Long non-coding RNAs in female infertility: Advancing from molecular insights to clinical relevance

- Search | Clin Exp Reprod Med > Epub ahead of print | A broad range of genetic and epigenetic factors contributes to female infertility, a substantial proportion of which is related to ovulatory disorders. Any factor that disrupts the normal function of key ovarian components, including the follicle, the enclosed oocyte, and surrounding somatic cells, may contribute to female infertility. Investigating the molecular factors involved in folliculogenesis and reproductive pathways may substantially improve the treatment of diseases affecting the female reproductive system. Long non-coding RNAs (lncRNAs), as key regulators of molecular and biological processes, play important roles in ovarian function and female fertility. These effects are mediated through interactions with DNA, RNA, and proteins, and lncRNAs are involved in processes such as granulosa cell differentiation, follicular growth, and ovarian hormonal regulation. Altered lncRNA expression may contribute to reproductive disorders such as polycystic ovary syndrome, endometriosis, and primary ovarian insufficiency. In addition, several lncRNAs have been proposed as potential biomarkers for the diagnosis of female reproductive disorders and as novel therapeutic targets. However, many functional mechanisms of these molecules remain unclear. This review summarizes recent scientific findings on the role of lncRNAs in the pathophysiology of female infertility and evaluates their potential for the development of novel diagnostic and therapeutic approaches. A better understanding of these molecular pathways may support more effective strategies for managing and treating female infertility. Infertility, defined as the inability to achieve pregnancy after 12 months of regular unprotected intercourse, affects approximately 15% of reproductive-age couples and remains a multifaceted clinical challenge [1,2]. Female-factor infertility encompasses a broad spectrum of etiologies, including anatomic, endocrine, and infectious causes, as well as specific conditions such as endometriosis. Polycystic ovary syndrome (PCOS) is a prevalent and complex cause of female infertility and accounts for approximately 70% of cases associated with ovulatory dysfunction [3-5]. Despite comprehensive diagnostic investigations, the underlying molecular regulatory networks remain insufficiently characterized. In particular, the functional and translational implications of long non-coding RNAs (lncRNAs) in folliculogenesis, granulosa cell (GC) function, and the hormonal imbalances characteristic of conditions such as PCOS and idiopathic infertility remain underexplored [6,7]. The ovarian follicle, the main functional unit of the female reproductive system, connects the oocyte with surrounding follicular cells, including granulosa and theca cells, through gap junctions. These connections allow the exchange of small molecules, including ions, metabolites, nutrients, and molecular messengers, between adjacent cells [8]. GCs play key roles in regulating the growth and maturation of mammalian ovarian follicles. By surrounding the oocyte and secreting growth factors, these cells support oocyte growth and development, regulate follicular growth, and guide follicular development toward mature oocyte formation. Oocyte quality therefore depends strongly on interactions with surrounding GCs [9]. Ovarian function and folliculogenesis are regulated by growth factors and cytokines, including transforming growth factor beta family members such as bone morphogenetic proteins, growth differentiation factors, and anti-Müllerian hormone (AMH), through paracrine and autocrine mechanisms. Disruption of these signaling pathways may lead to impaired oocyte development and infertility [10]. Therefore, investigating the molecular pathways responsible for GC function, proliferation, and differentiation is essential for understanding the mechanisms underlying folliculogenesis [11]. In addition, ovarian GCs play key roles in the pathogenesis of ovarian disorders such as PCOS and primary ovarian insufficiency (POI). Disrupted GC function and abnormal proliferation are major characteristics of PCOS. Therefore, studying GCs may help clarify the molecular mechanisms underlying these complex disorders [12]. Molecular biomarkers are important for evaluating oocyte quality and monitoring the effectiveness of assisted reproductive technology. These biomarkers can be classified into two main categories: protein-coding genes, including luteinizing hormone receptor (LHR), growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), gap junction protein connexin 43 (Cx43), apoptosis pathway proteins, and serpin family E member 2 (SERPINE2); and non-coding genes, including lncRNAs and microRNAs (miRNAs). LncRNAs perform regulatory functions through interactions with proteins, transcription factors, messenger RNAs (mRNAs), and miRNAs, and they show tissue-specific and condition-specific expression patterns [13]. Although interest in lncRNAs has increased in recent years, their regulatory mechanisms remain incompletely understood and, in some contexts, continue to be debated [14]. Despite substantial advances in understanding the molecular mechanisms involved in infertility, the role of lncRNAs in regulating reproductive processes requires further investigation. Increasing evidence suggests that these regulatory molecules play key roles in controlling follicular development, ovarian gene expression, and ovarian function. This review explores recent findings on the regulatory roles of lncRNAs in the pathophysiology of infertility, examines their molecular mechanisms in reproductive regulation, and evaluates their potential applications as diagnostic biomarkers and therapeutic targets. Non-coding RNAs (ncRNAs) are pivotal regulators of gene expression and cellular homeostasis. A large proportion of the higher eukaryotic genome is transcribed into ncRNAs. These RNAs are divided into two functional groups: structural RNAs, including ribosomal RNA and transfer RNA, and regulatory RNAs, including miRNAs, lncRNAs, circular RNAs, Piwi-interacting RNAs, small interfering RNAs (siRNAs), and small nucleolar RNAs (snoRNAs). The marked diversity of ncRNAs in size, structure, and function reflects their key roles in regulating cellular processes [15]. Only approximately 2% of the genome encodes protein-coding RNAs, whereas much of the remaining genome is transcribed into diverse ncRNAs, many of which have important regulatory functions. In addition to their housekeeping roles in essential cellular processes, ncRNAs actively regulate gene expression at transcriptional and post-transcriptional levels [16]. This review examines the multiple functions of lncRNAs and their roles in the pathogenesis of female infertility. miRNAs are ncRNA molecules of 19 to 24 nucleotides that primarily regulate gene expression post-transcriptionally by binding to the 3′ untranslated regions of target mRNAs, leading to translational repression or mRNA degradation. They can also modulate gene expression at the transcriptional and chromatin levels [17,18]. LncRNAs are transcripts longer than 200 nucleotides that are generally not translated into proteins. They may undergo splicing, polyadenylation, and capping, although some lncRNAs lack these modifications. Their functions depend partly on intracellular localization [16,19] and include the regulation of chromatin modifications, facilitation of chromosomal looping, modulation of DNA transcription, mRNA processing, and interactions with proteins and other RNAs [20]. LncRNAs are ncRNAs that, despite lacking conventional protein-coding capacity, play critical regulatory roles in diverse cellular processes. Based on their genomic location relative to protein-coding genes, lncRNAs are divided into six main groups: sense, antisense, bidirectional, intronic, intergenic, and enhancer-associated lncRNAs [21]. Based on mechanism of action, lncRNAs are classified as decoys, scaffolds, signals, or guides. These functional categories reflect their capacity to interact with chromatin, transcription factors, miRNAs, and RNA-binding proteins, which gives rise to broad regulatory versatility. Recent studies have shown that some ncRNAs contain open reading frames, may encode functional micropeptides, and play key roles in regulating physiological and pathological processes, including homeostasis, inflammation, metabolism, and tumor progression, in a tissue-specific manner. This finding highlights the complexity of lncRNA functions and their potential implications in disease development and lncRNA-targeted therapy [22-25]. The key roles of these molecules in disease pathogenesis have prompted researchers to develop new technologies and tools for targeting lncRNAs and designing lncRNA-based drugs. This approach has opened new avenues in drug development. Despite substantial progress, challenges remain, including the lack of successful reference cases and limited clinical data on the safety and efficacy of lncRNA-targeting drugs [26]. Among important lncRNAs and lncRNA-related mechanisms that regulate translational machinery and modulate the function of other ncRNAs, including miRNAs and snoRNAs, are competing endogenous RNAs (ceRNAs), metastasis associated lung adenocarcinoma transcript 1 (MALAT1), maternally expressed 3 (MEG3), homeobox A11 antisense RNA (HOXA11-AS), H19 imprinted maternally expressed transcript (H19), myocardial infarction associated transcript (MIAT), profilin 2 (PFL), HOX transcript antisense RNA (HOTAIR), plasmacytoma variant translocation 1 (PVT1), and activated in RCC with sunitinib resistance (ARSR) [16]. Recent studies have demonstrated the key roles of these molecules in the pathophysiology of a wide range of diseases, including cardiovascular and neurological disorders, cancers, and immune and metabolic diseases, through their effects on cellular activities [27]. LncRNAs are distinguished from other RNAs by their unique regulatory mechanisms, structural features, and biosynthetic pathways. However, many aspects of their structure and function remain unknown [28,29]. LncRNAs are a large group of ncRNA species that lack substantial protein-coding capacity. They exhibit cell-specific expression and regulatory functions. Studies suggest that the human genome contains more than 16,000 lncRNA genes, although computational analyses indicate that the actual number may reach 100,000, depending on annotation criteria and transcript-identification methods [30,31]. Most lncRNAs are transcribed by RNA polymerase II and include transcripts arising from intergenic regions, as well as sense and antisense transcripts from genes that overlap with other genes. These transcriptional processes generate long RNAs that often share characteristics with mRNAs: they are capped with 7-methylguanosine (m7G) at the 5′ end, polyadenylated at the 3′ end, and spliced similarly to mRNAs. Enhancer and promoter regions can also be independently transcribed into RNAs, which are known as enhancer RNAs and promoter upstream transcripts [32]. Although many lncRNAs resemble mRNAs, several types are processed from long primary RNA transcripts to produce mature lncRNAs without 5′ caps or 3′ polyadenylated tails. The production of these lncRNAs is closely associated with eukaryotic RNA processing. This feature allows many lncRNAs to remain predominantly in the nucleus and perform regulatory functions in diverse biological processes, such as gene-expression regulation and interactions with chromatin or other RNA molecules. As a result, lncRNAs are involved primarily in regulatory processes and differ functionally and biologically from mRNAs [32]. The functions of lncRNAs are closely linked to their structural features, which enable interactions with proteins, DNA, and other RNA molecules [20]. Their structural diversity allows them to act through multiple mechanisms. One of the most extensively studied structural features of lncRNAs is secondary structure. Secondary structures are formed through base-pairing interactions within an RNA molecule and affect stability, localization, and interactions with other molecules [33]. Recent studies have identified specific secondary structures in lncRNAs that are critical for their function. For example, stem-loop structures in certain lncRNAs facilitate binding to proteins involved in transcriptional regulation [34]. Tertiary structures also contribute to lncRNA function. These structures arise from long-range interactions between distant regions of the RNA molecule and may substantially affect its stability and activity. Recent advances in high-throughput sequencing technologies have enabled the identification of complex tertiary structures in lncRNAs. These studies have shown that specific tertiary interactions are essential for proper lncRNA folding and function [35]. Emerging evidence further suggests that the spatial organization of lncRNA molecules in the nucleus plays an important role in their function. Nuclear compartmentalization enables precise gene-expression regulation by bringing regulatory elements, such as enhancers and promoters, into spatial proximity and by allowing lncRNAs to act as scaffolds or guides for chromatin-remodeling complexes. Therefore, the three-dimensional structure of lncRNAs is crucial for facilitating long-range interactions between distant genomic regions [36]. LncRNAs regulate gene expression through five main mechanisms. At the transcriptional level, they regulate gene expression by binding to promoter regions, interacting with chromatin complexes, and modulating histone modifications and DNA methylation. At the level of histone modification, they alter histone methylation and acetylation patterns by recruiting histone-modifying enzymes to target-gene promoters. At the DNA methylation level, they regulate promoter methylation patterns through interactions with DNA methyltransferases and demethylases. Through interactions with transcription factors, lncRNAs can modulate transcriptional activity by recruiting or sequestering these factors at target-gene loci. Finally, lncRNAs can participate in bidirectional feedback loops through reciprocal regulatory interactions with target genes, resulting in mutual reinforcement of gene expression. These complex regulatory mechanisms indicate the central role of lncRNAs in gene-expression control [37-40]. The diverse mechanisms of lncRNAs enable their involvement in nearly all physiological activities of living cells and link them to a wide range of diseases, including fertility disorders. Increasing evidence suggests that lncRNAs act as master regulators and molecular coordinators of ovarian reproductive function. These regulatory molecules control a wide range of physiological processes through complex signaling networks, including ovulation, ovarian growth and development, sex steroid hormone biosynthesis and secretion, and corpus luteum formation and function. Follicular development and maturation are complex multistep processes that require precise, coordinated interactions among three major structural and functional components: the oocyte, GCs, and theca cells. These cellular interactions are regulated through paracrine and autocrine signaling pathways. Disruption of this organized regulatory network may lead to abnormalities in follicular growth and development and contribute to reproductive dysfunction [41]. Through transcriptional, post-transcriptional, and epigenetic regulatory mechanisms, lncRNAs play pivotal roles in maintaining homeostasis in essential reproductive processes. These regulatory molecules influence female reproductive physiology broadly, including sexual maturation, reproductive cycling during the fertile years, and physiological changes during menopause. In addition, they play important roles in fertility, successful conception, and pregnancy maintenance [42]. Extensive epigenetic research has shown that lncRNAs are involved in a wide range of processes, including histone and chromatin modification, DNA structural organization, and gene-expression regulation [43]. These epigenetic changes play fundamental roles in many reproductive biological processes, including spermatogenesis and ovulation [44]. At the transcriptional level, lncRNAs substantially affect mRNA production by modulating the activity of transcription factor complexes [45]. Beyond transcriptional control, these regulatory molecules also contribute to post-transcriptional gene regulation and participate in RNA splicing, processing, transport, translation, and degradation [46]. Regulation of chromatin structure and function through post-translational histone modifications is a central mechanism of gene-expression control. LncRNAs play prominent roles in this process and can alter chromatin structure and protein-binding patterns through mechanisms such as methylation, acetylation, and ubiquitination. In addition, these molecules can interfere with transcription by preventing the RNA polymerase II complex from binding to promoters [47]. Recent animal-model studies have revealed a pivotal role for lncRNA-GAS2 in regulating the Notch signaling pathway in ovarian tissue. Disruption of this signaling pathway has broad consequences for reproductive function, including reduced reproductive capacity, structural damage and rupture of ovarian cysts, reduced numbers of antral follicles and corpora lutea, and damage to the basement membrane surrounding developing follicles. Together, these abnormalities disrupt normal folliculogenesis and may contribute to infertility [48]. These findings indicate that precise regulation of lncRNAs is essential for maintaining ovarian tissue homeostasis and normal reproductive function [48]. Oocyte maturation is a fundamental process in follicular growth and development and plays a critical role in determining fertility potential and fertilization competence after ovulation. Molecular studies have shown that lncRNAs tightly regulate oocyte maturation through complex mechanisms [49]. Several studies have delineated specific roles for individual lncRNAs. For example, significantly reduced lncRNA-Y00062 expression in cumulus cells from low-quality embryos correlates with altered NIMA-related kinase 7 (NEK7) expression, suggesting a potential role in spindle assembly and meiotic progression [50]. Broadly, four major lncRNAs—X-inactive specific transcript (XIST), NEAT1, MALAT1, and growth arrest specific 5 (GAS5)—are involved in follicle development through epigenetic control and molecular scaffolding [51]. In addition, analysis of 89 differentially expressed lncRNAs across maturation stages, particularly the 12 located within host-gene introns, has highlighted their regulatory significance in steroidogenesis, growth