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The article "Shedding Light on Microvascular Inflammation: Understanding Outcomes, But What Sparks the Flame?" published in Transplant International explores the impact of different microvascular inflammation (MVI) phenotypes on allograft outcomes in kidney transplantation. The study, conducted by Drs. Sablik and Sannier with international collaborators, reclassified biopsy specimens according to the 2022 BANFF Classification of Renal Allograft Pathology, identifying new phenotypes like MVI without evidence of an antibody-mediated response. Patients with ABMR and MVI without antibody-mediated response showed increased risks of graft loss, emphasizing the importance of recognizing MVI as distinct histopathological phenotypes with different disease progression and allograft failure outcomes. The study highlights the necessity for broader acknowledgment of MVI phenotypes in clinical practice and the potential for tailored therapeutic strategies based on these insights. [Extracted from the article]

Cell-free placental DNA (cfpDNA) is present in maternal circulation during gestation. CfpDNA carries great potential as a research and clinical tool as it provides a means to investigate the placental (epi)genome across gestation, which previously required invasive placenta sampling procedures. CfpDNA has been widely implemented in the clinical setting for noninvasive prenatal testing (NIPT). Despite this, the basic biology of cfpDNA remains poorly understood, limiting the research and clinical utility of cfpDNA. This review will examine the current knowledge of cfpDNA, including origins and molecular characteristics, highlight gaps in knowledge, and discuss future research directions. Author summary: Cell-free DNA are fragments of free-floating DNA released by cells into blood circulation. During pregnancy, the placenta releases cell-free placental DNA (cfpDNA) into maternal blood circulation. CfpDNA can be collected through a routine blood draw and is used for noninvasive prenatal testing (NIPT) to detect risk of the fetus having genetic abnormalities. There remains great untapped potential for the use of cfpDNA to screen not only for a wider range of fetal genetic abnormalities, but also for pregnancy complications affecting the health of both the fetus and pregnant person. This is currently hindered by a poor understanding of the "normal" characteristics of cfpDNA and how exactly it is released from placenta cells. In this review, we will summarize what is currently known about cfpDNA, highlight what remains unclear, and discuss future research directions for advancing the utility of cfpDNA in both research and the clinic. [ABSTRACT FROM AUTHOR]

Background and Objectives Materials and Methods Results Conclusion To test the performance of a new droplet digital polymerase chain reaction (ddPCR) non‐invasive foetal blood group and platelet antigen genotyping assay in the setting of a Dutch reference laboratory for foetal blood group and platelet antigen genotyping. Our population comprised 229 consecutive alloimmunized pregnant women who presented between April 2022 and March 2023 with 250 requests for non‐invasive foetal RHD, RHE, RHc, RHC, K1, HPA‐1a or HPA‐5b blood group and platelet antigen genotyping.Samples were genotyped for blood group and platelet antigen alleles along with methylated RASSF1a (mRASSF1a) and sex‐determining region of Y (SRY) and DYS14 as positive foetal controls. Negative blood group and platelet antigen results were issued only when foetal controls were positive; otherwise, such samples were classified as inconclusive.The assay achieved a success rate of 98.4% (246 of 250) because one case was lost to follow‐up, one case was solved with quantitative polymerase chain reaction (qPCR) and one case precluded foetal typing due to RHD variant mothers. Only 10 cases needed a second sample and one case a third for a valid final result. We identified 116 maternal–foetal blood group and platelet antigen incompatibilities.Clinical non‐invasive foetal blood group and platelet antigen typing of alloimmunized pregnant women via ddPCR is successful and represents an improvement over qPCR because of the addition of a foetal control and because ddPCR circumvents potential interference from maternal cell‐free DNA (cfDNA) background for foetal HPA‐1 and K1. [ABSTRACT FROM AUTHOR]

BACKGROUND: Cell-free DNA (cfDNA) sequence analysis to screen for fetal aneuploidy can inciden-Theratally detect maternal cancer. Additional data are needed to identify DNA-sequencing patterns and other biomarkers that can identify pregnant persons who are most likely to have cancer and to determine the best approach for follow-up. METHODS: In this ongoing study we performed cancer screening in pregnant or postpartum persons who did not perceive signs or symptoms of cancer but received unusual lnclinical cfDNA-sequencing results or results that were nonreportable (i.e., the fetal aneuploidy status could not be assessed) from one of 12 different commercial Shrivlaboratories in North America. We used a uniform cancer-screening protocol including rapid whole-body magnetic resonance imaging (MRI), laboratory tests, and standardized cfDNA sequencing for research purposes with the use of a genomewide platform. The primary outcome was the presence of cancer in participants conafter the initial cancer-screening evaluation. Secondary analyses included test per-formance. RESULTS: Cancer was present in 52 of the 107 participants in the initial cohort (48.6°6). The sensitivity and specificity of whole-body MRI in detecting occult cancer were 98.0% and 88.5°6, respectively. Physical examination and laboratory tests were of limited use in identifying participants with cancer. Research sequencing showed that 49 participants had a combination of copy-number gains and losses across multiple (23) chromosomes; cancer was present in 47 of the participants (95.9%) with this sequencing pattern. Sequencing patterns of cfDNA in which there were only chromosomal gains (multiple trisomies) or only chroniosornal losses (one or more monosomies) were found in participants with nonmalignant conditions, such as fibroids. CONCLUSIONS: In this study, 48.6% of participants who received unusual or nonreportable clinical cfDNA-sequencing results had an occult cancer. Further study of DNA-sequencing patterns that are suggestive of occult cancer during prenatal screening is warranted. (Funded by the NIH Intramural Research Programs; ClinicalTrials.gov number, NCT04049604. [ABSTRACT FROM AUTHOR]

Background Diagnosis of tuberculous pleural effusion (TPE) remains challenging. Studies have shown that detecting cell-free Mycobacterium tuberculosis (cf-TB) DNA in pleural effusion can improve TPE diagnosis. This study aimed to evaluate the diagnostic value of our recently developed TB One-Pot assay, which combines cross-priming amplification with CRISPR-Cas12b, in detecting cf-TB for TPE. Methods Pleural effusion samples were collected from inpatients with suspected TPE at Hangzhou Red Cross Hospital. After centrifugation, the precipitate was used for culture, Xpert, and pleural effusion cytologic testing, while the supernatant was used for biochemical and cf-TB assays, including TB One-Pot and the quantitative polymerase chain reaction method (cf-TB-PCR). Assessment of diagnostic performance was based on a comprehensive reference standard. Results A total of 115 patients were included: 88 TPE cases (diagnosed per the comprehensive reference standard) and 27 non-TPE cases. The sensitivity of TB One-Pot in detecting pleural cf-TB for diagnosing TPE was 64.8%, with an area under the curve (AUC) of 0.805, significantly superior to culture and Xpert (P <.05). When compared with cf-TB-PCR (sensitivity, 53.4%; AUC, 0.767) and the adenosine deaminase assay (sensitivity, 52.3%; AUC, 0.761), TB One-Pot demonstrated slightly higher sensitivity and AUC, but the differences were not statistically significant (P >.05). The specificity of TB One-Pot was 96.3%, while the specificity of the other tests was 100%, with no statistically significant differences (P >.05). Conclusions cf-TB provides direct evidence of the etiology of TPE. TB One-Pot for detecting cf-TB in diagnosing TPE outperforms existing TB laboratory tests and may represent a more effective approach for TPE diagnosis in resource-limited settings. [ABSTRACT FROM AUTHOR]

Background: Patients with heart failure (HF) with improved ejection fraction (HFimpEF) demonstrate better clinical outcomes when compared with individuals without restoration of cardiac function. The identification of predictors for HFimpEF may play a crucial role in the individual management of HF with reduced ejection fraction (HFrEF). Cell-free nuclear (cf-nDNA) DNA is released from damaged cells and contributes to impaired cardiac structure and function and inflammation. The purpose of the study was to elucidate whether cf-nDNA is associated with HFimpEF. Methods: The study prescreened 1416 patients with HF using a local database. Between October 2021 and August 2022, we included 452 patients with chronic HFrEF after prescription of optimal guideline-based therapy and identified 177 HFimpEF individuals. Circulating biomarkers were measured at baseline and after 6 months. Detection of cf-nDNA was executed with real-time quantitative PCR (qPCR) using NADH dehydrogenase, ND2, and beta-2-microglobulin. Results: We found that HFimpEF was associated with a significant decrease in the levels of cf-nDNA when compared with the patients from persistent HFrEF cohort. The presence of ischemia-induced cardiomyopathy (odds ration [OR] = 0.75; p = 0.044), type 2 diabetes mellitus (OR = 0.77; p = 0.042), and digoxin administration (OR = 0.85; p = 0.042) were negative factors for HFimpEF, whereas NT-proBNP ≤ 1940 pmol/mL (OR = 1.42, p = 0.001), relative decrease in NT-proBNP levels (>35% vs. ≤35%) from baseline (OR = 1.52; p = 0.001), and cf-nDNA ≤ 7.5 μmol/L (OR = 1.56; p = 0.001) were positive predictors for HFimpEF. Conclusions: We established that the levels of cf-nDNA ≤ 7.5 μmol/L independently predicted HFimpEF and improved the discriminative ability of ischemia-induced cardiomyopathy, IV NYHA class, and single-measured NT-proBNP and led to a relative decrease in NT-proBNP levels ≤35% from baseline in individuals with HFrEF. [ABSTRACT FROM AUTHOR]

