly, this downregulated expression was strongly correlated with reduced patient survival. Additionally, overexpression of tRF-20-M0NK5Y93 was found to inhibit the proliferation and migration capabilities of NSCLC cells, leading to suppressed tumor growth and accelerated apoptosis. Furthermore, tRF-20-M0NK5Y93 was capable of binding to PLOD1, thereby negatively regulating its expression. Notably, the restoration of PLOD1 expression was able to counteract the inhibitory effects of enforced tRF-20-M0NK5Y93 on NSCLC cell proliferation, migration, and apoptosis.

CONCLUSION

The expression level of tRF-20-M0NK5Y93 was found to be decreased in NSCLC. Overexpressed tRF-20-M0NK5Y93 exhibited inhibitory effects on NSCLC cell proliferation and migration, accelerated apoptosis, and suppressed tumor growth by targeting PLOD1. These findings highlight tRF-20-M0NK5Y93 as a promising target for NSCLC therapy.

A Novel tRF, HCETSR, Derived From tRNA-Glu/TTC, Inhibits HCC Malignancy by Regulating the SPBTN1-catenin Complex Axis

tRNA-derived fragments (tRFs), a novel class of small non-coding RNAs cleaved from transfer RNAs, have been implicated in tumor regulation. In this study, the role of a specific tRF, HCETSR is investigated, which is significantly downregulated in hepatocellular carcinoma (HCC) and correlates with advanced tumor burden and higher HCC mortality. Functional analyses revealed that HCETSR inhibits HCC malignancy and serves as an independent predictor of poor prognosis. Mechanistically, a novel SPTBN1/catenin complex axis regulated by HCETSR is identified. HCETSR binds to a critical domain of SPTBN1, disrupting its interaction with the catenin complex (comprising β-catenin, α-catenin, and P120-catenin), and facilitates the transfer of the catenin complex from the cell membrane to the nucleus. Specifically, HCETSR decreases the proteasomal degradation of β-catenin and inhibits the synthesis of nascent β-catenin. Furthermore, HCETSR suppresses the transcriptional activity of LEF1 through P120-catenin rather than α-catenin, thereby reducing β-catenin's influence on LEF1 activity. It is demonstrated that HCETSR is spliced from tRNA-Glu/TTC. The biogenesis of HCETSR and tRNA-Glu/TTC is regulated by the spliceosome and Dicer1. In conclusion, These findings suggest that HCETSR, derived from tRNA-Glu/TTC, inhibits HCC malignancy via modulation of the SPTBN1/catenin axis and may represent a promising prognostic marker and therapeutic strategy for HCC.

Circulating non-coding RNAs as a tool for liquid biopsy in solid tumors

Solid tumors are significant causes of global mortality and morbidity. Recent research has primarily concentrated on finding pathology-specific molecules that can be acquired non-invasively and that can change as the disease progresses or in response to treatment. The focus of research has moved to RNA molecules that are either freely circulating in body fluids or bundled in microvesicles and exosomes because of their great stability in challenging environments, ease of accessibility, and changes in level in response to therapy. In this context, there are many non-coding RNAs that can be used for this purpose in liquid biopsies. Out of these, microRNAs have been extensively studied. However, there has been an increase of interest in studying long non-coding RNAs, piwi interacting RNAs, circular RNAs, and other small non-coding RNAs. In this article, an overview of the most researched circulating non-coding RNAs in solid tumors will be reviewed, along with a discussion of the significance of these molecules for early diagnosis, prognosis, and therapeutic targets. The publications analyzed were extracted from the PubMed database between 2008 and June 2024.

The Role of the Fox Gene in Breast Cancer Progression

Forkhead box (FOX) genes are a family of transcription factors that participate in many biological activities, from early embryogenesis to the formation of organs, and from regulation of glucose metabolism to regulation of longevity. Given the extensive influence in the multicellular process, FOX family proteins are responsible for the progression of many types of cancers, especially lung cancer, breast cancer, prostate cancer, and other cancers. Breast cancer is the most common cancer among women, and 2.3 million women were diagnosed in 2020. So, various drugs targeting the FOX signaling pathway have been developed to inhibit breast cancer progression. While the role of the FOX family gene in cancer development has not received enough attention, discovering more potential drugs targeting the FOX signaling pathway is urgently demanded. Here, we review the main members in the FOX gene family and summarize their signaling pathway, including the regulation of the FOX genes and their effects on breast cancer progression. We hope this review will emphasize the understanding of the role of the FOX gene in breast cancer and inspire the discovery of effective anti-breast cancer medicines targeting the FOX gene in the future.