factor signaling, and apoptosis control. Because oocyte quality depends strongly on GC function, these lncRNA expression profiles may serve as biomarkers of in vitro fertilization (IVF) success and as potential therapeutic targets [52]. Recent evidence indicates that lncRNA AK124742 may act as a regulator of embryonic development, with increased expression correlating with improved embryo quality and success rates through modulation of proliferation, differentiation, and implantation pathways [53]. The differential expression of 633 lncRNAs in cumulus cells further underscores their role in regulating metabolic processes, particularly unsaturated fatty acid biosynthesis, and cell division required for follicular growth and energy supply [50]. Cell-specific expression patterns across follicular compartments suggest a precise, multifaceted regulatory role: coordinated expression of breast cancer anti-estrogen resistance 4 (BCAR4), TCL1 upstream neural differentiation-associated RNA (TUNAR), and cancer susceptibility 8 (CASC8) in metaphase II oocytes, together with MALAT1 expression in cumulus cells, establishes a network that regulates follicle development, apoptosis-related clearance, extracellular matrix function, and chromatin remodeling necessary for oocyte developmental potential [49]. AMH acts as a key regulator of sexual development and follicular homeostasis. By participating in GC proliferation, AMH plays a central role in regulating ovarian follicle growth and development [54]. Molecular studies have shown that lncRNAs, particularly lncRNA-H19, play critical roles in regulating AMH expression. In a pioneering mouse-model study, deletion of the lncRNA-H19 gene led to a marked reduction in AMH expression, with several consequences, including accelerated follicular atresia, shortened growth cycles of secondary, preantral, and antral follicles, and disruption of the estrous cycle. These findings indicate that lncRNAs have essential roles in ovarian function by regulating AMH expression and influencing follicular growth dynamics and menstrual cycle regulation [55]. Furthermore, NEAT1, which is highly expressed in the corpus luteum, plays a key role in steroid hormone production and pregnancy maintenance [56]. In this context, H19 is also an important regulator of fertility. Studies have shown that H19 expression is significantly higher in the ectopic endometrium of patients with endometriosis than in eutopic endometrium. Suppression of H19 inhibits proliferation and invasion of endometriotic cells through regulation of the miR-124-3p/integrin subunit beta 3 (ITGβ3) axis [57]. In women with diminished ovarian reserve (DOR), circulating and ovarian tissue levels of H19 are markedly decreased. In addition, women with low serum AMH levels have lower serum H19 levels, which may limit the number of mature estradiol-producing follicles and impair ovulation. These findings suggest that H19 plays an important role in AMH regulation [55]. Epigenetic changes, particularly DNA methylation, play fundamental roles in reproductive function. Imprinted genes show parent-of-origin-specific expression patterns regulated by differential methylation. Extensive research has demonstrated that lncRNAs serve as critical regulators of steroidogenesis and the female reproductive cycle. Among these molecules, H19 is a key imprinted gene that is transcribed exclusively from the maternal allele, whereas the paternal allele remains silent through methylation. Studies have shown that steroid hormones regulate H19 expression in various hormone-responsive tissues. In endometrial tissue, H19 transcripts are localized specifically to the stroma and are absent from the glandular and luminal epithelium. H19 expression varies throughout the menstrual cycle, increasing before decidualization and peaking late in the secretory phase [58]. Comprehensive studies have shown that H19 acts as a ceRNA by binding miRNA let-7 and thereby regulates the insulin-like growth factor (IGF) signaling pathway. This regulation is essential for the proliferation and differentiation of endometrial stromal cells (ESCs) during the menstrual cycle. During the normal menstrual cycle, H19 expression is coordinated with hormonal changes, particularly estrogen and progesterone, and peaks during the secretory phase. This increased expression coincides with preparation of the endometrium for embryo receptivity. Aberrant H19 expression is associated with reproductive disorders, including unexplained infertility and endometriosis. In patients with endometriosis, decreased H19 expression leads to downregulation of insulin-like growth factor 1 receptor (IGF1R), which in turn impairs the proliferation and differentiation of ESCs. In addition, through regulation of let-7, H19 affects the expression of genes involved in cell adhesion, such as integrin beta-3 (ITGB3), which is essential for successful implantation. This complex regulation suggests that H19 is a key regulator of endometrial homeostasis and fertility [59-61]. Recent studies have shown that, in addition to H19, LINC00473 is a key regulator of endometrial decidualization through the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) signaling pathway. Unlike other menstrual cycle regulators, LINC00473 expression is independent of steroid hormones, including estrogen and progesterone, and is instead regulated by the cAMP/PKA pathway. This lncRNA regulates key decidualization genes, including prolactin (PRL), insulin-like growth factor-binding protein 1 (IGFBP1), progesterone receptor (PGR), and homeobox (HOX) genes, which are critical for endometrial development. Meanwhile, HOXA11 antisense RNA acts as an additional regulator whose expression pattern is synchronized with the menstrual cycle, reaching a maximum during the proliferative phase and decreasing as progesterone levels increase. This complex regulatory network demonstrates how LINC00473 and other lncRNAs cooperate to regulate endometrial receptivity (ER) and implantation success. Disruption of these regulatory pathways may lead to infertility and other reproductive disorders [62,63]. One study investigated the role of lncRNAs in gene-expression control in relation to fertility and maternal age. Using NanoString technology, the researchers examined the expression profiles of 68 lncRNAs in cumulus cells isolated from metaphase II oocytes from younger and older women. The results showed that 28 lncRNAs were significantly downregulated in cumulus cells from older women. Using databases such as miRNet, TarPmiR, and Kyoto Encyclopedia of Genes and Genomes (KEGG), the investigators identified ceRNA networks and found that miRNAs binding to 11 of these lncRNAs were involved in important signaling pathways, including phosphoinositide 3-kinase (PI3K)-protein kinase B (Akt), forkhead box O (FOXO), and p53. These pathways are essential for ovarian folliculogenesis and female germ-cell maturation. The researchers concluded that reduced expression of these lncRNAs in cumulus cells from older women could affect the expression of genes encoding proteins associated with reproductive aging. A better understanding of these regulatory networks may support the development of new therapies and improve reproductive outcomes in older women [64]. Infertile couples account for approximately 15% of married couples, and female factors are estimated to contribute to approximately 40% of infertility cases. Although many factors can contribute to infertility, molecular research on female infertility remains important for clarifying disease mechanisms and identifying potential diagnostic and therapeutic targets [65]. PCOS is the most common endocrine and metabolic disorder in women of reproductive age. This heterogeneous syndrome is characterized by a range of symptoms and signs, including hyperandrogenism, which may manifest as hirsutism, acne, hair loss, and elevated serum androgen concentrations. Women with PCOS may also present with polycystic ovarian morphology, irregular menstruation, obesity or overweight, mood disorders, and infertility [66]. The pathogenesis of this syndrome remains unclear, but research into its genetic and molecular causes has increased in recent years because of growing interest in molecular interactions affecting genes involved in PCOS development [67]. Recent studies have demonstrated a significant role for lncRNAs in the pathogenesis of PCOS. Although next-generation sequencing has identified numerous differentially expressed lncRNAs in PCOS-associated tissues, functional and mechanistic research on these regulatory molecules remains in its early stages. Current studies have focused mainly on lncRNA expression patterns and functional mechanisms in several key tissues and cell types, including peripheral blood leukocytes, which may serve as non-invasive biomarkers; cumulus cells, which play critical roles in oocyte development; GCs, which contribute to steroid hormone production; and follicular fluid, which provides the microenvironment for follicular growth and development (Figure 1). Recent findings suggest that lncRNAs are involved in PCOS pathogenesis through several molecular pathways, including regulation of steroid biosynthesis leading to hyperandrogenism, modulation of steroid receptor activity affecting hormonal homeostasis, regulation of lipid metabolism and insulin resistance associated with PCOS-related obesity, and control of