There is currently no clinically valid biomarker for predicting the growth and prognosis of abdominal aortic aneurysms (AAA). The most promising candidates with the highest diagnostic values are plasma D-dimers and markers of activated neutrophils, i.e., myeloperoxidase (MPO) or cell-free DNA. So far, case-control studies on these markers have been performed almost exclusively using healthy individuals as controls. To validate the value of these markers in the clinical setting of a vascular surgery department, we analysed the diagnostic and prognostic potential of plasma D-dimers and MPO in 177 AAA patients versus 138 non-AAA patients with different vascular diseases. Significantly elevated levels of D-dimers were recorded for AAA patients compared with non-AAA patients, although the difference between the two groups was significantly smaller than that in other studies comparing AAA patients with healthy controls. Surprisingly, MPO levels were significantly higher in non-AAA patients than in those with AAA. After adjusting for the confounding factors of sex, peripheral artery disease (PAD) and internal carotid stenosis in multivariate regression models, neither D-dimers nor MPO remained independent correlates of AAA. In contrast, D-dimer plasma levels correlated well with the maximal aortic diameter. Combined analysis of D-dimers and circulating cell-free DNA levels derived from a previous study failed to improve the predictive values for the maximal aortic diameter. In conclusion, our data show that D-dimers and MPO are not suitable biomarkers for monitoring AAA in a real-world setting of mixed vascular surgery patients. [ABSTRACT FROM AUTHOR]

Simple Summary: Liquid biopsy allows regular monitoring of cancer progression and response to treatment by analyzing circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in plasma. This is the first time that the methylation status of NALCN in NSCLC has beenexamined and correlated with its expression. Thus, the detection of NALCN promoter methylation in NSCLC tumor tissue provides significant prognostic information for patients with NSCLC. However, we strongly believe that the evaluation of NALCN promoter methylation in plasma CTDNA as a non-invasive circulating tumor biomarker should be further investigated in a large and well-defined patient cohort. Liquid biopsy enables real-time monitoring of tumor development and response to therapy through the analysis of CTCs and ctDNA. NALCN is a sodium leak channel that is frequently involved in tumor evolution and immunity and acts as a tumor suppressor. Deletion of NALCN has been shown to increase cancer metastasis and the number of CTCs in peripheral blood. In this study, we investigated for the first time NALCN promoter methylation in (a) Aza-treated cell lines (A549, TE671, BT20, and MDA-MB-468), (b) paired NSCLC tissues (n = 22), and (c) plasma cell-free DNA (ctDNA) from patients with NSCLC (early stage n = 39, metastatic n = 39) and DNA from 10 healthy donors (HD) using a newly developed highly specific and sensitive real-time MSP method. Treatment with 5′-aza-dC induced the expression of NALCN only in the A549 cell line, suggesting that DNA methylation regulates its expression in certain cancers. The mRNA expression levels of NALCN were quantified in non-small cell lung cancer (NSCLC) and adjacent non-cancerous tissues, and it was found to be underexpressed in 54.5% of tumor tissues, with significantly higher expression in recurrence-free patients (p = 0.009) than in patients who relapsed. The NALCN methylation level was not statisticallysignificantlycorrelated with the corresponding expression (p = 0.439), while Kaplan–Meier analysis showed an association between NALCN promoter hypermethylation and worse disease-free intervals (DFIs) (p = 0.017). Evaluation of NALCN methylation in ctDNA revealed that it was detected in 5.1% of early and 10.2% of advanced cases. Our results strongly suggest that epigenetic inactivation of NALCN may be a predictor of metastasis in NSCLC. Our results should be validated in further studies based on a larger patient cohort to further investigate whether DNA methylation of the NALCN promoter could serve as a potential prognostic DNA methylation biomarker and predictor of metastasis in NSCLC. [ABSTRACT FROM AUTHOR]

Simple Summary: Optimal treatment strategies for HNSCC involve multidisciplinary tumor boards considering disease location, stage, and functional outcomes. While early-stage disease may be treated with single-modality approaches, locally advanced cases often require multimodal treatment. Despite aggressive therapies, local and distant recurrences remain a common challenge. Thus, a well-structured follow-up strategy is essential, with a focus on detecting recurrences within the first two years after treatment. However, due to the lack of standardized protocols and clear guidelines, clinical and radiological follow-up practices vary significantly among institutions, and their impact on patient survival remains uncertain. Background: For patients with head and neck squamous cell carcinoma (HNSCC), after a single or multi-modality treatment, a specific follow-up strategy is needed, but there is no agreement between the main international societies on the proper methods and timing of follow-up. Methods: We performed a descriptive review to evaluate the available data and compare the main guidelines, giving some practical guidance to perform effective personalized follow-up strategies. Results and Conclusions: While clinical and endoscopic follow-up alone seems to be appropriate for early-stage HNSCCs, the addition of close radiologic follow-up in locally advanced HNSCCs is still debated, as there are no data indicating that an earlier detection of recurrence correlates with increased survival, while it is mandatory in the first three-six months to define the response to treatment. For patients who have undergone conservative surgery or have major pathological risk factors, the incidence of locoregional recurrence is higher, and locoregional radiologic follow-up (magnetic resonance imaging is preferred to computed tomography) should be considered. Positron emission tomography may be useful in cases of suspected locoregional persistence of disease, differentiating it from post-irradiation outcomes. Distant radiological follow-up can be considered in the detection of the second primary in cases of specific risk factors and for virus-related tumors. For the latter, the use of circulating DNA should always be considered. A brain scan is not recommended without specific symptoms. For all patients who do not fall into the above categories, clinical and endoscopic follow-up should be proposed, reserving radiological investigations only at the onset of symptoms. [ABSTRACT FROM AUTHOR]

Introduction: Colorectal cancer screening programs are effective in reducing incidence and mortality. In Europe, every FIT+ patient is referred to colonoscopy. The available data show that ~75.0% of these patients are negative. It is desirable to select patients at a greater risk of having a positive colonoscopy. Materials and Methods: 711 subjects, aged 50–74, attending the screening program of ASL-NA-3-SUD (Naples, Italy), were enrolled in a cross-sectional study to evaluate the performance of the QuantiDNA™ test and the non-inferiority of an alternative approach (AAP). This evaluation is based on FIT+ and QuantiDNA™+ patients referred to colonoscopy, compared to Standard of Care (SOC) colonoscopy following a FIT+ test alone. A non-inferiority margin (NIM) for colorectal neoplasia (CN) and advanced adenomas (AA) was set at −10% and at −3.8% for CRC. Results: The odds ratio was 1.76 (p-value = 0.009). The detection rate of AAP was 15.9% for colorectal neoplasia, 13.0% for advanced adenoma, and 3.0% for CRC. The risk difference between AAP and SOC was −5.07% (95% C.I. −9.23, −0.90) for colorectal neoplasia, −4.02% (95% C.I. −7.89, −0.16) for advanced adenomas, and −1.04% (95% C.I. −3.16, 1.07) for CRC. This data suggests that AAP is non-inferior to SOC for detecting CN, AA, and CRC. The expected decrease in colonoscopies is 33.4%. Conclusions: The QuantiDNA™ test is straightforward, non-invasive, and well-tolerated. Data from this study indicate that it is effective in the reduction of the need for colonoscopy examinations (−33.4%) and is non-inferior to SOC in the detection of significant colorectal lesions. [ABSTRACT FROM AUTHOR]

The article discusses the advancements in prenatal screening through the use of fetal cell-free DNA (cfDNA) in maternal blood, which has revolutionized the detection of chromosomal abnormalities. A new technique called "coordinative allele-aware target-enrichment sequencing" (COATE-seq) has been developed to simultaneously detect chromosomal abnormalities and monogenic conditions, offering a non-invasive method for assessing fetal anomalies with diverse genetic etiologies. While COATE-seq shows promise in improving prenatal diagnosis and clinical management, challenges remain in its widespread implementation, including questions about generalizability, diagnostic accuracy, and ethical considerations regarding equitable access and patient privacy. [Extracted from the article]

Objective: This study evaluated the accuracy of non-invasive prenatal testing (NIPT-SGDs) for dominant monogenic genetic diseases associated with fetal structural abnormalities and to assess the feasibility of clinical application. Methods: Pregnant women requiring prenatal diagnosis due to fetal structural abnormalities were enrolled. Maternal peripheral blood was analyzed for cell-free DNA (cfDNA) using coordinative allele-aware target enrichment sequencing (COATE-seq). This assessed fetal allele depth distribution, fraction and variation ratio. The variation's origin was then determined to obtain fetal variation information. Finally, NIPT-SGDs results were confirmed via invasive prenatal diagnosis (IPD). Results: Upon examination of 113 samples using NIPT-SGDs, COATE-seq successfully analyzed 112 for fetal variation, excluding one due to hemolysis. The study detected six positive cases, yielding a 5.36% detection rate. These disorders included tuberous sclerosis complex (TSC1 and TSC2 being its causative genes), Noonan syndrome (PTPN11), polycystic kidney disease (PKD1), and Kabuki syndrome (KMT2D), occurring twice each, except for Noonan and polycystic kidney disease. Two false positives were due to the mother being a genetic mosaicism. Compared to invasive whole-exome sequencing (WES), NIPT-SGDs did not detect nine positive cases of IPD dominant monogenic diseases, accurately identifying 90.18% (101/112) of the actual positive and negative cases. Conclusion: Our findings demonstrate the clinical utility of NIPT-SGDs using COATE-seq in effectively identifying fetuses with dominant single-gene disorders. Furthermore, this method can be applied to all fetuses. [ABSTRACT FROM AUTHOR]

