Genomic alterations of cerebrospinal fluid cell-free DNA in leptomeningeal metastases of gastric cancer.

BACKGROUND: Leptomeningeal metastases (LM) were rare in gastric cancer (GC), and GC patients with LM (GCLM) generally suffer from poor prognosis. Nevertheless, the clinical utility of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) was underinvestigated in GCLM. METHODS: We retrospectively studied 15 GCLM patients, and all patients had paired primary tumor tissue samples and post-LM CSF samples while 5 patients also had post-LM plasma samples. All samples were analyzed using next-generation sequencing (NGS), and the molecular and clinical features were correlated with clinical outcomes. RESULTS: CSF had higher mutation allele frequency (P = 0.015), more somatic mutations (P = 0.032), and more copy-number variations (P < 0.001) than tumor or plasma samples. Multiple genetic alterations and aberrant signal pathways were enriched in post-LM CSF, including CCNE1 amplification and cell cycle-related genes, and CCNE1 amplification was significantly associated with patients' overall survival (P = 0.0062). More potential LM progression-related markers were detected in CSF samples than in tumor samples, including PREX2 mutation (P = 0.014), IGF1R mutation (P = 0.034), AR mutation (P = 0.038), SMARCB1 deletion (P < 0.001), SMAD4 deletion (P = 0.0034), and TGF-beta pathway aberration (P = 0.0038). Additionally, improvement in intracranial pressure (P < 0.001), improvement in CSF cytology (P = 0.0038), and relatively low levels of CSF ctDNA (P = 0.0098) were significantly associated with better PFS. Lastly, we reported a GCLM case whose CSF ctDNA dynamic changes were well correlated with his clinical assessment. CONCLUSIONS: CSF ctDNA could more sensitively detect molecular markers and metastasis-related mechanisms than tumor tissues in GCLM patients, and our study sheds light on utilizing CSF ctDNA in prognostic estimation and clinical assessment in GCLM.

Cerebrospinal fluid circulating tumour DNA genotyping and survival analysis in lung adenocarcinoma with leptomeningeal metastases.

PURPOSE: The prognosis of patients with leptomeningeal metastasis (LM) remains poor. Circulating tumour DNA (ctDNA) has been proven to be abundantly present in cerebrospinal fluid (CSF); hence, its clinical implication as a biomarker needs to be further verified. METHODS: We conducted a retrospective study of 35 lung adenocarcinoma (LUAD) patients with LM, and matched CSF and plasma samples were collected from all patients. All paired samples underwent next-generation sequencing (NGS) of 139 lung cancer-associated genes. The clinical characteristics and genetic profiling of LM were analysed in association with survival prognosis. RESULTS: LM showed genetic heterogeneity, in which CSF had a higher detection rate of ctDNA (P = 0.003), a higher median mutation count (P < 0.0001), a higher frequency of driver mutations (P < 0.01), and more copy number variation (CNV) alterations (P < 0.001) than plasma. The mutation frequencies of the EGFR, TP53, CDKN2A, MYC and CDKN2B genes were easier to detect in CSF than in LUAD tissue (P < 0.05), possibly reflecting the underlying mechanism of LM metastasis. CSF ctDNA is helpful for analysing the mechanism of EGFR-TKI resistance. In cohort 1, which comprised patients who received 1/2 EGFR-TKIs before the diagnosis of LM, TP53 and CDKN2A were the most common EGFR-independent resistant mutations. In cohort 2, comprising those who progressed after osimertinib and developed LM, 7 patients (43.75%) had EGFR CNV detected in CSF but not plasma. Furthermore, patient characteristics and various genes were included for interactive survival analysis. Patients with EGFR-mutated LUAD (P = 0.042) had a higher median OS, and CSF ctDNA mutation with TERT (P = 0.013) indicated a lower median OS. Last, we reported an LM case in which CSF ctDNA dynamic changes were well correlated with clinical treatment. CONCLUSIONS: CSF ctDNA could provide a more comprehensive genetic landscape of LM, indicating the potential metastasis-related and EGFR-TKI resistance mechanisms of LM patients. In addition, genotyping of CSF combined with clinical outcomes can predict the prognosis of LUAD patients with LM.