fundamental cellular processes such as proliferation, differentiation, and apoptosis in ovarian cells that may lead to polycystic ovarian morphology. These molecular mechanisms act in concert and ultimately contribute to the complex phenotype of PCOS [65]. Functional studies have shown that various lncRNAs play critical regulatory roles in GC proliferation and apoptosis, both of which are essential for normal ovarian function. These regulatory molecules also contribute to cell development, differentiation, and proliferation and are particularly active during the follicular phase of the menstrual cycle, directly implicating them in PCOS pathogenesis [68]. One important mechanism of lncRNA action is interaction with miRNAs. These interactions can affect both miRNA synthesis and activity. The importance of this complex regulatory network between lncRNAs and miRNAs in modulating biological processes, including cellular development, nutrient metabolism, and responses to biotic and abiotic stress, has been well documented [69]. These findings suggest that deeper understanding of lncRNA roles and mechanisms may support the development of novel therapeutic approaches for PCOS (Table 1) [70-83]. Studies have shown that lncRNAs are involved in PCOS pathogenesis through several molecular pathways. One of the most important pathways is regulation of steroid biosynthesis, which contributes to hyperandrogenism. These molecules also modulate steroid receptor activity, thereby affecting hormonal homeostasis, and regulate lipid metabolism and insulin resistance, both of which are associated with PCOS-related obesity [65]. ZNFX1 antisense RNA 1 (ZFAS1) is a key regulator of steroidogenesis. Studies have shown that reduced ZFAS1 expression increases the secretion of steroid hormones, including progesterone and estradiol, in GCs [79]. This finding indicates that ZFAS1 acts as a negative regulator of steroid hormone production. Studies have also shown that inhibition of lncRNA-ovarian cancer associated 1 (Lnc-OC1) in human GCs is associated with increased aromatase mRNA expression, which subsequently increases estradiol production [77]. Recently, a novel molecule named hormone disturbance in PCOS associated regulator of RNA-binding protein with multiple splicing (HUPCOS) was identified as a 495-bp intergenic lncRNA at position 15q22. This molecule showed a positive association with follicular-fluid testosterone levels through inhibition of cytochrome P450, family 11 (CYP11) activity, a key enzyme in steroid biosynthesis [84]. Regarding glucose metabolism, H19 showed a positive correlation with fasting plasma glucose levels, although no direct correlation with insulin resistance was observed [75]. In contrast, patients with PCOS and insulin resistance showed decreased GAS5 expression along with a significant increase in interleukin-18, suggesting a possible role for these two molecules in insulin resistance pathogenesis [73]. Recent studies have also shown that lncRNA HLA complex group 26 (HCG26) has a dual role in steroidogenesis regulation. Inhibition of this molecule increases aromatase gene expression and subsequently estradiol production. These findings suggest that HCG26 is a key regulator of steroidogenesis and that its dysregulation may contribute to PCOS pathogenesis [85]. The balance between GC apoptosis and proliferation in PCOS is regulated by several lncRNAs through distinct molecular mechanisms. Lnc-CCNL1-3:1 contributes to the PCOS phenotype by initiating metabolic dysfunction through interference with glucose transporters (GLUTs), which then acts as an upstream trigger of the apoptotic cascade. This metabolic link distinguishes Lnc-CCNL1-3:1 from other lncRNAs implicated in GC apoptosis [86]. In contrast to general p53 activation, BRAF activated non-coding RNA (BANCR) specifically modulates GC fate by controlling downstream transcriptional targets of the p53 pathway. This regulation produces a confirmed signature of increased apoptosis and reduced proliferation in PCOS samples [74]. Granulosa-cells-differentiation-associated RNA (GDAR) provides another distinct axis of control by acting upstream of classical cell-death execution and regulating the ratio of pro-apoptotic to anti-apoptotic proteins. This level of regulation significantly correlates with overall PCOS severity and impairs normal folliculogenesis [87]. Complex regulatory networks between lncRNAs and miRNAs play important roles in PCOS pathogenesis. NEAT1 is one of the most important lncRNAs in these networks. This molecule binds directly to miR-16, inhibiting its function and regulating target-gene expression. In addition, NEAT1 interacts with miR-483 and miR-324-3p, thereby contributing to glucose and lipid metabolism regulation. Studies have shown that increased NEAT1 expression in patients with PCOS is associated with impaired glucose homeostasis and insulin resistance [83,88]. MALAT1 functions as a ceRNA within a regulatory network by binding to various miRNAs, inhibiting their function, and regulating target-gene expression. MALAT1 sequesters miRNAs, preventing them from suppressing target mRNAs and thereby influencing key cellular processes. Studies have shown that MALAT1 regulates genes involved in steroid metabolism through interaction with miR-125b. This molecule also contributes to GC proliferation and apoptosis by forming regulatory networks with other miRNAs, such as miR-200c and miR-145 [89]. H19 is another key lncRNA involved in glucose metabolism regulation. Through interaction with the let-7 family of miRNAs, H19 regulates genes involved in the insulin signaling pathway. Studies have shown that H19 may act as a molecular sponge for miR-29a-3p, thereby regulating high-mobility group AT-hook 2 (HMGA2) expression. HMGA2, a non-histone chromatin protein, plays crucial roles in cell proliferation, differentiation, and metabolic regulation by modulating gene transcription and chromatin structure, processes that are relevant to PCOS pathogenesis. Its involvement in these cellular mechanisms contributes to insulin resistance and glucose metabolism disturbances commonly observed in patients with PCOS. This mechanism plays an important role in insulin sensitivity and glucose metabolism regulation. Increased H19 expression in patients with PCOS is associated with increased fasting glucose levels and impaired glucose metabolism [75,90]. Recent studies have shown that these regulatory networks can act in concert and form a complex gene-regulatory system. For example, NEAT1 and MALAT1 may cooperate and enhance their regulatory effects through co-regulation of specific miRNAs. These findings indicate that a complete understanding of lncRNA roles in PCOS pathogenesis requires comprehensive examination of these regulatory networks and their interactions [83]. Blood-based lncRNA biomarkers may be particularly important for PCOS diagnosis and prognosis. Studies have shown that steroid receptor RNA activator (SRA) and MIRLET7BHG are significantly overexpressed in the peripheral blood of patients with PCOS, and this overexpression is directly correlated with body mass index. Research has shown that expression levels of these molecules could be used as biomarkers to predict obesity risk in patients with PCOS. Significant correlations have also been observed between their expression levels and metabolic parameters, such as insulin resistance and lipid profile [68,71]. GAS5 is an important biomarker associated with insulin resistance. Reduced GAS5 expression in the peripheral blood of patients with PCOS is associated with increased interleukin-18 levels, indicating a potential role in systemic inflammation and insulin resistance. Studies have shown that GAS5 expression levels can be used as an independent predictor of insulin resistance in patients with PCOS. Changes in GAS5 expression are also associated with responses to insulin-sensitizing treatments [73]. XIST is recognized as an important biomarker for predicting pregnancy outcomes in women with PCOS. Increased XIST expression in peripheral blood is associated with an increased risk of pregnancy complications, such as gestational diabetes and preeclampsia. Studies have shown that monitoring XIST levels during pregnancy may help identify patients at risk of pregnancy complications at an early stage [91]. Sorafenib resistance-associated lncRNA in renal cell carcinoma (SRLR) has also recently been identified as a novel biomarker associated with GC apoptosis. Peripheral blood SRLR expression is directly related to GC apoptosis and the severity of folliculogenesis disorders. Studies have shown that SRLR plays an important role in PCOS pathogenesis by regulating apoptotic signaling pathways. Changes in SRLR expression are also associated with responses to ovulation-induction treatments [81]. Recent multi-marker panels that combine these lncRNAs have shown higher diagnostic accuracy. These panels can provide more comprehensive information on patients’ metabolic, hormonal, and inflammatory status and may therefore support more accurate clinical decision-making [88]. Dual regulators in PCOS demonstrate multifunctional activity by simultaneously influencing proliferation, steroidogenesis, and cellular homeostasis through distinct signaling networks. HCG26 acts as a central coordinator of the PI3K/AKT and mitogen-activated protein kinase (MAPK) cascades, integrating growth and steroidogenic signals within