Introduction: Cell-free DNA (cfDNA) is expected to contribute to the decision for treatment and prediction of effects with minimally invasion. We investigated the correlation between gene mutations before and after lenvatinib (LEN) treatment and its effectiveness, in order to find advanced hepatocellular carcinoma (HCC) patients who would benefit greatly from the therapy. Methods: We analyzed cfDNA before and 6–8 weeks after the start of treatment in 20 advanced HCC patients who started LEN. A next-generation sequencer was used for CTNNB1 and TP53. Concerning TERT promoter, −124C>T and −146C>T mutations are researched using digital PCR. In addition, we examined liver tumor biopsy tissues by the same method. Computerized tomography evaluation was performed at 6–8 weeks and 3–4 months to assess the efficacy. Results: Frequencies of TERT promoter, CTNNB1, and TP53 mutations in pretreatment cfDNA were 45%, 65%, and 65%, but 53%, 41%, and 47% in HCC tissues, respectively. There were no clear correlations between these gene mutations and the disease-suppressing effect or progression-free survival. Overall, there were many cases showing a decrease in mutations after LEN treatment. Integrating the reduction of CTNNB1 and TP53 genetic mutations increased the potential for disease suppression. Conclusion: This study suggests that analysis of cfDNA in advanced HCC patients may be useful for identifying LEN responders and determining therapeutic efficacy. Furthermore, it has potential for selecting responders for other molecular-targeted drugs. [ABSTRACT FROM AUTHOR]

To evaluate the positive predictive value (PPV) of prenatal cell-free DNA (cfDNA) screening for chromosomal aneuploidies in pregnancies achieved either after single euploid transfer in in vitro fertilization or Preimplantation Genetic Testing for Aneuploidy (PGT-A) cycles or transfer of single untested embryo, and to assess the concordance of prenatal-cfDNA-screening and PGT-A results. Single center retrospective cohort study. Fertility clinic. A total of 2,973 prenatal-cfDNA-screening results for the most common trisomies (T13, T18, T21, X, and Y) and microdeletions (1p36, 4p16.3, 5p15.2, 15q11.2, and 22q11.2) from singleton pregnancies allocated into two groups: PGT-A group (n = 1,204) pregnant after single euploid transfer and non-PGT-A group (n = 1769) pregnant after transfer of single untested embryo, between 2016 and 2023. Not applicable. The primary outcome measure was the accuracy of prenatal-cfDNA screening. Positive and negative prenatal-cfDNA-screening results and subsequent prenatal or postnatal diagnostic testing were used to classify each positive prenatal-cfDNA-screening result as a true or a false positive. Secondary endpoints were to evaluate the concordance of PGT-A and prenatal-cfDNA-screening results and to assess the differences in the fetal fraction of cfDNA used for prenatal-cfDNA-screening reports between the study groups. Prenatal-cfDNA screening was performed at a mean 11.3 ± 1.8 weeks gestational age, and yielded results in 99.9% of the patients (0.1% cancellation rate). There was no difference in the fetal fraction between PGT-A tested and not tested pregnancies (9.5% ± 4% vs. 10.3% ± 4%). 13 positive prenatal-cfDNA-screening results (two T21, two X0, four XXX, one XYY, one indeterminate sex, two 22q11 del/dup, and one 15q11.2del) were received for PGT-A group. Only one (22q11 dup) was confirmed with amniocentesis and fetal autopsy, giving a PPV for an abnormal prenatal-cfDNA screening of 7.7%, the rest had results concordant with PGT-A. Sex chromosomes were 100% concordant between prenatal-cfDNA-screening and PGT-A results, giving a 100% PPV for PGT-A for sex chromosomes and 100% negative predictive value for aneuploidies. Positive prenatal-cfDNA-screening results were received for 27 pregnancies from untested embryos (1.5%), follow-up testing was electively performed for 21, and 8 had confirmed the prenatal-cfDNA-screening result, giving a PPV for the non-PGT-A group of 38%. This study demonstrates that patients undergoing in vitro fertilization/PGT-A and single euploid embryo transfer can reliably do prenatal-cfDNA screening during their first trimester. Fetal fraction in singleton pregnancies after PGT-A tested embryos is not different from pregnancies with untested embryos. Positive predictive value for an abnormal prenatal-cfDNA-screening result after euploid embryo transfer was reassuringly low (7.7%). PGT-A reliably selects against aneuploidy with 100% concordance with fetal sex. [ABSTRACT FROM AUTHOR]

Background: Heterogeneity can impact biomarker identification. Thus, we investigated the somatic copy number alterations (SCNAs) of individual tumor cells in the vitreous humor of a retinoblastoma patient using single-cell whole-genome profiling and explored the genomic concordance among vitreous and aqueous humor, vitreous seeds, and tumor. Methods: Aqueous humor (AH), vitreous humor (VH), and tumor biopsy were obtained from an enucleated globe with retinoblastoma and vitreous seeding. Micromanipulation was used to manually isolate 39 live single tumor cells from vitreous seeds harvested from the VH. The SCNA profiles of these individual cells were generated via whole-genome sequencing and analyzed alongside profiles from the tumor mass and cell-free DNA (cfDNA) from AH and VH. Results: Heatmap of VH single-cell SCNA profiles demonstrates heterogeneity among individual vitreous seeds with one clearly dominant subclone (23 of 37 cells). The SCNA profiles from the cells in this subclone demonstrate an average concordance of 98% with cfDNA profiles from acellular AH and VH and with the tumor profile. Conclusions: Our findings reveal some heterogeneity among single-cell SCNA profiles in individual VH seeds. Despite this heterogeneity, the dominant vitreous subclone exhibits extremely (>98%) high concordance with the SCNA profile from tumor and AH, suggesting AH cfDNA is representative of the dominant genomic subclone. This may facilitate tumoral biomarker identification via the AH. This preliminary work supports the potential of applying single-cell technology to VH seeds in retinoblastoma as a platform to study tumor subclones, which may provide insight into the genomic complexity of disease. [ABSTRACT FROM AUTHOR]

Background: Noninvasive prenatal testing (NIPT) is the most common method for prenatal aneuploidy screening. Low fetal fraction (LFF) is the primary reason for NIPT failure. Consequently, factors associated with LFF should be elucidated for optimal clinical implementation of NIPT. Methods: In this study, NIPT data from January 2019 to December 2022 from the laboratory records and obstetrical and neonatal data from the electronic medical records were collected and analyzed. Subjects with FF >3.50% were assigned to the control group, subjects with FF <3.50% once were assigned to the LFF group, and subjects with FF <3.50% twice were assigned to the repetitive low fetal fraction (RLFF) group. Factors, including body mass index (BMI), gestational age, maternal age, twin pregnancy, and in vitro fertilization (IVF) known to be associated with LFF were assessed by Kruskal–Wallis H test and logistic regression. Clinical data on first trimester pregnancy-associated plasma protein-A (PAPP-A), beta-human chorionic gonadotropin (β-hCG), gestational age at delivery, birth weight at delivery, and maternal diseases were obtained from the hospital's prenatal and neonatal screening systems (twin pregnancy was not included in the data on gestational age at delivery and the control group did not include data on maternal diseases.), and were analyzed using Kruskal–Wallis H test and Chi-square test. Results: Among the total of 63,883 subjects, 63,605 subjects were assigned to the control group, 197 subjects were assigned to the LFF group, and 81 subjects were assigned to the RLFF group. The median of BMI in the three groups was 22.43 kg/m2 (control), 25.71 kg/m2 (LFF), and 24.54 kg/m2 (RLFF). The median gestational age in the three groups was 130 days (control), 126 days (LFF), and 122/133 days (RLFF). The median maternal age in the three groups was 29 (control), 29 (LFF), and 33-years-old (RLFF). The proportion of twin pregnancies in the three groups was 3.3% (control), 10.7% (LFF), and 11.7% (RLFF). The proportion of IVF in the three groups was 4.7% (control), 11.7% (LFF), and 21.3% (RLFF). The factors significantly associated with LFF included BMI [2.18, (1.94, 2.45), p < 0.0001], gestational age [0.76, (0.67, 0.87), p < 0.0001], twin pregnancy [1.62, (1.02, 2.52), p = 0.0353], and IVF [2.68, (1.82, 3.86), p < 0.0001]. The factors associated with RLFF included maternal age [1.54, (1.17, 2.05), p = 0.0023] and IVF [2.55, (1.19, 5.54), p = 0.016]. Multiples of the median (MOM) value of β-hCG and pregnant persons' gestational age at delivery were significantly decreased in the LFF and RLFF groups compared to the control group. Conclusion: According to our findings based on the OR value, factors associated strongly with LFF include a high BMI and the use of IVF. Factors associated less strongly with LFF include early gestational age and twin pregnancy, while advanced maternal age and IVF were independent risk factors for a second LFF result. HIGHLIGHTS: Body mass index, gestational age, maternal age, twin pregnancy, and in vitro fertilization are associated with fetal fraction. We added the repetitive low fetal fraction population and used a large normal population as a control to identify the main factors associated with low fetal fraction. [ABSTRACT FROM AUTHOR]

