Abstract Background Precocious puberty (PP) in girls is traditionally defined as the onset of breast development before the age of 8 years. The specific biomarkers of premature thelarche (PT) and central precocious puberty (CPP) girls are uncertain, and little is known about their metabolic characteristics driven by perfluorinated compounds (PFCs) and clinical phenotype. This study aimed to screen specific biomarkers of PT and CPP and elucidate their underlying pathogenesis. The relationships of clinical phenotype-serum PFCs-metabolic characteristics were also explored to reveal the relationship between PFCs and the occurrence and development of PT and CPP. Methods Nuclear magnetic resonance (NMR)-based cross-metabolomics strategy was performed on serum from 146 PP (including 30 CPP, 40 PT, and 76 unspecified PP) girls and 64 healthy girls (including 36 prepubertal and 28 adolescent). Specific biomarkers were screened by the uni- and multivariate statistical analyses. The relationships between serum PFCs and clinical phenotype were performed by correlation analysis and weighted gene co-expression network analysis to explore the link of clinical phenotype-PFCs-metabolic characteristics in PT and CPP. Results The disordered trend of pyruvate and butyrate metabolisms (metabolites mapped as formate, ethanol, and 3-hydroxybutyrate) were shared and kept almost consistent in PT and CPP. Eight and eleven specific biomarkers were screened for PT and CPP, respectively. The area under curve of specific biomarker combination was 0.721 in CPP vs. prepubertal, 0.972 in PT vs. prepubertal, 0.646 in CPP vs. prepubertal integrated adolescent, and 0.822 in PT vs. prepubertal integrated adolescent, respectively. Perfluoro-n-heptanoic acid and perfluoro-n-hexanoic acid were statistically different between PT and CPP. Estradiol and prolactin were significantly correlated with PFCs in CPP and PT. Clinical phenotypes and PFCs drive the metabolic characteristics and cause metabolic disturbances in CPP and PT. Conclusions The elevation of formate, ethanol, and 3-hydroxybutyrate may serve as the early diagnostic indicator for PP in girls. But the stratification of PP still needs to be further determined based on the specific biomarkers. Specific biomarkers of CPP and PT exhibited good sensitivity and can facilitate the classification diagnosis of CPP and PT. PFC exposure is associated with endocrine homeostasis imbalance. PFC exposure and/or endocrine disturbance directly or indirectly drive metabolic changes and form overall metabolic network perturbations in CPP and PT. Supplementary Information The online version contains supplementary material available at 10.1186/s12916-023-03032-0. Keywords: Premature thelarche, Central precocious puberty, Specific biomarkers, Metabolic network, Perfluorinated compounds Background Pubertal timing is usually regulated by complex interplay of genetic, environmental, nutritional, and epigenetic factors. Therefore, the criteria for normal pubertal timing and thus the definition of precocious puberty are hard to determine. Precocious puberty (PP) in girls is traditionally defined as the onset of breast development before the age of 8 years [[41]1]. Its underlying pathophysiology may be gonadotropin-releasing hormone (GnRH)-dependent for central precocious puberty (CPP) girls or GnRH-independent for premature thelarche (PT) girls. CPP is mainly induced by the continuous pulse secretion of GnRH to prematurely activate the hypothalamic-pituitary-gonadal (HPG) axis; however, the exact mechanisms remain unclear. The main clinical manifestation of the PT girls is simple breast development due to exposure to the peripheral estrogen environment. When PT is accompanied by the significant advance growth of bone age, it is more likely to evolve into secondary CPP. CPP can lead to short- and long-term complications in girls, including increased risk of psychosocial distress, short stature, obesity, cardiovascular disease, and type 2 diabetes in adulthood [[42]2]. Therefore, it is vital to understand the etiology of PT and CPP for accurate diagnosis and prompt intervention. Some researchers tried to quantify PP with the help of clinical phenotype such as luteinizing hormone (LH), follicular-stimulating hormone (FSH), and estradiol to determine the index threshold for CPP diagnosis, but it is still confronted with great controversy and challenge at this moment [[43]3, [44]4]. Some evidences have indicated the changes of metabolic profile during puberty. Qi et al. found that catecholamine metabolic pathway, tryptophan metabolic pathway, and TCA cycle were disturbed in CPP girls by GC/LC-MS-based urinary metabolomics analysis [[45]5]. Yang et al. used LC-MS technology to characterize the urinary metabolomes of CPP girls and found that amino acids, especially aromatic amino acids, were closely related to the pathogenesis of CPP by activating the HPG axis and inhibiting the hypothalamic-pituitary-adrenal axis [[46]6]. However, the clinical differential diagnosis of CPP and PT is still in a vague interface, and the lack of powerful molecular biomarkers is a long-term bottleneck in the clinical diagnosis and evaluation of PP. Recently, ubiquitous exposures to polyfluorinated compounds (PFCs) have attracted concerns regarding their possible harmful effects during critical periods of development in early-life and long-term consequences on