theca cells. Its elevated expression correlates with increased androgen synthesis and theca-cell hyperplasia, primarily through transcriptional regulation of the steroidogenic enzyme CYP17A1 [92]. Unlike the general steroidogenic modulation observed in other contexts, this dual regulation by HCG26 directly links metabolic and proliferative imbalance to the androgen excess characteristic of PCOS. Prader-Willi region non-protein coding RNA 2 (PWRN2) exerts a distinct regulatory influence on the follicular milieu by maintaining ionic and metabolic equilibrium. Through modulation of proton pump and ion channel gene expression, PWRN2 regulates follicular-fluid acidity, a parameter critical for oocyte maturation and quality. Furthermore, its involvement in glucose metabolism within GCs connects local energy dynamics to follicular growth outcomes, an association specific to the altered metabolic setting of PCOS [72]. Telomeric repeat-containing RNA (TERRA) differs mechanistically by controlling chromosomal integrity and cellular longevity. It interacts directly with telomerase and telomere-binding proteins to sustain telomere length, thereby preventing premature cellular aging observed in PCOS ovarian tissues. Impaired TERRA expression correlates not only with telomere shortening but also with reduced oocyte competence in IVF patients, underscoring its systemic role in ovarian maintenance and reproductive potential [93]. Importantly, these dual regulators appear to cooperate rather than act redundantly. The metabolic-environmental interplay between HCG26 and PWRN2 may fine-tune granulosa-cell function and follicular pH, whereas TERRA cross-communication with other regulators may help maintain genomic stability and coordinated resistance to ovarian cellular aging. Collectively, their complementary regulation delineates a network in which distinct signaling axes converge to sustain follicular viability under the dysregulated endocrine state of PCOS [72]. POI, also referred to historically as premature ovarian failure, is a hypergonadotropic ovarian disorder characterized by cessation of menstruation or ovarian dysfunction before the natural age of menopause, typically before age 40 years. According to European Society of Human Reproduction and Embryology (ESHRE) guidelines, a definitive diagnosis of POI requires follicle-stimulating hormone (FSH) levels greater than 25 IU/L on two occasions measured at least 4 weeks apart, accompanied by amenorrhea or oligomenorrhea for at least 4 months. Patients with POI present with multiple features, including decreased estrogen levels, early menopausal manifestations, elevated FSH levels, amenorrhea, and infertility. Despite therapeutic efforts, such as estrogen therapy in severe cases of POI, infertility remains a major challenge [94,95]. Although impaired estrogen production is the main underlying cause of POI symptoms, multiple factors, including genetic variation, adverse effects of medical treatments, environmental exposures, viral infections, and chronic diseases, contribute to its pathogenesis, which remains partly unknown. In a whole-exome sequencing study of 1,030 patients with POI, mutations in genes involved in gonadal development and folliculogenesis pathways were associated with disease pathology and were identified as key factors in disease occurrence and progression [96]. In addition to protein-coding genes, lncRNAs play diverse biological roles in POI pathogenesis, although the functions of many of these molecules in POI development and progression remain unknown. The role of lncRNAs in regulating GC apoptosis in POI has been established through several molecular pathways. Studies have demonstrated that nuclear paraspeckle assembly transcript 1 (NEAT1) plays a crucial role in apoptosis regulation by modulating p53 expression. According to Li et al. [97], NEAT1 expression is significantly reduced in ovarian tissue from patients with POI, leading to increased p53 expression and subsequent initiation of cellular apoptosis. Similarly, Sun et al. [98] showed that differentiation antagonizing non-protein coding RNA (DANCR) acts through interaction with heterogeneous nuclear ribonucleoprotein C (hNRNPC) and p53. Reduced DANCR expression in GCs from patients with POI disrupts hNRNPC binding to p53, increasing p53 protein levels and initiating GC senescence [98]. Wang et al. [99] demonstrated that PVT1 plays a role in regulating GC apoptosis. Hypermethylation-induced PVT1 downregulation leads to GC apoptosis by inhibiting FOXO3a phosphorylation and enhancing FOXO3a transcriptional activity [99]. Xiong et al. [100], in a study examining the effects of cyclophosphamide on GCs, identified a role for MEG3 in apoptosis regulation. Cyclophosphamide-induced MEG3 upregulation enhances the expression of apoptotic markers, including p53, p66Shc, p16, and activated caspase-3, through activation of the MEG3-p53-p66Shc pathway. This cascade ultimately inhibits cell proliferation and contributes to POI progression [100,101]. These findings suggest that lncRNAs play pivotal roles in regulating GC apoptosis and POI progression through multiple molecular pathways. Understanding these pathways could facilitate the development of novel therapeutic strategies to regulate apoptosis in POI. Recent studies have revealed roles for several lncRNAs in regulating GC proliferation and differentiation. GC-associated transcript 1 (GCAT1), also known as LINC02690, is one important regulator. Reduced GCAT1 expression in GCs from patients with POI is significantly correlated with serum FSH and AMH levels. The mechanism of GCAT1 action involves regulation of p27-dependent polypyrimidine tract-binding protein 1 (PTBP1), ultimately inhibiting GC proliferation [102]. Another lncRNA, ZNF674-AS1, is downregulated in GCs from patients with POI and is correlated with serum ovarian-reserve markers. This molecule is produced in response to stress and plays an important role in regulating glycolysis and GC proliferation. ZNF674-AS1 acts by regulating aldolase A (ALDOA) activity, which leads to follicular dysfunction [103]. Long noncoding RNA RP4-545C24.1 (designated DDGC), also known as lncRNA RP4-545C24.1, plays a dual role in GCs by contributing to both DNA repair and cellular differentiation. It regulates RAD51 mRNA stability by competing with miR-589 for binding to this transcript. In addition, DDGC modulates Wilms' tumor 1 (WT1) protein stability through interaction with heat shock protein 90 (HSP90). Therefore, DDGC can mitigate etoposide-induced DNA damage and apoptosis [104]. These findings indicate that lncRNAs play key roles in regulating GC proliferation and differentiation through diverse molecular mechanisms and could be considered potential therapeutic targets in POI. Complex regulatory networks between lncRNAs and miRNAs have been identified in POI pathogenesis. Deleted in lymphocytic leukemia 1 (DLEU1) is one of the most important regulators in these networks and targets miR-146b through a sponge function. Studies have shown that decreased DLEU1 expression in GCs from patients with POI leads to increased miR-146b levels, which are associated with decreased expression of target genes such as TNF receptor-associated factor 6 (TRAF6) and interleukin-1 receptor-associated kinase 1 (IRAK1). These changes ultimately disrupt the nuclear factor κB signaling pathway and increase GC apoptosis [105]. Similarly, translation regulatory long non-coding RNA 1 (TRERNA1) regulates GC survival by targeting miR-23a. Decreased TRERNA1 expression in POI increases miR-23a levels, which in turn suppresses X-linked inhibitor of apoptosis protein (XIAP) expression and increases GC sensitivity to apoptosis. This regulatory pathway plays an important role in maintaining follicular homeostasis [95]. Like DLEU1, lncRNA gamma-butyrobetaine hydroxylase 1 antisense transcript 1 (BBOX1-AS1) targets miR-146b through its sponge function, but its mechanism of action differs. This lncRNA regulates TRAF6 expression by competing with TRAF6 for binding to miR-146b. Decreased BBOX1-AS1 expression in POI increases free miR-146b levels and consequently decreases TRAF6 expression, disrupting the PI3K/AKT signaling pathway and reducing cell survival [105]. These regulatory networks also play important roles in DNA repair and genomic integrity by controlling the expression of genes involved in DNA repair pathways, which are essential for maintaining GC health and preventing POI progression. Maintaining genomic integrity and proper DNA repair is essential for normal GC function, and lncRNAs play important roles in these processes. HLA complex P5 (HCP5) is one key regulator in this context and acts through interactions with two important proteins, MutS homolog 5 (MSH5) and Y-box binding protein 1 (YB1). Studies have shown that decreased HCP5 expression in GCs from patients with POI is associated with decreased MSH5 expression. MSH5 is essential for mismatch repair, and its reduction leads to DNA-damage accumulation. In addition, HCP5 helps maintain genomic stability by regulating YB1, a transcription factor involved in the DNA-damage response [106]. DDGC is also a dual regulator of DNA repair pathways and acts through interactions with RAD51 and WT1. This lncRNA functions as a ceRNA for miR-589 and regulates RAD51 transcript stability. RAD51 is a key protein in homologous recombination repair (HR), and its reduction causes defects