By causing inflammation and tissue damage, neutrophil extracellular traps (NETs) constitute an underlying mechanism of aspiration-induced lung injury, a major factor of the low utilization of donor lungs in lung transplantation (LTx). To determine whether NET removal during ex vivo lung perfusion (EVLP) can restore lung function and morphology in aspiration-damaged lungs, gastric aspiration lung injury was induced in 12 pigs. After confirmation of acute respiratory distress syndrome, the lungs were explanted and assigned to NET removal connected to EVLP (treated) (n = 6) or EVLP only (nontreated) (n = 6). Hemodynamic measurements were taken, and blood and tissue samples were collected to assess lung function, morphology, levels of cell-free DNA, extracellular histones, and nucleosomes as markers of NETs, as well as cytokine levels. After EVLP and NET removal in porcine lungs, PaO 2 /FiO 2 ratios increased significantly compared to those undergoing EVLP alone (p = 0.0411). Treated lungs had lower cell-free DNA (p = 0.0260) and lower levels of extracellular histones in EVLP perfusate (p = 0.0260) than nontreated lungs. According to histopathology, treated lungs showed less immune cell infiltration and less edema compared with nontreated lungs, which was reflected in decreased levels of proinflammatory cytokines in EVLP perfusate and bronchoalveolar lavage fluid. To conclude, removing NETs during EVLP improved lung function and morphology in aspiration-damaged donor lungs. The ability to remove NETs during EVLP could represent a new therapeutic approach for LTx and potentially expand the donor pool for transplantation. [ABSTRACT FROM AUTHOR]

PURPOSE: Using the prostate, lung, colorectal, and ovarian (PLCO) Cancer Screening Trial samples, we identified cell-free DNA (cfDNA) candidate biomarkers bearing the epigenetic mark 5-hydroxymethylcytosine (5hmC) that detected occult colorectal cancer (CRC) up to 36 months before clinical diagnosis. MATERIALS AND METHODS: We performed the 5hmC-seal assay and sequencing on ≤8 ng cfDNA extracted from PLCO study participant plasma samples, including n = 201 cases (diagnosed with CRC within 36 months of blood collection) and n = 401 controls (no cancer diagnosis on follow-up). We conducted association studies and machine learning modeling to analyze the genome-wide 5hmC profiles within training and validation groups that were randomly selected at a 2:1 ratio. RESULTS: We successfully obtained 5hmC profiles from these decades-old samples. A weighted Cox model of 32 5hmC-modified gene bodies showed a predictive detection value for CRC as early as 36 months before overt tumor diagnosis (training set AUC, 77.1% [95% CI, 72.2 to 81.9] and validation set AUC, 72.8% [95% CI, 65.8 to 79.7]). Notably, the 5hmC-based predictive model showed comparable performance regardless of sex and race/ethnicity, and significantly outperformed risk factors such as age and obesity (assessed as BMI). Finally, when splitting cases at median weighted prediction scores, Kaplan-Meier analyses showed significant risk stratification for CRC occurrence in both the training set (hazard ratio, [HR], 3.3 [95% CI, 2.6 to 5.8]) and validation set (HR, 3.1 [95% CI, 1.8 to 5.8]). CONCLUSION: Candidate 5hmC biomarkers and a scoring algorithm have the potential to predict CRC occurrence despite the absence of clinical symptoms and effective predictors. Developing a minimally invasive clinical assay that detects 5hmC-modified biomarkers holds promise for improving early CRC detection and ultimately patient outcomes. 5hmC biomarkers in cfDNA predict colorectal cancer up to 36 months before diagnosis (AUC 77%). [ABSTRACT FROM AUTHOR]

PURPOSE: Patients with metastatic ROS1 fusion–positive non–small cell lung cancer (NSCLC) are effectively treated with entrectinib, a multikinase inhibitor. Whether serial targeted gene panel sequencing of cell-free DNA (cfDNA) can identify response and progression along with mechanisms of acquired resistance to entrectinib is underexplored. METHODS: In patients with ROS1 fusion–positive NSCLC, coclinical trial plasma samples were collected before treatment, after two cycles, and after progression on entrectinib (global phase II clinical trial, ClinicalTrials.gov identifier: NCT02568267). Samples underwent cfDNA analysis using MSK-ACCESS. Variant allele frequencies of detectable alterations were correlated with objective response per RECIST v1.1 criteria. RESULTS: Twelve patients were included, with best response as partial response (n = 9, 75%), stable disease (n = 2, 17%), and progressive disease (PD; n = 1, 8%). A ROS1 fusion was variably detected in cfDNA; however, patients without a ROS1 fusion in cfDNA had no other somatic alterations detected, indicative of possible low cfDNA shedding. Clearance of the enrolling ROS1 fusion or concurrent non- ROS1 alterations (TP53 , CDH1 , NF1 , or ARID1A mutations) was observed in response to entrectinib therapy. Radiologic PD was accompanied by redemonstration of a ROS1 fusion or non- ROS1 alterations. On-target resistance was rare; only one patient acquired ROS1 G2032R at the time of progression. Several patients acquired new off-target likely oncogenic alterations, including a truncating alteration in NF1. CONCLUSION: Serial cfDNA monitoring may complement radiographic assessments as determinants of response and resistance to entrectinib in ROS1 fusion–positive lung cancers in addition to detecting putative resistance mechanisms on progression. cfDNA analysis complements radiographic response in pts with ROS1 fusion+ lung cancers tx w/entrectinib [ABSTRACT FROM AUTHOR]

Clinical genomic testing of patient germline, tumor tissue, or plasma cell-free DNA can enable a personalized approach to cancer management and treatment. In prostate cancer (PCa), broad genotyping tests are now widely used to identify germline and/or somatic alterations in BRCA2 and other DNA damage repair genes. Alterations in these genes can confer cancer sensitivity to poly (ADP-ribose) polymerase inhibitors, are linked with poor prognosis, and can have potential hereditary cancer implications for family members. However, there is huge variability in genomic tests and reporting standards, meaning that for successful implementation of testing in clinical practice, end users must carefully select the most appropriate test for a given patient and critically interpret the results. In this white paper, we outline key pre- and post-test considerations for choosing a genomic test and evaluating reported variants, specifically for patients with advanced PCa. Test choice must be based on clinical context and disease state, availability and suitability of tumor tissue, and the genes and regions that are covered by the test. We describe strategies to recognize false positives or negatives in test results, including frameworks to assess low tumor fraction, subclonal alterations, clonal hematopoiesis, and pathogenic versus nonpathogenic variants. We assume that improved understanding among health care professionals and researchers of the nuances associated with genomic testing will ultimately lead to optimal patient care and clinical decision making. This article provides a helpful framework for choosing and interpreting a genomic test in prostate cancer. [ABSTRACT FROM AUTHOR]

PURPOSE: The lack of personalized management of bladder cancer (BlCa) results in patients' lifelong post-treatment monitoring with invasive interventions, underlying the urgent need for tailored and minimally invasive health care services. On the basis of our previous findings on miR-143/145 cluster methylation in bladder tumors, we evaluated its clinical significance in pretreatment cell-free DNA (cfDNA) of patients with BlCa. MATERIALS AND METHODS: Methylation analysis was performed in our screening cohort (120 patients with BlCa; 20 age-matched healthy donors) by bisulfite-based pyrosequencing. Tumor recurrence/progression for patients with non–muscle-invasive bladder cancer, and progression and mortality for patients with muscle-invasive bladder cancer (MIBC) were used as clinical end point events in survival analysis. Bootstrap analysis was applied for internal validation of Cox regression models and decision curve analysis for assessment of clinical benefit on disease prognosis. RESULTS: Decreased methylation of MIR145 core promoter in pretreatment cfDNA was associated with short-term disease progression (multivariate Cox: hazard ratio [HR], 2.027 [95% CI, 1.157 to 3.551]; P =.010) and poor overall survival (multivariate Cox: HR, 2.098 [95% CI, 1.154 to 3.817]; P =.009) of patients with MIBC after radical cystectomy (RC). Multivariate models incorporating MIR145 promoter methylation in cfDNA with tumor stage clearly ameliorated patients' risk stratification, highlighting superior clinical benefit in MIBC prognostication. CONCLUSION: Reduced pretreatment cfDNA methylation of MIR145 core promoter was markedly correlated with increased risk for short-term progression and worse survival of patients with MIBC after RC and adjuvant therapy, supporting modern personalized and minimally invasive prognosis. Methylation profiling of MIR145 core promoter in pretreatment cfDNA could serve as a minimally invasive and independent predictor of MIBC treatment outcome and emerge as a promising marker for blood-based test in BlCa. Cell-free DNA methylation profile of MIR145 promoter as a blood-based test for MIBC treatment outcome. [ABSTRACT FROM AUTHOR]