Next-generation sequencing in the diagnosis of neurobrucellosis: a case series of eight consecutive patients.

BACKGROUND: Neurobrucellosis (NB) presents a challenge for rapid and specific diagnosis. Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) has showed power in detection of causative pathogens, even some infrequent and unexpected pathogens. In this study, we presented 8 cases of NB diagnosed by the NGS of CSF. METHODS: Between August 1, 2018 and September 30, 2020, NGS was used to detect causative pathogens in clinically suspected central nervous system (CNS) infections. Data on demographics, clinical features, and laboratory tests, imaging results and NGS results were collected and reviewed. RESULTS: Among the presented 8 patients, Brucella was rapidly detected using NGS of CSF within 1-4 days, despite those eight patients had variable medical history, disease course, clinical manifestations, laboratory tests and imaging findings. NGS showed the sequence reads corresponded to Brucella species were 8 to 448, with genomic coverage of 0.02 to 0.87%. The relative abundance was 0.13% to 82.40% and sequencing depth was 1.06 to 1.24. Consequently, patients were administered with 3 to 6 months of doxycycline, ceftriaxone and rifampicin, double or triple combination, supplemented with symptomatic therapy and were fully recovered except for case 1. CONCLUSION: NGS of CSF provides a powerful tool in detection of Brucella in a prompt and specific manner, and can be considered for first-line diagnostic use in practice.

Locating through dynamic scattering media based on speckle correlations.

In complex imaging settings, optical scattering often prohibits the formation of a clear target image, and instead, only a speckle without the original spatial structure information is obtained. Scattering seriously interferes with the locating of targets; especially, when the scattering medium is dynamic, the dynamic nature leads to rapid decorrelation of optical information in time, and the challenge increases. Here, a locating method is proposed to detect the target hidden behind a dynamic scattering medium, which uses the a priori information of a known reference object in the neighborhood of the target. The research further designs an automatic calibration method to simplify the locating process, and analyzes the factors affecting positioning accuracy. The proposed method enables us to predict the position of a target from the autocorrelation of the captured speckle pattern; the angle and distance deviations of the target are all within 2.5%. This approach can locate a target using only a single-shot speckle pattern, and it is beneficial for target localization in dynamic scattering conditions.

NSCLC extracellular vesicles containing miR-374a-5p promote leptomeningeal metastasis by influencing blood‒brain barrier permeability.

Leptomeningeal metastasis (LM) is a devastating complication of advanced non-small cell lung cancer (NSCLC). Diagnosis and monitoring of LM can be challenging. Extracellular vesicles (EVs) microRNAs (miRNAs) have become a new noninvasive diagnostic biomarker. The purpose of this study was to examine the clinical value and role of EVs miRNAs in NSCLC-LM. According to next-generation sequencing (NGS), miRNAs with differential expression of EVs in serum of NSCLC patients with LM and non-LM were detected to find biological markers for the diagnosis of LM. Cellular and in vivo experiments were conducted to explore the pathogenesis of EVs miRNA promoting LM in NSCLC. In the present study, we first demonstrated the serum level of EV-associated miR-374a-5p in patients with LM of lung cancer was much higher than that in patients without LM and was correlated with the survival time of patients with LM. Further studies showed that EVs miR-374a-5p efficiently destroys tight junctions and the integrity of the cerebral microvascular endothelial cell barrier, resulting in increased blood-brain barrier (BBB) permeability. Mechanistically, miR-374a-5p regulates the distribution of ZO-1 and occludin in endothelial cells by targeting ADD3, increasing vascular permeability and promoting LM. Implications: These results suggest that serum NSCLC-derived EVs miR-374a-5p is involved in premetastatic niche formation by regulating the permeability of BBB to promote NSCLC-LM, and can be used as a blood biomarker for the diagnosis and prognosis of NSCLC-LM.

Next-generation sequencing for the diagnosis of Listeria monocytogenes meningoencephalitis: a case series of five consecutive patients.

