Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

Etiological stratification and prognostic assessment of haemophagocytic lymphohistiocytosis by machine learning on onco-mNGS data and clinical data

Introduction

Hemophagocytic lymphohistiocytosis (HLH) is a rare, complicated and life threatening hyperinflammatory syndrome that maybe triggered by various infectious agents, malignancies and rheumatologic disorders. Early diagnosis and identification of the cause is essential to initiate appropriate treatment and improve the quality of life and survival of patients. The recently developed Onco-mNGS technology can be successfully used for simultaneous detection of infections and tumors.

Methods

In the present study, 92 patients with clinically confirmed HLH were etiologically subtyped for infection, tumor and autoimmunity based on CNV and microbial data generated by Onco-mNGS technology, and a predictive model was developed and validated for the differential diagnosis of the underlying disease leading to secondary HLH. Furthermore, the treatment outcomes of patients with HLH triggered by EBV infection and non-EBV infection were evaluated, respectively.

Results

The current study demonstrated that the novel Onco-mNGS can identify the infection and malignancy- related triggers among patients with secondary HLH. A random forest classification model based on CNV profile, infectious pathogen spectrum and blood microbial community was developed to better identify the different HLH subtypes and determine the underlying triggers. The prognosis for treatment of HLH patients is not only associated with CNV, but also with the presence of pathogens and non- pathogens in peripheral blood. Higher CNV burden along with frequent deletions on chromosome 19, higher pathogen burden and lower non-pathogenic microbes were prognosis factors that significantly related with unfavorable treatment outcomes.

Discussion

Our study provided comprehensive knowledge in the triggers and prognostic predictors of patients with secondary HLH, which may help early diagnosis and appropriate targeted therapy, thus improving the survival and prognosis of the patients.

Liquid Biopsy Based on Cell-Free DNA and RNA

This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.

Comparison of the diagnostic significance of cerebrospinal fluid metagenomic next-generation sequencing copy number variation analysis and cytology in leptomeningeal malignancy

BACKGROUND

Diagnosis and monitoring of leptomeningeal malignancy remain challenging, and are usually based on neurological, radiological, cerebrospinal fluid (CSF) and pathological findings. This study aimed to investigate the diagnostic performance of CSF metagenomic next-generation sequencing (mNGS) and chromosome copy number variations (CNVs) analysis in the detection of leptomeningeal malignancy.

METHODS

Of the 51 patients included in the study, 34 patients were diagnosed with leptomeningeal malignancies, and 17 patients were diagnosed with central nervous system (CNS) inflammatory diseases. The Sayk's spontaneous cell sedimentation technique was employed for CSF cytology. And a well-designed approach utilizing the CSF mNGS-CNVs technique was explored for early diagnosis of leptomeningeal malignancy.

RESULTS

In the tumor group, 28 patients were positive for CSF cytology, and 24 patients were positive for CSF mNGS-CNVs. Sensitivity and specificity of CSF cytology were 82.35% (95% CI: 66.83-92.61%) and 94.12% (95% CI: 69.24-99.69%). In comparison, sensitivity and specificity of CSF mNGS-CNV were 70.59% (95% CI: 52.33-84.29%) and 100% (95% CI: 77.08-100%). There was no significant difference in diagnostic consistency between CSF cytology and mNGS-CNVs (p = 0.18, kappa = 0.650).

CONCLUSIONS

CSF mNGS-CNVs tend to have higher specificity compared with traditional cytology and can be used as a complementary diagnostic method for patients with leptomeningeal malignancies.

Epstein-Barr virus-positive iris diffuse large B-cell lymphoma detected by metagenomic next-generation sequencing

PURPOSE

Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) is a relatively rare subtype of DLBCL. Herein, we report a case of a patient with EBV-positive iris DLBCL after undergoing penetrating keratoplasty and discuss its possible pathogenesis.

METHODS

A 72-year-old male patient presented to our hospital with progressive blurring of vision in the left eye for the past 4 months. Small white nodular lesions were observed on the iris and retinal surface of the left eye, with a white cloud-like opacity in the vitreous cavity.

RESULTS

The patient was eventually diagnosed with EBV-positive iris DLBCL after undergoing pathological and metagenomic tests. After injecting methotrexate in the left vitreous cavity and administering systemic and local antiviral treatments, the ocular lesions disappeared.