in DNA double-strand break repair. In addition, DDGC regulates WT1 protein stability through interaction with HSP90, which is involved in regulating the expression of genes related to DNA repair. Studies have shown that DDGC expression is reduced in GCs from patients with POI and that this reduction is associated with increased DNA damage and apoptosis [104]. These findings suggest that lncRNAs play pivotal roles in maintaining GC genomic integrity by regulating key proteins involved in DNA repair pathways. Disruption of these regulatory pathways can lead to DNA-damage accumulation, ultimately causing cell death and POI progression (Figure 2). Endometriosis is a benign disease of the female reproductive system characterized by the presence, growth, and infiltration of functional endometrial or endometrial-like tissue outside the uterus [107]. This estrogen-dependent disease has a prevalence of 6%–10% and affects 50%–60% of women with pelvic pain and/or infertility. Its main clinical manifestations include dysmenorrhea, infertility, and pelvic pain [108]. Although several theories have been proposed to explain the etiology of endometriosis, its pathogenesis remains unclear. Proposed mechanisms include retrograde menstruation, coelomic metaplasia, and blood or lymphatic dissemination [109]. Although complex biological processes involving various genes contribute to endometriosis, studies have shown that multiple lncRNAs also play important roles in its occurrence and progression. Extensive studies have shown that master regulatory lncRNAs play key roles in endometriosis pathogenesis. Using microarray chip technology, Sun and colleagues first identified differential lncRNA expression patterns in ectopic and eutopic endometrium from patients with ovarian endometriosis. In this comprehensive study, 948 lncRNAs and 4,088 mRNAs were dysregulated, among which lncRNA cell adhesion molecule L1 like antisense RNA 2 (CHL1-AS2) showed the most significant change [110]. Furthermore, Zhang et al. [111] showed using quantitative reverse transcription polymerase chain reaction that CHL1-AS2 expression was reduced in the eutopic endometrium but increased in ectopic lesions and adjacent tissues. Notably, the menstrual cycle did not affect CHL1-AS2 expression, supporting the interpretation that aberrant expression of this molecule is directly related to endometriosis pathogenesis [111]. H19, a 2.3-kb lncRNA located on chromosome 11p15.5, plays an important role in regulating endometrial and ovarian tissue. Ghazal et al. [59] examined H19 levels in normal and pathological endometrial tissue and showed that H19 expression was significantly reduced in endometriosis. Molecular pathway analysis showed that the H19/let-7/IGF1R pathway plays a key role in repairing damaged endometrium and that decreased H19 expression leads to impaired ER and, consequently, infertility [59]. Liu et al. [112] identified a novel mechanism involving MALAT1. They found that MALAT1 expression was increased alongside increased autophagy in ectopic endometriotic tissues. This increased expression was positively correlated with hypoxia-inducible factor 1-alpha (HIF-1α). These findings indicate that MALAT1 acts as a key mediator of hypoxia-induced autophagy and plays an important role in endometriosis progression [112]. The link among hypoxia, autophagy, and MALAT1 suggests a novel mechanism in endometriosis pathogenesis and may represent a potential therapeutic target for this disease. These key regulators act in concert to form a complex regulatory network that contributes to endometriosis pathogenesis. A better understanding of how these molecules function and interact may support the development of more effective treatments for endometriosis. Several studies have shown that lncRNAs play important roles in regulating cell proliferation and migration in endometriosis. Sha et al. [113] identified lncRNA LINC00261 and described a novel mechanism controlling cell behavior. This molecule inhibits cell proliferation and migration in the endometriosis cell line CRL-7566 while inducing apoptosis in these cells [113]. This finding suggests that LINC00261 may act as a negative regulator of cell growth in endometriosis. In a comprehensive study, Lin et al. [114] showed that lncRNA SRA and steroid receptor RNA activator protein (SRAP) levels were significantly lower in normal endometrium than in tissues affected by endometriosis. In ovarian endometriosis, increased SRA expression was associated with increased estrogen receptor alpha expression in periovarian tissues. This increased expression occurred alongside decreased vascular endothelial growth factor levels, which may help explain mechanisms of endometriosis progression and recurrence [114,115]. Liu et al. [116] investigated the role of LINC01279 in endometriosis pathogenesis in two separate studies. They found that this lncRNA was abnormally expressed in patients with endometriosis and was closely associated with cyclin-dependent kinase 14 (CDK14) and CXC motif chemokine ligand 12 (CXCL12) [117]. Their complementary study showed that LINC01279 downregulates HOXA10 expression by targeting miR-135b, a pathway that plays a key role in endometriosis initiation and progression [116]. These findings identify LINC01279 as a potential therapeutic target for endometriosis. Overall, these regulators form a complex network that controls cell proliferation and migration. A better understanding of this network may support the development of targeted therapies for endometriosis. The interplay of these molecules with hormonal signaling pathways and growth factors highlights the complexity of cellular-behavior regulation in this disease. Recent research on lncRNAs has identified several promising biomarkers and therapeutic targets for endometriosis. In a comprehensive study, Yin et al. [118] showed that lncRNA C8orf49 expression was significantly increased in endometriotic tissue and plasma from patients, and this increase was directly related to dysmenorrhea severity. They also found that inhibiting C8orf49 in ESCs could suppress cell proliferation and migration. This effect occurred through the C8orf49/miR-1323/phosphatase and tensin homolog (PTEN)/frizzled class receptor 4 (FZD4) pathway, in which C8orf49 regulates PTEN/FZD4 expression and controls ESC activity by recruiting miR-1323. These findings support C8orf49 as a reliable biomarker and prognostic factor for endometriosis [118]. LINC01279 is recognized as a key regulator in endometriosis pathogenesis. Studies have shown that this molecule reduces expression of HOXA10, a key gene in endometrial development and function, by targeting miR-135b. This regulatory pathway plays an important role in endometriosis initiation and progression [116]. The close relationship of LINC01279 with cyclin-dependent kinase 14 and CXC motif chemokine ligand 12 also suggests that this molecule is a potential therapeutic target for endometriosis [119]. H19, a 2.3-kb lncRNA located on chromosome 11p15.5, plays critical roles in fertility and endometrial function. Ghazal et al. [59] examined H19 levels in normal and pathological endometrial tissues and reported significantly reduced H19 expression in endometriosis. Their mechanistic studies showed that the H19/let-7/IGF1R pathway plays a key role in repairing damaged endometrium. Reduced H19 expression disrupts this pathway, resulting in impaired ER, which may explain infertility in these patients [59]. These biomarkers not only contribute to a better understanding of endometriosis pathophysiology but also may support early diagnosis, prognosis, and targeted therapy design. Simultaneous evaluation of these markers can provide a more comprehensive picture of disease status and treatment response and may support the development of personalized therapeutic approaches. Molecular regulatory networks in endometriosis play complex and multifaceted roles in controlling cellular processes. The C8orf49/miR-1323/PTEN/FZD4 pathway is one of the most important regulatory networks in endometriosis pathogenesis. Studies have shown that C8orf49 acts as a molecular sponge for miR-1323 and controls cellular activities by regulating PTEN and FZD4 expression. Increased C8orf49 expression in endometriotic tissues decreases miR-1323 levels and consequently increases PTEN and FZD4 expression. These changes ultimately lead to abnormal proliferation and migration of ESCs [118]. The H19/let-7/IGF1R regulatory pathway plays a key role in tissue repair and maintenance of endometrial homeostasis. H19 controls IGF1R levels by regulating let-7, an evolutionarily conserved miRNA. Under normal conditions, this pathway is essential for proper endometrial tissue repair. Studies have shown that in endometriosis, reduced H19 expression disrupts this regulatory pathway. This disruption is associated with reduced tissue repair capacity and increased risk of ectopic adhesion formation [59]. Disruption of this pathway may also explain some fertility problems in patients with endometriosis. The MALAT1/HIF-1α regulatory network plays a pivotal role in controlling cellular autophagy. LncRNA MALAT1 is upregulated under hypoxic conditions and regulates cellular responses to oxidative stress by stabilizing HIF-1α. In endometriotic tissues, increased MALAT1 expression is associated with increased autophagic activity, which may contribute to endometrial cell survival in adverse