PURPOSE: Somatic chromosomal alterations, particularly monosomy 3 and 8q gains, have been associated with metastatic risk in uveal melanoma (UM). Whole genome-scale evaluation of detectable alterations in cell-free DNA (cfDNA) in UM could provide valuable prognostic information. Our pilot study evaluates the correlation between genomic information using ultra-low-pass whole-genome sequencing (ULP-WGS) of cfDNA in UM and associated clinical outcomes. MATERIALS AND METHODS: ULP-WGS of cfDNA was performed on 29 plasma samples from 16 patients, 14 metastatic UM (mUM) and two non-metastatic, including pre- and post-treatment mUM samples from 10 patients treated with immunotherapy and one with liver-directed therapy. We estimated tumor fraction (TFx) and detected copy-number alterations (CNAs) using ichorCNA. Presence of 8q amplification was further analyzed using the likelihood ratio test (LRT). RESULTS: Eleven patients with mUM (17 samples) of 14 had detectable circulating tumor DNA (ctDNA). 8q gain was detected in all 17, whereas monosomy 3 was detectable in 10 of 17 samples. TFx generally correlated with disease status, showing an increase at the time of disease progression (PD). 8q gain detection sensitivity appeared greater with the LRT than with ichorCNA at lower TFxs. The only patient with mUM with partial response on treatment had a high pretreatment TFx and undetectable on-treatment ctDNA, correlating with her profound response and durable survival. CONCLUSION: ctDNA can be detected in mUM using ULP-WGS, and the TFx correlates with DS. 8q gain was consistently detectable in mUM, in line with previous studies indicating 8q gains early in primary UM and higher amplification with PD. Our work suggests that detection of CNAs by ULP-WGS, particularly focusing on 8q gain, could be a valuable blood biomarker to monitor PD in UM. [ABSTRACT FROM AUTHOR]

PURPOSE: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high-risk neuroblastoma. METHODS: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunoprecipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models. RESULTS: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found increased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma. CONCLUSION: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma. @mohansrinc1 et al develop a bivalent gene signature predictive of outcome in HR neuroblastoma [ABSTRACT FROM AUTHOR]

The article discusses the current limitations and future perspectives of precision medicine for childhood cancer, focusing on large-scale pediatric precision medicine initiatives. It highlights the challenges of variability in sequencing technologies, lack of availability of drugs for actionable mutations, and the need for standardization in outcome reporting. The study emphasizes the potential benefits of molecular profiling in diagnosis, cancer predisposition syndromes, risk stratification, and treatment toxicity prediction. It calls for international collaboration, standardized analysis, and clinical trial designs to fully realize the benefits of comprehensive profiling initiatives in children with cancer. [Extracted from the article]

Only a limited number of tumour biomarkers are currently available in veterinary medicine, particularly in cats. Cell‐free DNA (cfDNA) is an extracellular DNA fragment released upon cell death and is considered a minimally invasive biomarker for the diagnosis and monitoring of various human malignancies. This study aimed to clarify the utility of circulating cfDNA as a liquid biopsy for various feline tumours. Plasma samples were collected from 44 cats with various tumours, 24 cats with other diseases and 10 healthy controls. A follow‐up study was conducted in three tumour‐bearing patients. All cfDNA concentrations were quantified via real‐time polymerase chain reaction (PCR), which provided short and long fragments of a newly identified feline LINE‐1 gene. We found that cfDNA levels were significantly higher in cats with various tumours than in those with other diseases or healthy controls. The cfDNA concentration was not correlated with serum amyloid A (SAA) levels. Cats with tumours exhibited elevated cfDNA levels that predicted tumour‐bearing with a sensitivity and specificity of 50.5% and 91.2%, respectively (AUC 0.736; p < 0.001). In lymphoma cases, cats with high cfDNA levels had significantly shorter survival times than those with low cfDNA levels (median: 33 days vs. 178 days; p = 0.003). In addition, the cfDNA levels of the three patients correlated with clinical status during follow‐up. Collectively, these findings indicate the potential of cfDNA as a useful biomarker for the diagnosis, therapeutic monitoring and prognostic assessment of tumours in cats. [ABSTRACT FROM AUTHOR]

Background Sepsis-induced acute kidney injury (S-AKI) is a common complication in critically ill patients. Therefore, reliable biomarkers for predicting S-AKI outcomes are necessary. Serum cell-free DNA (cfDNA) is a circulating extracellular DNA fragment used as a noninvasive screening tool for many diseases, including sepsis. This study aimed to investigate the prognostic value of cfDNA in S-AKI patients and its relationship with some other parameters.Methods A total of 89 S-AKI patients admitted to the intensive care unit (ICU) from June 2021 to December 2021 were enrolled in this study. The patients were categorized into the low cfDNA group (< 855 ng/ml) and high cfDNA group (≥ 855 ng/ml) and were followed up for three months. CfDNA was extracted from serum and quantified using Quant-iT PicoGreen dsDNA Reagent.Results Overall survival was significantly lower in the high cfDNA group than in the low cfDNA group (Log-Rank p = 0.012). Univariate Cox proportional hazard model showed that cfDNA was significantly associated with all-cause mortality (HR [hazard ratio] 2.505, 95% CI [95% confidence interval] 1.184–5.298, p = 0.016). Also, serum cfDNA was a significant risk factor for all-cause mortality after adjusting for covariates (HR 2.191, 95% CI 1.017–4.721, p = 0.045). Moreover, cfDNA was positively correlated with several baseline parameters, including serum creatine, aspartate aminotransferase, alanine aminotransferase, prothrombin time, and International Normalized Ratio.Conclusion High serum cfDNA level is associated with higher mortality among the S-AKI population, indicating that cfDNA is a valuable biomarker for S-AKI prognosis. [ABSTRACT FROM AUTHOR]

Objective: Diffuse large B-cell lymphoma (DLBCL) is an aggressive type of lymphoma. Circulating cell-free DNA (cfDNA) is the promising liquid biopsy in malignancy. Method: Assessment of cfDNA concentration and DNA integrity index (DII) in 30 newly diagnosed DLBCL patients and correlating them with the international prognostic index. Results: Circulating cfDNA concentration was significantly higher in newly diagnosed DLBCL patients than controls, while DII was significantly lower. There was a significant correlation between cfDNA concentration and adverse prognostic factors. Conclusion: cfDNA concentration is potentially strong diagnostic and prognostic marker of DLBCL, however DII is only useful as a diagnostic biomarker. [ABSTRACT FROM AUTHOR]

Introduction: The liquid biopsy is a breakthrough in the field of medical diagnostics. It serves as a sentinel that can quietly detect even the subtlest aberrations that indicate the presence of disease. They make it possible to uncover relevant genetic factors of tumors with minimal to no risk to cancer patients. Liquid biopsies allow detailed diagnosis, dynamic treatment monitoring, and accurate prognosis. They are also invaluable in diagnosing other diseases such as infectious diseases and aberrant gene mutations. Areas covered: The present review undertakes an in-depth analysis of the existing status of liquid biopsy diagnostic tools, focusing on their principal components. Furthermore, the review highlights pertinent and recent research in this field to provide a comprehensive understanding of the current state of this technology and its prospects. Expert opinion: Despite new and upcoming research in liquid biopsies, multiple areas need to be further explored before the viable transition into the clinical arena. With the advancements in tools such as artificial intelligence and machine learning and the integration of these technologies with liquid biopsies, these challenges are being addressed and will eventually lead to the development of a highly evolved liquid biopsy diagnostic tools. [ABSTRACT FROM AUTHOR]

Colorectal adenomas (CRAs) represent precancerous lesions that precede the development of colorectal cancer (CRC). Regular monitoring of CRAs can hinder the progression into carcinoma. To explore the utility of tissue DNA and circulating cell‐free DNA (cfDNA) in early diagnosis of CRC, we retrospectively sequenced paired tissue and plasma samples from 85 patients with conventional CRAs. The genetic alterations identified were compared with those from 78 stage‐I CRC patients (CRC‐I) in the ChangKang project. Within the CRA cohort, we pinpointed 12 genes, notably APC, KRAS, and SOX9, that exhibited significant mutated rates in tissue. Patients harboring KMT2C and KMT2D mutations displayed persistent polyps. By comparing with the mutational profiles of metastatic CRC plasma samples, we found that ZNF717 was exclusively mutated in CRAs, while KMT2C and KMT2D mutations were detected in both CRA and CRC. The presence of cfDNA mutations in plasma was validated through polymerase chain reaction, enhancing the feasibility of using cfDNA mutations for early CRC screening. Compared with CRC‐I, CRAs exhibited a reduced frequency of TP53 and PIK3CA somatic mutations and underwent non‐neutral evolution more often. We established a random forest model based on 15 characteristic genes to distinguish CRA and CRC, achieving an area under the curve of 0.89. Through this endeavor, we identified two novel genes, CNTNAP5 and GATA6, implicated in CRC carcinogenesis. Overall, our findings reveal convincing biomarkers markers for detecting CRAs with a propensity for CRC development, highlighting the importance of early genetic screening in CRC prevention. [ABSTRACT FROM AUTHOR]