Research progress on the tsRNA biogenesis, function, and application in lung cancer

In recent years, there has been a mounting occurrence of lung cancer, which stands as one of the most prevalent malignancies globally. This rise in incidence poses a significant hazard to human health, making lung cancer a matter of grave concern. It has been shown that tRNA-derived small non-coding RNA (tsRNA) is involved in the development of tumors, especially lung cancer, through mechanisms such as regulating mRNA stability, influencing protein translation, and acting as epigenetic regulators. Recent studies have shown that tsRNA is abnormally expressed in the plasma and tissues of lung cancer patients, and its expression level is closely related to the malignancy degree and postoperative recurrence of lung cancer. Therefore, for lung cancer patients, tsRNA represents a promising non-invasive biomarker, exhibiting significant potential for facilitating early diagnosis and prognostic evaluation, and for achieving precision treatment of lung cancer by regulating its expression. This article focuses on the biogenesis of tsRNA and its ability to promote lung cancer cell proliferation and invasion. In addition, the specific clinical significance of tsRNA in lung cancer was discussed. Finally, we discuss the need for further improvement of small RNA sequencing technology, and the future research directions and strategies of tsRNA in lung cancer and tumor diseases were summarized.

The tRF-33/IGF1 axis dysregulates mitochondrial homeostasis in HER2-negative breast cancer

Transfer RNA-derived small RNAs (tsRNAs), a recently identified noncoding RNA subset, are mainly classified into transfer RNA (tRNA)-derived small RNA fragments (tRFs) and tRNA-derived stress-induced RNAs (tiRNAs). tsRNAs dysregulation is frequently observed in numerous cancer types, suggesting involvement in tumorigenesis. However, their functions in breast cancer (BC) remain to be fully understood. Here, it was discovered that tRF-33-MEF91SS2PMFI0Q (tRF-33), derived from mature tRNA-LysTTT, was markedly upregulated in human epidermal receptor 2 (HER2)-negative BC cells and tissue samples. tRF-33 stimulated the proliferation, migration, and invasiveness of BC cells in vitro and facilitated tumor progression in vivo. Mechanistically, tRF-33 was found for the first time to bind directly to the 3'-UTR of IGF1, resulting in downregulation of both its mRNA and protein and thus affecting mitochondrial homeostasis and progression of BC. These results demonstrate a novel tsRNA modulatory mechanism and a potential direction for treating HER2-negative BC.NEW & NOTEWORTHY In this study, we identified differential expression of tRNA fragments in HER2-negative BC tissues compared with adjacent normal tissues, observing significant upregulation of an i-tRF type tRF-33-MEF91SS2PMFI0Q (tRF-33) in the tumor tissue. We also found that tRF-33 promoted tumorigenesis in BC cells. We demonstrated for the first time that IGF1 was a target gene of tRF-33 and also showed that the tRF-33/IGF1 axis impaired mitochondrial dynamics, thus affecting mitochondrial homeostasis and promoting HER2-negative BC progression.

Systematic assessment of serum i-tRF-AsnGTT in gastric cancer: a potential clinical biomarker

Since gastric cancer (GC) shows no apparent signs in its early stages, most patients are diagnosed later with a poor prognosis. We therefore seek more sensitive and specific GC biomarkers. Small RNAs formed from tRNAs represent a novel class of non-coding RNAs that are highly abundant in bodily fluids and essential to biological metabolism. This study explores the potential of i-tRF-AsnGTT in gastric cancer diagnostics. To begin with, we sequenced i-tRF-AsnGTT using high-throughput methods. i-tRF-AsnGTT expression levels in GC were determined using real-time fluorescence polymerase chain reaction. Agarose gel electrophoresis, Sanger sequencing, and repeated freezing and thawing were performed to verify molecular properties. A correlation was found between clinical and pathological parameters and i-tRF-AsnGTT expression levels through the χ2 test, and receiver operating characteristic was used to analyze its diagnostic value in GC. In serum, i-tRF-AsnGTT has a low and stable expression level. It can differentiate between patients with gastric cancer and gastritis and healthy donors with better diagnostic efficacy. In combination with clinicopathological parameters, i-tRF-AsnGTT correlates with tumor differentiation; infiltration depth of tumors; tumor, node, metastasis stage; lymph node metastases; and neural/vascular invasion. Serum i-tRF-AsnGTT expression is low in GC patients. Serum from postoperative patients shows increased i-tRF-AsnGTT expression levels. Potentially, this could be used as a biomarker to help diagnose gastric cancer and monitor its prognosis.