Introduction. The prompt and specific diagnosis of Listeria monocytogenes meningoencephalitis (LMM) is challenging. Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) is an emerging technique for diagnosing infrequent causative pathogens.Hypothesis/Gap statement. We hypothesized that NGS of CSF is an effective approach for diagnosing LMM.Aim. To evaluate the effectiveness of NGS, we present five cases of LMM diagnosed using NGS of the CSF.Methodology. Between August 2017 and 30 September 2020, we used NGS of the CSF to detect pathogens in patients with clinically suspected central nervous system infections. The clinical characteristics, laboratory tests, imaging findings and NGS results are reviewed.Results. Five patients were diagnosed with LMM using NGS of the CSF within 2 to 4 days, although the clinical manifestations, medical history and imaging findings varied strikingly. NGS of CSF showed sequence reads corresponding to L. monocytogenes species ranging from 118 to 1997 bp, genomic coverage of 0.29-5.96 %, relative abundance of 14.83-32.16 % and sequencing depth of 1.12 to 1.35. The prompt diagnosis resulted in targeted and effective treatment with the appropriate antibiotics, although two patients with the most severe cerebral parenchymal lesions showed little improvement.Conclusion. Our results demonstrate the power of NGS of CSF for the prompt diagnosis of LMM. NGS of CSF is an important complementary tool for identifying L. monocytogenes.

Metagenomic next-generation sequencing of cell-free and whole-cell DNA in diagnosing central nervous system infections.

Background: Central nervous system (CNS) infections pose a fatal risk to patients. However, the limited sample volumes of cerebrospinal fluid (CSF) and low detection efficiency seriously hinder the accurate detection of pathogens using conventional methods. Methods: We evaluated the performance of metagenomics next-generation sequencing (mNGS) in diagnosing CNS infections. CSF samples from 390 patients clinically diagnosed with CNS infections were used for the mNGS of cell-free DNA (cfDNA) (n =394) and whole-cell DNA (wcDNA) (n =150). Results: The sensitivity of mNGS using cfDNA was 60.2% (237/394, 95% confidence interval [CI] 55.1%-65.0%), higher than that of mNGS using wcDNA (32.0%, 95% [CI] 24.8%-40.2%, 48/150) and conventional methods (20.9%, 95% [CI] 16.2%-26.5%, 54/258) (P < 0.01, respectively). The accuracy of mNGS using cfDNA in positive samples was 82.6%. Most of viral (72.6%) and mycobacterial (68.8%) pathogens were only detected by the mNGS of cfDNA. Meningitis and encephalitis with Streptococcus pneumoniae infection might be more likely to result in critically ill diseases, while Human alphaherpesvirus 3 was prone to cause non-critically ill diseases. Conclusions: This is the first report on evaluating and emphasizing the importance of mNGS using CSF cfDNA in diagnosing CNS infections, and its extensive application in diagnosing CNS infections could be expected, especially for viral and mycobacterial CNS infections.

Technical Efficiency of Regional Public Hospitals in China Based on the Three-Stage DEA.

Many countries are facing the increasing cost of healthcare services and the low efficiency of public hospitals. These issues are also evident in China. This paper offers a comprehensive assessment of the efficiency of public hospitals operating in China's 31 regions. The impact of the third round of reform of the health system in 2009 is assessed based on the three-stage data envelopment analysis procedure. The time period from 2011 to 2018 is covered in this study. Due to different functions performed by the public hospitals and other ones, the number of patients with infectious diseases is incorporated as an output variable reflecting the social function. The outpatient visits and inpatient visits are considered to reflect the outputs related to the private functions. The results imply an increase in the mean efficiency of public hospitals from 0.927 to 0.981 after taking the impact of environmental variables and statistic noise into account. These results indicate that the efficiency of public hospitals is dependent in the operational environment. There are 11 regions whose hospitals operate on the efficiency frontier during the whole period covered. Therefore, the Chinese government should reasonably design and apply the regulatory tools to improve the efficiency of public hospitals.