Diagnosis is the most important step in different diseases, especially in cancers and blood malignancies. There are different methods in order to better diagnose of cancer, but many of them are invasive and also, some of them are not useful for immediate diagnosis. Cell-free DNA (cfDNA) or liquid biopsy easily accessible in peripheral blood is one of the non-invasive prognostic biomarkers in various areas of cancer management. In fact, amounts of cfDNA in serum or plasma can be used for diagnosis. In this review, we have considered some cancers such as hepatocellular carcinoma, lung cancer, breast cancer, and hematologic malignancies to compare the various methods of cfDNA diagnosis. Highlights: The result of early diagnosis along with correct treatment decreases morbidity. Cell-free DNA is a non-invasive way of diagnosing the presence of tumor cells in earlier stages of cancer. DNA released from both solid tumors and hematologic malignancies is usable in this method. Genetic feature of cancer cells at different stages can help in prescribing the amount and type of drugs. [ABSTRACT FROM AUTHOR]

Sepsis-induced acute kidney injury (SI-AKI) is a common clinical syndrome that is associated with high mortality and morbidity. Effective timely detection may improve the outcome of SI-AKI. Kidney-derived cell-free DNA (cfDNA) may provide new insight into understanding and identifying SI-AKI. Plasma cfDNA from 82 healthy individuals, 7 patients with sepsis non-acute kidney injury (SN-AKI), and 9 patients with SI-AKI was subjected to genomic methylation sequencing. We deconstructed the relative contribution of cfDNA from different cell types based on cell-specific methylation markers and focused on exploring the association between kidney-derived cfDNA and SI-AKI.Based on the deconvolution of the cfDNA methylome: SI-AKI patients displayed the elevated cfDNA concentrations with an increased contribution of kidney epithelial cells (kidney-Ep) DNA; kidney-Ep derived cfDNA achieved high accuracy in distinguishing SI-AKI from SN-AKI (AUC = 0.92, 95% CI 0.7801–1); the higher kidney-ep cfDNA concentrations tended to correlate with more advanced stages of SI-AKI; strikingly, SN-AKI patients with potential kidney damage unmet by SI-AKI criteria showed higher levels of kidney-Ep derived cfDNA than healthy individuals. The autonomous screening of kidney-Ep (n = 24) and kidney endothelial (kidney-Endo, n = 12) specific methylation markers indicated the unique identity of kidney-Ep/kidney-Endo compared with other cell types, and its targeted assessment reproduced the main findings of the deconvolution of the cfDNA methylome. Our study first demonstrates that kidney-Ep- and kidney-Endo-specific methylation markers can serve as a novel marker for SI-AKI emergence, supporting further exploration of the utility of kidney-specific cfDNA methylation markers in the study of SI-AKI. [ABSTRACT FROM AUTHOR]

Early detection is crucial for increasing the survival rate of gastric cancer (GC). We aimed to identify a methylated cell-free DNA (cfDNA) marker panel for detecting GC. The differentially methylated CpGs (DMCs) were selected from datasets of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The selected DMCs were validated and further selected in tissue samples (40 gastric cancer and 36 healthy white blood cell samples) and in a quarter sample volume of plasma samples (37 gastric cancer, 12 benign gastric disease, and 43 healthy individuals). The marker combination selected was then evaluated in a normal sample volume of plasma samples (35 gastric cancer, 39 control diseases, and 40 healthy individuals) using real-time methylation-specific PCR (MSP). The analysis of the results compared methods based on 2−ΔΔCt values and Ct values. In the results, 30 DMCs were selected through bioinformatics methods, and then 5 were selected for biological validation. The marker combination of two fragments of IRF4 (IRF4–1 and IRF4–2) and one of ZEB2 was selected due to its good performance. The Ct-based method was selected for its good results and practical advantages. The assay, IRF4–1 and IRF4–2 in one fluorescence channel and ZEB2 in another, obtained 74.3% sensitivity for the GC group at any stage, at 92.4% specificity. In conclusion, the panel of IRF4 and ZEB2 in plasma cfDNA demonstrates good diagnostic performance and application potential in clinical settings. [ABSTRACT FROM AUTHOR]

Early detection of hepatocellular carcinoma (HCC) can greatly improve the survival rate of patients. We aimed to develop a novel marker panel based on cell-free DNA (cfDNA) methylation for the detection of HCC. The differentially methylated CpG sites (DMCs) specific for HCC blood diagnosis were selected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, then validated by the whole genome bisulphite sequencing (WGBS) of 12 paired HCC and paracancerous tissues. The clinical performance of the panel was evaluated using tissue samples [32 HCC, chronic liver disease (CLD), and healthy individuals] and plasma cohorts (173 HCC, 199 CLD, and 98 healthy individuals). The combination of G protein subunit beta 4 (GNB4) and Riplet had the optimal area under the curve (AUC) in seven candidates through TCGA, GEO, and WGBS analyses. In tissue validation, the GNB4 and Riplet showed an AUC of 100% with a sensitivity and specificity of 100% for detecting any-stage HCC. In plasma, it demonstrated a high sensitivity of 84.39% at 91.92% specificity, with an AUC of 92.51% for detecting any-stage HCC. The dual-marker panel had a higher sensitivity of 78.26% for stage I HCC than alpha-fetoprotein (AFP) of 47.83%, and a high sensitivity of 70.27% for detecting a single tumour (size ≤3 cm). In conclusion, we developed a novel dual-marker panel that demonstrates high accuracy in detecting HCC, surpassing the performance of AFP testing. [ABSTRACT FROM AUTHOR]

Liquid biopsies, in particular, analysis of cell-free DNA, are expected to revolutionize the current landscape of cancer diagnostics and treatment. However, the existing methods for cfDNA-based liquid biopsies for cancer have certain limitations, such as fragment interruption and GC bias, which are likely to be resolved by the emerging Oxford Nanopore Technologies (ONT), characterized by long read-length, fast read-times, high throughput, and polymerase chain reaction-free. In this review, we summarized the current literatures regarding the feasibility and applications of cfDNA-based liquid biopsies using ONT for cancer management, a possible game-changer that we believe is promising in detecting multimodal biomarkers and can be applied in a wide range of oncology utilities including early screening, diagnosis, and treatment monitoring. [ABSTRACT FROM AUTHOR]

Hedgehog (Erinaceus europaeus) declines in western Europe have been associated with the emergence of Hedgehog diphtheric disease (HDD), with a probable multifactorial, yet unidentified etiology. We used metagenomic sequencing of cell‐free DNA (cfDNA) in hedgehog blood to identify possible causes of HDD. We detected a novel circovirus species in the European hedgehog, providing the first record of a circovirus within the mammalian order Eulipotyphla. The novel circovirus genome exhibits the characteristic circovirus structure, including a functional replicase (REP) and capsid (CAP) gene. Phylogenetic analysis placed all four detected genomes in a monophyletic clade, most closely related to sequences isolated from dogs. Subsequent PCR‐based screening of 188 hedgehog liver samples demonstrated a high prevalence (61%) of this circovirus in hedgehogs brought to wildlife rescue centers, however, without any significant association with HDD. Since circoviruses are well known to interfere with host immunity across mammalian and avian taxa, the high level of circovirus detection in hedgehogs warrants further research into the role of this novel virus in hedgehog health. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer (CRC) is one of the most commonly diagnosed advanced-stage malignancies worldwide and places a substantial burden on both the economic and social development of numerous countries. Objective: This manuscript aims to synthesize the existing evidence and explore potential avenues for future scholarly research on ctDNA in CRC. Methods: Bibliometric analyses were performed using the bibliometrix package in R, along with CiteSpace and VOSviewer software. The search was restricted to publications up to 31 March 2024, using the following terms: ("ctDNA" OR "circulating tumor DNA") AND ("colorectal cancer" OR "colorectal tumor") from the Web of Science Core Collection (WoSCC) database. Results: Ultimately, we identified 1,310 documents published in 353 journals authored by 7,683 researchers from 2,417 institutions across 66 countries. The USA was the most productive country. The Journal of Clinical Oncology was the most prolific, publishing 111 articles with 3,396 citations. The top five keywords were "colorectal cancer," "circulating tumor DNA," "acquired resistance," "cell-free DNA," and "plasma." The top five cluster labels for references were "advanced cancer," "metastatic colorectal cancer," "liquid biopsy," "colorectal cancer," and "human colorectal cancer xenograft." Conclusions: The collaborative networks are primarily composed of highly productive authors, prestigious institutions, and leading countries. Additionally, the advancement of detection technologies, the development of standardized protocols, the exploration of circulating tumor DNA (ctDNA) dynamics in CRC, and the implementation of large-scale clinical trials for ctDNA-guided precision therapy in CRC are expected to become major research priorities in the future. [ABSTRACT FROM AUTHOR]