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.

TRF-16 Inhibits Lung Cancer Progression by Hindering the N6-Methyladenosine Modification of CPT1A mRNA

Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs. Recent studies suggest that tRFs participate in some pathological processes. However, the biological activities and processes of tRFs in lung cancer cells remain mainly unclear. In the present investigation, we employed tRNA-derived small RNA (tsRNA) sequencing to predict differentially expressed tsRNAs in lung cancer cells, and nine tsRNAs with significant expression alterations were validated using qPCR. Wound healing, colony formation, transwell invasion and CCK-8 assays were performed to detect the effects of tRF-16 on cell function. Western blotting evaluated the relationship between tRF-16 and the IGF2BP1 axis. Our findings demonstrated that tRF-16 expression was substantially downregulated in lung cancer cells. TRF-16 could inhibit lung cancer cells' ability to increase, migrate, invade and obtain radiation resistance. Furthermore, tRF-16 decreases the stability of CPT1A by impairing the binding of IGF2BP1 to CPT1A. As a result, the fatty acid metabolism in lung cancer cells was inhibited. Finally, tRF-16 also inhibits lung cancer cell proliferation in vivo. This study shows that tRF-16 plays a crucial regulatory role in the proliferation of lung cancer cells and may represent a novel avenue for their regulation.

Small non-coding RNAs as diagnostic, prognostic and predictive biomarkers of gynecological cancers: an update

INTRODUCTION

Non-coding RNAs (ncRNAs) comprise a heterogeneous cluster of RNA molecules. Emerging evidence suggests their involvement in various aspects of tumorigenesis, particularly in gynecological malignancies. Notably, ncRNAs have been implicated as mediators within tumor signaling pathways, exerting their influence through interactions with RNA or proteins. These findings further highlight the hypothesis that ncRNAs constitute therapeutic targets and point out their clinical potential as stratification biomarkers.

AREAS COVERED

The review outlines the use of small ncRNAs, including miRNAs, tRNA-derived small RNAs, PIWI-interacting RNAs and circular RNAs, for diagnostic, prognostic, and predictive purposes in gynecological cancers. It aims to increase our knowledge of their functions in tumor biology and their translation into clinical practice.

EXPERT OPINION

By leveraging interdisciplinary collaborations, scientists can decipher the riddle of small ncRNA biomarkers as diagnostic, prognostic and predictive biomarkers of gynecological tumors. Integrating small ncRNA-based assays into clinical practice will allow clinicians to provide cure plans for each patient, reducing the likelihood of adverse responses. Nevertheless, addressing challenges such as standardizing experimental methodologies and refining diagnostic assays is imperative for advancing small ncRNA research in gynecological cancer.

Emerging roles of tRNA-derived small RNAs in injuries

tRNA-derived small RNAs (tsRNAs) are a novel class of small noncoding RNAs, precisely cleaved from tRNA, functioning as regulatory molecules. The topic of tsRNAs in injuries has not been extensively discussed, and studies on tsRNAs are entering a new era. Here, we provide a fresh perspective on this topic. We systematically reviewed the classification, generation, and biological functions of tsRNAs in response to stress, as well as their potential as biomarkers and therapeutic targets in various injuries, including lung injury, liver injury, renal injury, cardiac injury, neuronal injury, vascular injury, skeletal muscle injury, and skin injury. We also provided a fresh perspective on the association between stress-induced tsRNAs and organ injury from a clinical perspective.

The mechanism of MMP14-positive tumor-associated fibroblast subsets in inhibiting PD-1 immunotherapy for esophageal cancer through exosomal tsRNA-10522