environments. This pathway also contributes to angiogenesis and chronic inflammation regulation in endometriotic lesions [112]. A deeper understanding of these molecular regulatory networks may improve understanding of endometriosis pathophysiology and lead to the identification of new therapeutic targets. Targeted interference with these pathways, especially during early disease stages, could provide more effective strategies for controlling disease progression. Furthermore, simultaneous examination of multiple regulatory pathways may clarify the interrelationships among these networks and their effects on clinical outcomes (Figure 3). Recent data indicate that lncRNAs contribute to female infertility by linking mitochondrial, immunological, and endometrial regulatory mechanisms across the reproductive tract. In the ovary, lncRNAs interact with essential metabolic and apoptotic processes, thereby influencing mitochondrial activity, oxidative-stress responses, and oocyte quality. In the uterus, specific lncRNA networks modulate immune-cell recruitment, inflammatory signaling, and stromal–epithelial interactions, ultimately affecting ER, embryo implantation, and decidualization. Dysregulation of lncRNA-mediated processes is associated with prevalent female infertility disorders, including PCOS, endometriosis, and POI, underscoring their potential as biomarkers and therapeutic targets [120-122]. Figure 4 visualizes the links among lncRNA dysregulation, epigenetic regulation, and metabolic regulation in female infertility pathophysiology. Mitochondria are essential organelles responsible for energy production, oxidative-stress regulation, calcium homeostasis, and apoptosis regulation. They are critical for preserving redox equilibrium by controlling the generation and elimination of reactive oxygen species (ROS). Mitochondrial dysfunction causes oxidative-stress accumulation, resulting in DNA damage, genetic mutations, and apoptosis, which may contribute to POI development. LncRNAs modulate the transcription and translation of numerous genes and profoundly affect several physiological and pathological processes, including oxidative stress, inflammation, and apoptosis [123]. Transcriptomic profiling of GCs in PCOS has revealed distinct lncRNA signatures associated with oxidative phosphorylation, ROS regulation, and apoptotic pathways. A recent study showed significantly decreased lncRNA NONHSAT233728.1 expression in GCs from women with PCOS. Knockdown of NONHSAT233728.1 in the human granulosa-like tumor cell line (KGN) exacerbated mitochondrial dysfunction, as evidenced by increased ROS accumulation, disrupted mitochondrial membrane potential, and apoptosis activation through MAPK/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling, ultimately resulting in GC death [124]. Several lncRNAs, such as GCAT1, are downregulated in GCs, leading to disrupted cell-cycle regulation and increased follicular atresia [102]. Recent studies indicate that MEG3 downregulation inhibits the PI3K/AKT/mammalian target of rapamycin (mTOR) pathway, decreases autophagy in GCs, and normalizes GC proliferation. MEG3 can reduce hydrogen peroxide (H2O2)-induced oxidative-stress damage in GCs through regulation of the AMP-activated protein kinase (AMPK)/mTOR pathway. MALAT1 influences mitochondrial function, enhances ROS production, and causes mitochondrial depolarization, thereby activating apoptotic pathways. Another study found that CUFF.253988.1 enhances mitochondrial damage and apoptosis in ovaries after T-2 toxin exposure [125]. These findings indicate that lncRNA dysregulation makes GCs more sensitive to mitochondrial damage and stress, leading to degradation of ovarian reserve. Disease-specific lncRNA networks influence mitochondrial function, redox balance, and apoptosis in ovarian cells, highlighting the link between mitochondrial dysfunction and female infertility. LncRNAs serve as intermediaries between the nucleus and mitochondria and may influence aging and tumor formation. Their influence on mitochondrial function could lead to new methods for early diagnosis and targeted treatment of POI. Immune regulation in the endometrium is essential for maternal–fetal tolerance during early pregnancy, and lncRNAs serve as key regulators of immune-cell infiltration, inflammatory signaling, and stromal immunological crosstalk in female infertility [126]. In recurrent implantation failure (RIF), lncRNA–mRNA network analysis identified six hub lncRNAs—NONHSAT083203.2, NONHSAT212577.1, NONHSAT035952.2, NONHSAT193031.1, NONHSAT053761.2, and NONHSAT025064.2—that were upregulated in RIF endometrium and correlated with immune activity, leukocyte recruitment, and cytokine regulation [127]. H19 has important roles in controlling uterine immunological responses and facilitating embryo implantation. H19 interacts with miR-301a-3p, an important participant in the Hedgehog pathway and immunological processes, and acts as a ceRNA to regulate GAS1 expression. In patients with RIF, H19 is downregulated and immunological responses are altered, particularly in natural killer cells and T cells. These findings indicate an important role for H19 in regulating ER and immune activity [128]. MALAT1 is important for regulating immunological responses in chronic endometritis (CE) because it affects the miR-142-3p/PIK3R1 axis. MALAT1 increases PIK3R1 expression, which leads to further inflammation in endometrial cells, suggesting that MALAT1 could be a useful diagnostic and therapeutic target for CE [129]. ER is a brief and critical period during which the uterus is prepared for embryo implantation. LncRNAs regulate adhesion, differentiation, and remodeling pathways during this delicate process. Decreased H19 expression increases Let-7 levels, which post-transcriptionally inhibits IGF1R. This disruption impairs ESC development, reducing the endometrium’s receptivity to embryo implantation. This imbalance may impair the uterine milieu required for implantation, thereby contributing to infertility [130]. Current findings indicate that MEG3 is expressed at reduced levels in ectopic endometrial tissues and that its increased expression inhibits human endometrial stromal cell (hESC) proliferation and invasion. MEG3 functions as a ceRNA by influencing the miR-21-5p/DNA methyltransferase 3 beta (DNMT3B) pathway, which results in Twist methylation and subsequent downregulation of Twist expression. These mechanisms suggest that targeting MEG3 could be a valuable therapeutic approach for improving ER and addressing endometriosis-associated infertility [131]. Research indicates that lncRNA NEAT1 is crucial for enhancing endoplasmic reticulum function and proliferation of endometrial epithelial cells (EECs). Increased NEAT1 and HOXA10 levels have been observed in infertile patients and in mice with embryo implantation defects. NEAT1 downregulation accelerated EEC proliferation and increased ER marker expression. NEAT1 modulates HOXA10 expression through interaction with CCCTC-binding factor (CTCF) and thereby promotes embryo implantation [132]. Embryo implantation, including trophoblast adhesion and invasion into receptive endometrium, is strongly influenced by lncRNAs. H19 downregulates ITGB3 gene expression in endometrial tissue, which may reduce implantation rates. Embryo adhesion is one of the most critical steps in implantation, and ITGB3 supports this process while also promoting angiogenesis [133]. The peptide encoded by lncRNA LINC00339, LINC00339-205-49aa, enhances implantation rates by stimulating MAPK/PI3K-Akt signaling, thereby improving human choriocarcinoma cell line (JAR) trophoblast spheroid adhesion to Ishikawa endometrial cells [134]. CLRN1-AS1 modulates trophoblast cell adhesion to the extracellular matrix during early implantation by modifying CXCL10 and CXCL11 expression and therefore may play an important role in successful implantation [135]. These findings underscore lncRNAs as important mediators of maternal–fetal interaction establishment in human infertility. Decidualization of hESCs is a progesterone- and cAMP-driven differentiation process that is essential for supporting implantation, with lncRNAs acting as important transcriptional regulators. LINC00473 is rapidly activated in hESCs by decidual stimuli, including estradiol, medroxyprogesterone acetate, and dibutyryl cAMP, through the cAMP-PKA-interleukin-11-signal transducer and activator of transcription-3 (STAT3) pathway. LINC00473 knockdown significantly reduces expression of key decidual markers, including PRL, IGFBP1, PGR, FOXO1, HOXA10/11, and WNT4, confirming LINC00473 as essential for human decidualization [62]. The stability of bone morphogenetic protein receptor type 1B (BMPR1B)-AS1, regulated by IGF2BP2, facilitates SMAD1/5/9 signaling and augments decidualization in patients with endometriosis, thereby linking lncRNA dysregulation with implantation defects [136]. AC027288.3 has been identified as a novel regulator of Wnt signaling through FZD4/inhibin subunit beta A (INHBA) during hESC decidualization, thereby expanding the lncRNA repertoire involved in this process. Together, these lncRNAs regulate the decidual phenotype required for pregnancy establishment [137]. Developing reliable lncRNA-based biomarkers for female reproductive conditions such as PCOS, POI, and endometriosis remains a major challenge. This difficulty is largely attributable to small sample