health in consideration of their persistence and bioaccumulation potential. Massive researches have shown that PFCs can interfere with estrogen homeostasis and pose a risk of endocrine-disrupting effects [[47]7–[48]9], and they are association with dyslipidemia, renal function, and age at menarche [[49]7, [50]10–[51]12], but there is still inconsistency in the research results [[52]13] as well as certain gender differences [[53]14–[54]17]. In addition, evidences have shown that PFCs can affect the HPG axis [[55]18, [56]19] or directly affect the gonad axis through their weak estrogen or antiandrogen effects to disrupt the development of puberty [[57]20]. However, the correlation research of PFC exposure with the occurrence and development of PP is still in its infancy [[58]19, [59]21, [60]22], and therefore extensive in-depth research and exploration is urgently required to clarify the exact response mechanism. The correlation analysis between PFCs and the clinical phenotype in girls with PP as well as the endogenous metabolites driven by PFCs will help to reveal the impact of PFCs on the occurrence and development of precocious puberty in girls and the preliminary mechanisms. Based on this, the serum metabolic profiles of prepubertal, PP, PT, CPP, and adolescent girls were characterized by one-dimensional nuclear magnetic resonance hydrogen spectrum (^1H-NMR) technology, and the metabolic differences and connections were analyzed by cross-metabolomics analyses, aiming to screen the specific biomarkers of CPP and PT. Furthermore, to reveal the effect of PFCs on the occurrence of CPP and PT, the metabolic modules driven by PFCs and clinical phenotype were identified by weighted gene co-expression network analysis (WGCNA). Methods Subject selection and sampling The children were enrolled from the Department of Child Health, Women and Children’s Hospital, School of Medicine, Xiamen University. A total of 146 PP (including 30 CPP, 40 PT, and 76 unspecified PP) girls were enrolled at their first visit. The inclusion criteria of the patients are shown in detail in Fig. [61]1 according to the clinical guidelines and the related literatures [[62]23–[63]25]. In addition, 64 healthy girls were recruited as a control group for metabolic comparison, who were divided into 36 prepubertal and 28 adolescent girls based on their developmental status. Relevant clinical phenotypes were collected during the clinical examination. Morning fasting serum sample was collected from each girl through a clinical standard procedure and stood for 30 min, then centrifuged at 1000g for 10 min at 4 °C. The serum supernatant was transferred to a new centrifuge tube and stored at −80 °C until analysis. Fig. 1. [64]Fig. 1 [65]Open in a new tab Inclusion and screening process for study cohorts. *: Depending on the method of measurement. The detection method of basal LH and GnRH stimulation test in this study was immunochemiluminometric. LH: luteinizing hormone; FSH: follicular-stimulating hormone; BA: bone age (at the time of diagnosis); CA: chronologic age (at the time of diagnosis) Sample preparation, ^1H-NMR spectra acquisition and processing All serum samples were thawed at 4 °C, and 400 μL of serum was mixed with 200 μL of 60 mM phosphate buffer (pH 7.4, in 0.9% deuterated saline solution) and then vortexed for 10 s. After being centrifuged at 13,000g for 10 min at 4 °C, 550 μL of supernatant was transferred into a 5-mm NMR tube for ^1H-NMR spectral acquisition. The ^1H-NMR spectra of serum samples were obtained on a 600-MHz Bruker Advance nuclear magnetic resonance (NMR) spectrometer (Bruker BioSpin, Germany) equipped with a triple resonance cryogenic probe operating at 600.13 MHz and 298.0 K. A typical water-suppressed Carr-Purcell-Meiboom-Gill (CPMG, [RD-90°-(τ-180°-τ)[n]-ACQ]) pulse sequence with a spectral width of 12,019.2 Hz, an acquisition time of 1.36 s, a relaxation delay of 4.0 s, a scan accumulation of 64 times, and a data point of 16 K was adopted to acquire ^1H-NMR spectra. Spectral processing was performed on MestReNova (version 14.1.1, Mestrelab Research S.L., Spain). All the free induction decays were zero-filled to 64 K data points and multiplied by an exponential function of 1.0 Hz line-broadening factor. The ^1H-NMR spectra were manually phased, and baseline corrected, and then referenced to the doublet of endogenous lactate at δ1.33 after Fourier transformation. The spectral regions of δ4.70–δ5.17 and δ5.50–δ6.00 were removed to eliminate the interference of residual aquatic and urea signals. The remainder spectral regions (δ0.55–δ8.60) were integrally segmented into discrete regions of 0.002 ppm. To reduce the concentration difference between the samples, the obtained NMR spectral data were normalized to the total integrated area. LC-MS/MS detection of serum PFCs The serum PFCs of 40 PT and 30 CPP girls were measured by LC-MS/MS technique, and eleven kinds of PFCs, including perfluoro-n-octanoic acid (PFOA), potassium perfluoro-1-octanesulfonate (PFOS), perfluoro-n-butanoic acid (PFBA), perfluoro-n-undecanoic acid (PFUnDA), perfluoro-n-dodecanoic acid (PFDoDA), potassium perfluoro-1-butanesulfonate (PFBS), perfluoro-n-decanoic acid (PFDA), perfluoro-n-heptanoic acid (PFHpA), perfluoro-n-hexanoic acid (PFHA), potassium perfluoro-1-hexanesulfonate (TFHSA), and perfluoro-n-nonanoic acid (PFNA), were detected according to the references [[66]26,