Esophageal cancer (EC) continues to pose a significant health risk. Cancer-associated fibroblasts (CAFs), an essential part of the tumor microenvironment (TME), are viewed as potential therapeutic targets. However, their role in tumor mechanisms specific to esophageal cancer remains to be elucidated. This study identified MMP14+ CAFs and MMP14- CAFs using immunofluorescence staining. The cytotoxic activity of CD8 T cells was assessed via western blot and ELISA. Using a transwell test, the migratory potential of MMP14+ CAFs was evaluated. Using flow cytometry, apoptosis was found in the esophageal squamous cell carcinoma cell line KYSE30. To determine the important tsRNAs released by MMP14+ CAFs, tsRNA-seq was used. Two subgroups of EC receiving PD-1 immunotherapy were identified by our research: MMP14+ CAFs and MMP14- CAFs. MMP14+ CAFs showed improved migratory capacity and released more inflammatory factors linked to cancer. Through exosomes, these CAFs may prevent anti-PD-1-treated CD8 T cells from being cytotoxic. Furthermore, exosomal tsRNA from MMP14+ CAFs primarily targeted signaling pathways connected with cancer. Notably, it was discovered that tsRNA-10522 plays a critical role within inhibiting CD8 T cell tumor cell death. The tumor cell killing of CD8 T cells by exosomal tsRNA-10522 is inhibited by a subgroup of cells called MMP14+ CAFs inside the EC microenvironment during PD-1 immunotherapy. This reduces the effectiveness of PD-1 immunotherapy for EC. Our findings demonstrate the inhibitory function of MMP14+ CAFs within EC receiving PD-1 immunotherapy, raising the prospect that MMP14+ CAFs might serve as predictive indicators in EC receiving PD-1 immunotherapy.

tRNA-derived fragment 3'tRF-AlaAGC modulates cell chemoresistance and M2 macrophage polarization via binding to TRADD in breast cancer

BACKGROUND

Drug resistance, including Adriamycin-based therapeutic resistance, remains a challenge in breast cancer (BC) treatment. Studies have revealed that macrophages could play a pivotal role in mediating the chemoresistance of cancer cells. Accumulating evidence suggests that tRNA-Derived small RNAs (tDRs) are associated the physiological and pathological processes in multiple cancers. However, the underlying mechanisms of tDRs on chemoresistance of BC in tumor-associated macrophages remain largely unknown.

METHODS

The high-throughput sequencing technique was used to screen tDRs expression profile in BC cells. Gain- and loss-of-function experiments and xenograft models were performed to verify the biological function of 3'tRF-Ala-AGC in BC cells. The CIBERSORT algorithm was used to investigate immune cell infiltration in BC tissues. To explore the role of 3'tRF-Ala-AGC in macrophages, M2 macrophages transfected with 3'tRF-Ala-AGC mimic or inhibitor were co-cultured with BC cells. Effects on Nuclear factor-κb (NF-κb) pathway were investigated by NF-κb nuclear translocation assay and western blot analysis. RNA pull-down assay was performed to identify 3'tRF-Ala-AGC interacting proteins.

RESULTS

A 3'tRF fragment of 3'tRF-AlaAGC was screened, which is significantly overexpressed in BC specimens and Adriamycin-resistant cells. 3'tRF-AlaAGC could promote cell malignant activity and facilitate M2 polarization of macrophages in vitro and in vivo. Higher expression of M2 macrophages were more likely to have lymph node metastasis and deeper invasion in BC patients. Mechanistically, 3'tRF-AlaAGC binds Type 1-associated death domain protein (TRADD) in BC cells, and suppression of TRADD partially abolished the enhanced effect of 3'tRF-AlaAGC mimic on phenotype of M2. The NF-κb signaling pathway was activated in BC cells co-cultured with M2 macrophages transfected with 3'tRF-AlaAGC mimic.

CONCLUSIONS

3'tRF-AlaAGC might modulate macrophage polarization via binding to TRADD and increase the effect of M2 on promoting the chemoresistance in BC cells through NF-κb signaling pathway.

Signaling, cancer cell plasticity, and intratumor heterogeneity

Cancer's complexity is in part due to the presence of intratumor heterogeneity and the dynamic nature of cancer cell plasticity, which create substantial obstacles in effective cancer management. Variability within a tumor arises from the existence of diverse populations of cancer cells, impacting the progression, spread, and resistance to treatments. At the core of this variability is the concept of cellular plasticity - the intrinsic ability of cancer cells to alter their molecular and cellular identity in reaction to environmental and genetic changes. This adaptability is a cornerstone of cancer's persistence and progression, making it a formidable target for treatments. Emerging studies have emphasized the critical role of such plasticity in fostering tumor diversity, which in turn influences the course of the disease and the effectiveness of therapeutic strategies. The transformative nature of cancer involves a network of signal transduction pathways, notably those that drive the epithelial-to-mesenchymal transition and metabolic remodeling, shaping the evolutionary path of cancer cells. Despite advancements, our understanding of the precise molecular machinations and signaling networks driving these changes is still evolving, underscoring the necessity for further research. This editorial presents a series entitled "Signaling Cancer Cell Plasticity and Intratumor Heterogeneity" in Cell Communication and Signaling, dedicated to unraveling these complex processes and proposing new avenues for therapeutic intervention.