sizes, insufficient cross-population validation, and intrinsic biological characteristics of lncRNAs, particularly their tissue-specific expression patterns and molecular instability [125]. Their naturally low concentrations and rapid degradation in blood further hinder the development of robust non-invasive serum or plasma tests, especially for PCOS and endometriosis. At the same time, marked tissue heterogeneity within ovarian GCs in PCOS and POI and within ectopic endometrial lesions in endometriosis leads to inconsistent expression profiles across microarray and RNA-sequencing experiments. This variability is further compounded by the lack of standardized preanalytical protocols, including uniform RNA extraction techniques, consistent sample handling, and common normalization approaches [138]. In PCOS, altered lncRNA expression has been documented in GCs, cumulus cells, follicular fluid, peripheral blood, and adipose tissue. However, these expression patterns vary substantially according to the sampled tissue or fluid, clinical subtype, obesity status, and severity of insulin resistance. Consequently, a lncRNA signal detected in one tissue may not accurately reflect ovarian dysfunction or remain consistent across PCOS subgroups [139,140]. This limitation is even more pronounced in studies analyzing exosomal lncRNAs from follicular fluid of patients with obesity and PCOS, in which the transcripts originate from mixed cell populations. Without identification of the cell of origin, determining whether these lncRNAs indicate oocyte-quality defects, granulosa-cell impairment, or broader metabolic abnormalities is difficult, limiting their value as specific biomarkers [141]. Similar limitations are evident in endometriosis research. Plasma lncRNAs carried by extracellular vesicles have shown promise for distinguishing ovarian endometriosis from healthy controls, often with high area under the curve values. However, these findings generally come from small cohorts and focus exclusively on ovarian lesions, whereas superficial and deeply infiltrating forms of endometriosis are underrepresented. This raises concern that the identified candidates may reflect features specific to a particular lesion type rather than markers of the disease as a whole [108]. Although meta-analyses of bulk RNA-sequencing datasets have highlighted recurrent lncRNAs such as MALAT1, LINC02984, and GATA6-AS1, bulk transcriptomic data inevitably merge signals from stromal, epithelial, immune, and vascular cells, obscuring cell-specific patterns and complicating mechanistic interpretation. Although single-cell RNA sequencing offers a way to address this limitation, its application in reproductive lncRNA studies remains limited [142]. Importantly, most studies of lncRNAs in female infertility remain primarily descriptive. Only a small number of studies, such as those examining lnc-CCNL1-3:1 in PCOS GCs or small nucleolar RNA host gene 18 (SNHG18) in ovarian aging, provide functional evidence linking lncRNA expression to apoptosis, glycolytic regulation, or mitochondrial dysfunction [86,143]. Similarly, in DOR and POI, lncRNAs including NEAT1 and zinc finger E-box binding homeobox 2 (ZEB2)-AS1 have been proposed as potential biomarkers, yet their direct roles in follicular depletion or granulosa-cell survival remain insufficiently explored [101,144]. Without mechanistic validation, prioritizing lncRNA candidates for clinical translation remains challenging. Several lncRNAs, including XIST, NEAT1, MALAT1, GAS5, apolipoprotein A1 (APOA1)-AS, proteasome 20S subunit beta 8 (PSMB8)-AS1, and H19, have been proposed as candidate therapeutic targets. Nevertheless, most proposed strategies, including antisense oligonucleotides (ASOs), clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing, and lncRNA mimic molecules, remain future prospects rather than currently available clinical tools [130,145]. ASOs promote RNase H–mediated cleavage of complementary RNA strands. They are particularly effective against nuclear-localized lncRNAs, including newly transcribed lncRNAs, in contexts in which conventional RNA interference (RNAi) often has limited efficacy [146]. This advantage is especially relevant in reproductive biology, given that many disease-relevant lncRNAs are primarily nuclear localized and/or expressed at high levels. From a translational perspective, more than 100 ASO-based compounds targeting ncRNAs have reached clinical trials, and several have received U.S. Food and Drug Administration approval. This record highlights the technological maturity and clinical viability of ASO chemistry and delivery systems [147]. Genome-engineering tools such as CRISPR/Cas9 and CRISPR interference (CRISPRi) allow locus-specific control of lncRNA gene expression. Notably, a large-scale CRISPRi screen covering approximately 16,400 lncRNA loci identified nearly 500 functional lncRNAs with strong cell-type-specific effects on cell proliferation, underscoring the highly context-dependent nature of lncRNA activity [147]. However, comprehensive genomic assessments indicate that only approximately 38% of lncRNA loci can be considered “safe” CRISPR targets. Most overlap with promoter regions or transcriptional units of neighboring genes, raising the risk of unintended disruption of adjacent protein-coding sequences when DNA-level editing is used. Experimental evidence further shows that CRISPR-mediated knockout of certain lncRNAs, such as HOTAIR and NOP14-AS1, can inadvertently alter nearby gene expression. By contrast, transcript-targeting methods such as ASOs or small interfering RNA pools (siPOOLs), which are complex pools of siRNAs, do not produce comparable off-target genomic effects. Taken together, these observations suggest that, particularly within genomically dense reproductive regions, transcript-directed ASOs may offer a safer and more precise alternative to DNA-editing strategies for modulating lncRNA function [146]. Although ASO- and CRISPR-based approaches for lncRNA modulation have progressed considerably in oncology and cardiovascular research, their adoption in reproductive medicine remains at an early stage [148]. As of 2026, no lncRNA-targeted therapy has entered clinical trials for PCOS, POI, or endometriosis. The existing evidence remains largely preclinical. For example, CRISPR-mediated knockdown of H19 reduces endometriosis-like lesion formation in mouse models; silencing DANCR restores granulosa-cell function in ex vivo POI models; and ASO targeting of LINC00473 improves insulin sensitivity in PCOS cell-based systems. However, these promising results have not yet been translated into in vivo infertility models or human applications [125]. Recent advances in transcriptomics research have identified important functions of lncRNAs in the pathophysiology of female infertility. These regulatory molecules affect key processes such as folliculogenesis, oocyte maturation, steroidogenesis, and endometrial function. Numerous studies have linked dysregulated lncRNA expression to major disorders, including PCOS, POI, and endometriosis. These molecules function through diverse mechanisms, including epigenetic regulation, chromatin remodeling, miRNA interactions, and modulation of cellular signaling pathways. Despite substantial progress, major challenges remain. These include the complexity of molecular regulatory networks, limited sample sizes, and variability in research methodologies. In addition, many identified lncRNAs still require more thorough mechanistic investigation and functional validation. Nevertheless, lncRNAs show substantial promise as biomarkers and novel therapeutic targets for female infertility. Future research should focus on developing non-invasive diagnostic methods, creating targeted treatment strategies, and improving understanding of the molecular pathways underlying infertility. Further investigation of interactions between lncRNAs and other molecular regulators may also provide a more comprehensive understanding of female infertility pathophysiology and support improved therapeutic approaches. | LncRNA | Sample type | Sample size | Expression in PCOS | Reference | |---|---|---|---|---| | CTBP1-AS | Peripheral blood leukocytes | 23 PCOS, 17 controls | Upregulated | [70] | | SRA | Peripheral blood leukocytes | 23 PCOS, 17 controls | Upregulated | [71] | | PWRN2 | Cumulus cells | 30 PCOS, 30 controls | Upregulated | [72] | | GAS5 | Serum | 46 PCOS, 30 controls | Downregulated | [73] | | BANCR | Granulosa cells | 44 PCOS, 34 controls | Upregulated | [74] | | H19 | Peripheral blood leukocytes | 20 PCOS, 20 controls | Upregulated | [75] | | HOTAIR | Ovarian tissues | 80 PCOS rats, 10 control rats | Upregulated | [76] | | OC1 | Granulosa cells | 20 PCOS, 20 controls | Upregulated | [77] | | Xist | Serum | 46 PCOS, 30 controls | Downregulated | [73] | | H19 | Follicular fluid exosome samples | 25 PCOS, 25 controls | Upregulated | [78] | | ZFAS1 | Granulosa cells | 115 PCOS, 115 controls | Upregulated | [79] | | GAS5 | Plasma | 60 PCOS, 60 controls | Upregulated | [80] | | SRLR | Plasma | 52 PCOS, 48 controls | Upregulated | [81] | | MALAT1 | Granulosa cells | 68 PCOS, 30 controls | Downregulated | [82] | | NEAT1 | Peripheral blood leukocytes | 73 PCOS, 31 controls | Upregulated | [83] | | MALAT1 | Peripheral blood leukocytes | 73 PCOS, 31 controls | Downregulated | [83] | 1. 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