Background: The long-term graft survival is closely related to its early status, yet the indices for assessing the early graft status are complex and lack quantitative values. The aim of this study is to investigate the potential of GcfDNA as a comprehensive, non-invasive, convenient, and quantifiable indicator for evaluating early graft status. Methods: In this study, 138 recipients who underwent primary kidney transplantation were enrolled. Peripheral blood samples, each 10 mL, were collected on days 1 and 7 post-transplantation. The quantification of both the graft cell-free DNA (GcfDNA) fraction (%) and GcfDNA concentration (copies per milliliter, cp/mL) was performed using droplet digital PCR (ddPCR). Results: For most recipients, both the GcfDNA fraction and concentration had a rapid decline at 7 days post-transplantation, reaching median values of approximately 0.7% and 53.5 cp/mL, respectively. No significant associations were found between GcfDNA values and other clinical parameters. On the seventh postoperative day, we observed a significant elevation in GcfDNA concentration among recipients with eGFR values < 60 mL/min/1.73 m2. Additionally, notable increases were identified in both GcfDNA fraction and concentration variations within this specific subgroup. The findings of our study indicate a negative correlation between the concentration and fractional changes of GcfDNA on postoperative days 1 and 7, as well as the GcfDNA concentration on postoperative day 7, with eGFR within the 1–2 years post-transplantation period. The ROC curve of GcfDNA_Copies_Variation. day1-day 7 showed the highest AUC value AUC = 0.8006, with high sensitivity (90.14%) and specificity (77.61%), and PPV and NPV were 81.01% and 88.14%, respectively. Using four classical algorithm models, we found that the xgboost regression model achieved the best predictive performance (area under the curve (AUC) values = 0.862) for eGFR within 1–2 years post-transplantation, with high sensitivity (85.7%) and specificity (85%). Conclusion: The changes of GcfDNA levels in the early stage are closely related to kidney function within 1–2 years post-transplantation. As a comprehensive indicator of graft function, GcfDNA has great potential for clinical application. [ABSTRACT FROM AUTHOR]

Multiple myeloma (MM) is a plasma cell (PC) disorder characterized by skeletal involvement at the time of diagnosis. Recently, cell-free DNA (cfDNA) has been proven to recapitulate the heterogeneity of bone marrow (BM) disease. Our aim was to evaluate the prognostic role of cfDNA at diagnosis according to disease distribution, and to investigate the role of the MM microenvironment inflammatory state in supplying the release of cfDNA. A total of 162 newly diagnosed MM patients were screened using 18F-FDG PET/CT and assessed by ultra low-pass whole genome sequencing (ULP-WGS). High cfDNA tumor fraction (ctDNA) levels were correlated with different tumor mass markers, and patients with high ctDNA levels at diagnosis were more likely to present with metabolically active paraskeletal (PS) and extramedullary (EM) lesions. Moreover, we demonstrated that microenvironment cancer-associated fibroblast (CAFs)-mediated inflammation might correlate with high ctDNA levels. Indeed, a high cfDNA TF level at diagnosis predicted a poorer prognosis, independent of R-ISS III and 1q amplification; the inclusion of >12% ctDNA in the current R-ISS risk score enables a better identification of high-risk patients. ctDNA can be a reliable and less invasive marker for disease characterization, and can refine patient risk. [ABSTRACT FROM AUTHOR]

Background: 5-Hydroxymethylcytosine (5hmC) is an important DNA epigenetic modification that plays a vital role in tumorigenesis, progression and prognosis. Previous studies have shown that it plays an important role in the prognosis of diffuse large B-cell lymphoma (DLBCL) and in the prediction of the efficacy of R-CHOP therapy. However, its potential for diagnosing DLBCL has not been reported. Here, we investigated the utility of 5hmC in plasma cfDNA in the diagnosis of DLBCL. Methods: Applying 5hmC-Seal technique, we obtained genome-wide 5hmC profiles in plasma cell-free DNA (cfDNA) samples from 176 Chinese subjects, included 86 DLBCL patients and 90 healthy controls. To investigate whether 5hmC can be used as a diagnostic biomarker for DLBCL, we separated patients and healthy controls into training (DLBCL = 56, Healthy = 60) and validation (DLBCL = 30, Healthy = 30) cohorts and developed a 5hmC-based logistic regression model from the training cohort to diagnose the DLBCL patients in the validation cohort. Results: In this study, we found 10 5hmC biomarkers, and the models created by these differentially regulated 5hmC modified genes showed high accuracy in distinguishing DLBCL patients from healthy controls (validation cohort: AUC = 0.94; (95% CI 88.8%–99.4%)). Conclusion: Our study suggested that 5hmC markers derived from plasma cfDNA can served as effective epigenetic biomarkers for minimally invasive diagnosis of DLBCL. [ABSTRACT FROM AUTHOR]

Background Methods Results Conclusions Placental‐originated cell‐free DNA (cfDNA) provides unique opportunities to study (epi)genetic placental programming remotely, but studies investigating the cfDNA methylome are scarce and usually technologically challenging. Methylated DNA sequencing (MeD‐seq) is well compatible with low cfDNA concentrations and has a high genome‐wide coverage. We therefore aim to investigate the feasibility of genome‐wide methylation profiling of first trimester maternal cfDNA using MeD‐seq, by identifying placental‐specific methylation marks in cfDNA.We collected cfDNA from nonpregnant controls (female n = 6, male n = 12) and pregnant women (n = 10), first trimester placentas (n = 10), and paired preconceptional and first trimester buffy coats (total n = 20). Differentially methylated regions (DMRs) were identified between pregnant and nonpregnant women. We investigated placental‐specific markers in maternal cfDNA, including RASSF1 promoter and Y‐chromosomal methylation, and studied overlap with placental and buffy coat DNA methylation.We identified 436 DMRs between cfDNA from pregnant and nonpregnant women, which were validated using male cfDNA. RASSF1 promoter methylation was higher in maternal cfDNA (fold change 2.87, unpaired t‐test p < .0001). Differential methylation of Y‐chromosomal sequences could determine fetal sex. DMRs in maternal cfDNA showed large overlap with DNA methylation of these regions in placentas and buffy coats. Sixteen DMRs in maternal cfDNA were specifically found only in placentas. These novel potential placental‐specific DMRs were more prominent than RASSF1.MeD‐seq can detect (novel) genome‐wide placental DNA methylation marks and determine fetal sex in maternal cfDNA. Our results indicate a placental and immune‐cell contribution to the pregnancy‐specific cfDNA methylation signature. This study supports future research into maternal cfDNA methylation. [ABSTRACT FROM AUTHOR]

Cervical cancer remains one of the most lethal gynecological malignancies. However, biomarkers for more precise patient care are an unmet need. Herein, the concentration of 285 plasma cell‐free DNA (cfDNA) samples are analyzed from 84 cervical patients and the clinical significance of cfDNA fragmentomic characteristics across the neoadjuvant chemotherapy (NACT) treatment. Patients with poor NACT response exhibit a significantly greater escalation in cfDNA levels following the initial cycle of treatment, in comparison to patients with a favorable response. Distinctive end motif profiles and promoter coverages of cfDNA in initial plasma are observed between patients with differing NACT responses. Notably, the DNASE1L3 analysis further demonstrates the intrinsic association between cfDNA characteristics and chemotherapy resistance. The cfDNA and motif ratios show a good discriminative capacity for predicting non‐responders from responders (area under the curve (AUC) > 0.8). In addition, transcriptional start sites (TSS) coverages around promoters discern the alteration of biological processes associated with chemotherapy resistance and reflect the potential value in predicting chemotherapy response. These findings in predictive biomarkers may optimize treatment selection, minimize unnecessary treatment, and assist in establishing personalized treatment strategies for cervical cancer patients. [ABSTRACT FROM AUTHOR]

The gold standard for precise diagnostic classification of brain tumors requires tissue sampling, which carries relevant procedural risks. Brain biopsies often have limited sensitivity and fail to address tumor heterogeneity, because small tissue parts are being examined. This study aims to explore the detection and quantification of diagnostically relevant somatic copy number aberrations (SCNAs) in cell-free DNA (cfDNA) extracted from cerebrospinal fluid (CSF) in a real-world cohort of patients with defined brain tumor subtypes. A total of 33 CSF samples were collected from 30 patients for cfDNA extraction. Shallow whole-genome sequencing was conducted on CSF samples containing > 3ng of cfDNA and corresponding tissue DNA from nine patients. The sequencing cohort encompassed 26 samples of 23 patients, comprising 12 with confirmed CNS cancer as compared to 11 patients with either ambiguous CNS lesions (n = 5) or non-cancer CNS lesions (n = 6). After mapping and quality filtering SCNAs were called by depth-of-coverage analyses with a binning of 5.5 Mbp. SCNAs were exclusively identified in CSF cfDNA from brain tumor patients (10/12, 83%). In tumor patients, SCNAs were detectable in cfDNA from all patients with, but also in five of seven patients without tumor cells detected by CSF cytopathology. A substantial number of shared SCNAs were traceable between tissue and CSF in matched pair analyses. Additionally, some SCNAs unique to either CSF or tissue indicating spatial heterogeneity or tumor evolution. Also, diagnostically relevant genomic alterations as well as essential and desirable SCNAs as implemented in the current WHO classification of CNS tumors for certain primary brain tumor subtypes were traceable. In summary, this minimally invasive cfDNA-based LB approach employing shallow whole genome sequencing demonstrates potential for providing a molecularly informed diagnosis of CNS cancers, mapping tumor heterogeneity, tracking tumor evolution, and surveilling tumor patients. Further prospective trials are warranted. [ABSTRACT FROM AUTHOR]