tRNA-Derived Fragments as Biomarkers in Bladder Cancer

Bladder cancer (BC) diagnosis is reliant on cystoscopy, an invasive procedure associated with urinary tract infections. This has sparked interest in identifying noninvasive biomarkers in body fluids such as blood and urine. A source of biomarkers in these biofluids are extracellular vesicles (EVs), nanosized vesicles that contain a wide array of molecular cargo, including small noncoding RNA such as transfer RNA-derived fragments (tRF) and microRNA. Here, we performed small-RNA next-generation sequencing from EVs from urine and serum, as well as from serum supernatant. RNA was extracted from 15 non-cancer patients (NCPs) with benign findings in cystoscopy and 41 patients with non-muscle invasive BC. Urine and serum were collected before transurethral resection of bladder tumors (TUR-b) and at routine post-surgery check-ups. We compared levels of tRFs in pre-surgery samples to samples from NCPs and post-surgery check-ups. To further verify our findings, samples from 10 patients with stage T1 disease were resequenced. When comparing tRF expression in urine EVs between T1 stage BC patients and NCPs, 14 differentially expressed tRFs (DEtRFs) were identified. In serum supernatant, six DEtRFs were identified among stage T1 patients when comparing pre-surgery to post-surgery samples and four DEtRFs were found when comparing pre-surgery samples to NCPs. By performing a blast search, we found that sequences of DEtRFs aligned with genomic sequences pertaining to processes relevant to cancer development, such as enhancers, regulatory elements and CpG islands. Our findings display a number of tRFs that may hold potential as biomarkers for the diagnosis and recurrence-free survival of BC.

Unveiling the role of tRNA-derived small RNAs in MAPK signaling pathway: implications for cancer and beyond

tRNA-derived small RNAs (tsRNAs) are novel small non-coding RNAs originating from mature or precursor tRNAs (pre-tRNA), typically spanning 14 to 30 nt. The Mitogen-activated protein kinases (MAPK) pathway orchestrates cellular responses, influencing proliferation, differentiation, apoptosis, and transformation. tsRNAs influence the expression of the MAPK signaling pathway by targeting specific proteins within the pathway. Presently, four MAPK-linked tsRNAs have implications in gastric cancer (GC) and high-grade serous ovarian cancer (HGSOC). Notably, tRF-Glu-TTC-027 and tRF-Val-CAC-016 modulate MAPK-related protein expression, encompassing p38, Myc, ERK, CyclinD1, CyclinB, and c-Myc, hindering GC progression via MAPK pathway inhibition. Moreover, tRF-24-V29K9UV3IU and tRF-03357 remain unexplored in specific mechanisms. KEGG analysis posits varied tsRNAs in MAPK pathway modulation for diverse non-cancer maladies. Notably, high tRF-36-F900BY4D84KRIME and tRF-23-87R8WP9IY expression relates to varicose vein (VV) risk. Elevated tiRNA-Gly-GCC-001, tRF-Gly-GCC-012, tRF-Gly-GCC-013, and tRF-Gly-GCC-016 target spinal cord injury (SCI)-related brain-derived neurotrophic factor (BDNF), influencing MAPK expression. tRF-Gly-CCC-039 associates with diabetes foot sustained healing, while tRF-5014a inhibits autophagy-linked ATG5 in diabetic cardiomyopathy (DCM). Additionally, tsRNA-14783 influences keloid formation by regulating M2 macrophage polarization. Upregulation of tRF-Arg-ACG-007 and downregulation of tRF-Ser-GCT-008 are associated with diabetes. tsRNA-04002 alleviates Intervertebral disk degeneration (IDD) by targeting PRKCA. tsRNA-21109 alleviates Systemic lupus erythematosus (SLE) by inhibiting macrophage M1 polarization. The upregulated tiNA-Gly-GCC-002 and the downregulated tRF-Ala-AGC-010, tRF-Gln-CTG-005 and tRF-Leu-AAG-001 may be involved in the pathogenesis of Lupus nephritis (LN) by affecting the expression of MAPK pathway. Downregulation of tsRNA-1018, tsRNA-3045b, tsRNA-5021a and tsRNA-1020 affected the expression of MAPK pathway, thereby improving Acute lung injury (ALI). This review comprehensively dissects tsRNA roles in MAPK signaling across cancers and other diseases, illuminating a novel avenue for translational medical exploration.

Multiple structural flavors of RNase P in precursor tRNA processing

The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

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.