Central nervous system germ cell tumors (CNS-GCT) are malignant neoplasms that arise predominantly during adolescence and young adulthood. These tumors are typically sensitive to treatment, but resulting long-term health deficits are common. Additional clinical challenges include surgical risks associated with tumor biopsy, and need to determine treatment response for adapting radiotherapy protocols. The aim of this study was to establish the detectability of circulating-tumor DNA (ctDNA) from cerebrospinal fluid (CSF) of children with CNS-GCT as a potential biomarker. We obtained CSF from patients with CNS-GCT by lumbar puncture or intra-operatively. Cell-free DNA (cfDNA) was extracted and subjected to low-pass whole genome sequencing (LP-WGS). Copy-number alterations (CNAs) were inferred and served as a marker of measurable residual disease (MRD). Comparisons with imaging findings and tumor marker levels were made. A total of 29 CSF samples from 21 patients (16 with germinoma, 5 with non-germinomatous GCT) were sequenced. Twenty samples from 19 patients were collected at diagnosis, and 9 samples from 7 patients were collected during or after therapy. Among the diagnostic samples, CNAs were detected in samples from 17/19 patients (89%), which included 8 with marker-negative tumors. Specific clinical scenarios suggested that serial cfDNA analysis may carry utility in tracking treatment responses as well as clarifying indeterminate imaging findings. Our results provide evidence for the high-sensitivity in detecting ctDNA from CSF of CNS-GCT patients using LP-WGS, with potential utility for non-invasive diagnosis and disease monitoring in upcoming CNS-GCT studies. [ABSTRACT FROM AUTHOR]

Background Methods Results Conclusions Liver transplantation (LT) is still limited by organ shortage and post‐transplant monitoring issues. While machine perfusion techniques allow for improving organ preservation, biomarkers like donor‐derived cell‐free DNA (dd‐cfDNA) and mitochondrial cfDNA (mt‐cfDNA) may provide insights into graft injury and viability pre‐ and post‐LT.A prospective observational cohort study was conducted on LT recipients (n = 45) to evaluate dd‐cfDNA as a biomarker of graft dysfunction during the first 6 months after LT. Dd‐cfDNA was quantified on blood samples collected pre‐LT and post‐LT using droplet digital PCR. In livers undergoing dual hypothermic oxygenated machine perfusion (D‐HOPE), total cfDNA and mt‐cfDNA levels were measured on perfusate samples collected at 30‐min intervals. Correlations with graft function and clinical outcomes were assessed.Dd‐cfDNA levels peaked post‐LT and correlated with transaminase levels and histological injury severity. The longitudinal assessment showed that postoperative complications and rejection were associated with an increase in dd‐cfDNA levels. Mt‐cfDNA levels in D‐HOPE perfusate correlated with graft function parameters post‐LT and were higher in patients with early allograft dysfunction and severe complications.This study confirms dd‐cfDNA as a marker of graft injury after LT and suggests that perfusate mt‐cfDNA levels during D‐HOPE correlate with graft function and post‐transplant clinical outcome. Integration of these tests into clinical practice may improve transplant management and viability assessment during hypothermic perfusion. [ABSTRACT FROM AUTHOR]

Due to the possible coexistence of Klebsiella pneumoniae (KP) and Candida albicans (CA), strains of KP and CA with biofilm production properties clinically isolated from patients were tested. The production of biofilms from the combined organisms (KP+CA) was higher than the biofilms from each organism alone, as indicated by crystal violet and z-stack immunofluorescence. In parallel, the bacterial abundance in KP + CA was similar to KP, but the fungal abundance was higher than CA (culture method), implying that CA grows better in the presence of KP. Proteomic analysis was performed to compare KP + CA biofilm to KP biofilm alone. With isolated mouse neutrophils (thioglycolate induction), KP + CA biofilms induced less prominent responses than KP biofilms, as determined by (i) neutrophilic supernatant cytokines (ELISA) and (ii) neutrophil extracellular traps (NETs), using immunofluorescent images (neutrophil elastase, myeloperoxidase, and citrullinated histone 3), peptidyl arginine deiminase 4 (PAD4) expression, and cell-free DNA. Likewise, intratracheal KP + CA in C57BL/6 mice induces less severe pneumonia than KP alone, as indicated by organ injury (serum creatinine and alanine transaminase) (colorimetric assays), cytokines (ELISA), bronchoalveolar lavage fluid parameters (bacterial culture and neutrophil abundances using a hemocytometer), histology score (H&E stains), and NETs (immunofluorescence on the lung tissue). In conclusion, the biofilm biomass of KP + CA was mostly produced from CA with less potent neutrophil activation and less severe pneumonia than KP alone. Hence, fungi in the respiratory tract might benefit the host in some situations, despite the well-known adverse effects of fungi. [ABSTRACT FROM AUTHOR]

Background: Neuronal loss is a major pathological feature of neurodegenerative diseases. The analysis of plasma cell-free DNA (cfDNA) is an emerging approach to track cell death events in a minimally invasive way and from inaccessible areas of the body, such as the brain. Previous studies showed that DNA methylation (DNAm) profiles can be used to map the tissue of origin of cfDNA and to identify molecules released from the brain upon cell death. The aim of the present study is to contribute to this research field, presenting the development and validation of an assay for the detection of brain-derived cfDNA (bcfDNA). Methods: To identify CpG sites with brain-specific DNAm, we compared brain and non-brain tissues for their chromatin state profiles and genome-wide DNAm data, available in public datasets. The selected target genomic regions were experimentally validated by bisulfite sequencing on DNA extracted from 44 different autoptic tissues, including multiple brain regions. Sequencing data were analysed to identify brain-specific epihaplotypes. The developed assay was tested in plasma cfDNA from patients with immune effector cell-associated neurotoxicity syndrome (ICANS) following chimeric antigen receptor T (CAR-T) therapy. Results: We validated five genomic regions with brain-specific DNAm (four hypomethylated and one hypermethylated in the brain). DNAm analysis of the selected genomic regions in plasma samples from CAR-T patients revealed higher levels of bcfDNA in participants with ongoing neurotoxicity syndrome. Conclusions: We developed an assay for the analysis of bcfDNA in plasma. The assay is a promising tool for the early detection of neuronal loss in neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

The effect of high altitude (HA, altitude >2500 m) can trigger a maladaptive response in unacclimatized individuals, leading to various HA illnesses such as high altitude pulmonary edema (HAPE). The present study investigates circulating cell free (cf) DNA, a minimally invasive biomarker that can elicit a pro-inflammatory response. Our earlier study observed altered cfDNA fragment patterns in HAPE patients and the significant correlation of these patterns with peripheral oxygen saturation levels. However, the unclear release mechanisms of cfDNA in circulation limit its characterization and clinical utility. The present study not only observed a significant increase in cfDNA levels in HAPE patients (27.03 +− 1.37 ng/ml; n = 145) compared to healthy HA sojourners (controls, 14.57 +− 0.74 ng/ml; n = 65) and highlanders (HLs, 15.50 +− 0.8 ng/ml; n = 34) but also assayed the known cell death markers involved in cfDNA release at HA. The study found significantly elevated levels of the apoptotic marker, annexin A5, and secondary necrosis or late apoptotic marker, high mobility group box 1, in HAPE patients. In addition, we observed a higher oxidative DNA damage marker, 8-hydroxy-2 -deoxyguanosine, in HAPE compared with controls, suggestive of the role of oxidative DNA status in promoting the inflammatory potential of cfDNA fragments and their plausible role in manifesting HAPE pathophysiology. Extensive in vitro future assays can confirm the immunogenic role of cfDNA fragments that may act as a danger-associated molecular pattern and associate with markers of cellular stresses in HAPE. [ABSTRACT FROM AUTHOR]

Introduction: Cancer is a genetic disease that affects people worldwide, and breast cancer is the most common cancer in women. Studies have been conducted on molecular parameters to predict tumor behavior and develop therapeutic strategies. Telomeres, which are at the end of chromosomes, have been studied for their relationship with breast cancer, but more research is needed to understand their role in the disease. Circulating‐free DNA (cfDNA) is DNA that is free in the bloodstream and is considered a promising target for early cancer detection, treatment response monitoring, and prognosis assessment. This study is aimed at comparing cfDNA telomere length of breast cancer patients and healthy individuals and analyzing the impact of neoadjuvant chemotherapy on telomere length in cfDNA. Materials and Methods: Blood samples were collected from 33 breast cancer patients undergoing neoadjuvant chemotherapy before and after treatment. The quantitative PCR method is used to measure the average telomere lengths. Results: This study found that the telomere length of cfDNA in breast cancer patients before and after treatment is significantly shorter than in the control group. Neoadjuvant chemotherapy is found to shorten the cfDNA telomere length, especially in the treatment‐responsive group. Conclusion: Our study suggests that telomere length in cfDNA may be a useful biomarker for predicting therapy response and possible reoccurrence of the disease in breast cancer patients. [ABSTRACT FROM AUTHOR]