CONCLUSION

EBV infection, drug immunosuppression, and aging-related immune deterioration may play significant roles in the pathogenesis of EBV-positive iris DLBCL.

SYNOPSIS

Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) is a new subtype of DLBCL, which rarely occurs. Herein, we report a case of a patient with EBV-positive iris DLBCL after undergoing penetrating keratoplasty and discuss its possible pathogenesis.

Utility of metagenomic Next-Generation Sequencing for simultaneously detecting pathogens and neoplasms

Objectives

Clinicians often face the challenge of differentially diagnosing febrile patients who are suspected of infectious diseases, since the clinical manifestations of infection and cancer may overlap. A single test that can detect both pathogens and tumor could provide timely and accurate diagnostic clues to aid the treatment and management of these patients.

Methods

We enrolled eight patients to evaluate the utility of metagenomic Next-Generation Sequencing for simultaneously detecting pathogens and neoplasms using body fluids and tissue samples. Patients were selected by the following criteria: 1) Tumor was not considered upon hospitalization, but mNGS testing indicated neoplasm; 2) Tumor was not excluded, but microbial infection was primarily suspected according to initial clinical assessment.

Results

We detected potential pathogens in five patients, three of whom had progressed into critical infections. Moreover, abnormal chromosomal copy numbers were identified in all patients that indicated presence of neoplasms, which were pathologically confirmed.

Conclusions

Although copy number variations do not render a definitive cancer diagnosis, it can prompt clinicians to conduct more focused diagnostic testing for cancer, potentially saving time and cost. As a result, integrating copy number analysis with pathogen detection in mNGS may help establish rapid and accurate diagnosis for febrile patients.

Simultaneous diagnosis of tuberculous pleurisy and malignant pleural effusion using metagenomic next-generation sequencing (mNGS)

BACKGROUND

Metagenomic next-generation sequencing (mNGS) has become a powerful tool for pathogen detection, but the value of human sequencing reads generated from it is underestimated.

METHODS

A total of 138 patients with pleural effusion (PE) were diagnosed with tuberculous pleurisy (TBP, N = 82), malignant pleural effusion (MPE, N = 35), or non-TB infection (N = 21), whose PE samples all underwent mNGS analysis. Clinical TB tests including culture, Acid-Fast Bacillus (AFB) test, Xpert, and T-SPOT, were performed. To utilize mNGS for MPE identification, 25 non-MPE samples (20 TBP and 5 non-TB infection) were randomly selected to set human chromosome copy number baseline and generalized linear modeling was performed using copy number variant (CNV) features of the rest 113 samples (35 MPE and 78 non-MPE).

RESULTS

The performance of TB detection was compared among five methods. T-SPOT demonstrated the highest sensitivity (61% vs. culture 32%, AFB 12%, Xpert 35%, and mNGS 49%) but with the highest false-positive rate (10%) as well. In contrast, mNGS was able to detect TB-genome in nearly half (40/82) of the PE samples from TBP subgroup, with 100% specificity. To evaluate the performance of using CNV features of the human genome for MPE prediction, we performed the leave-one-out cross-validation (LOOCV) in the subcohort excluding the 25 non-MPE samples for setting copy number standards, which demonstrated 54.1% sensitivity, 80.8% specificity, 71.7% accuracy, and an AUC of 0.851.

CONCLUSION

In summary, we exploited the value of human and non-human sequencing reads generated from mNGS, which showed promising ability in simultaneously detecting TBP and MPE.

Utility of clinical metagenomics in diagnosing malignancies in a cohort of patients with Epstein-Barr virus positivity

Backgrounds

Differentiation between benign and malignant diseases in EBV-positive patients poses a significant challenge due to the lack of efficient diagnostic tools. Metagenomic Next-Generation Sequencing (mNGS) is commonly used to identify pathogens of patients with fevers of unknown-origin (FUO). Recent studies have extended the application of Next-Generation Sequencing (NGS) in identifying tumors in body fluids and cerebrospinal fluids. In light of these, we conducted this study to develop and apply metagenomic methods to validate their role in identifying EBV-associated malignant disease.

Methods

We enrolled 29 patients with positive EBV results in the cohort of FUO in the Department of Infectious Diseases of Huashan Hospital affiliated with Fudan University from 2018 to 2019. Upon enrollment, these patients were grouped for benign diseases, CAEBV, and malignant diseases according to their final diagnosis, and CNV analysis was retrospectively performed in 2022 using samples from 2018 to 2019.

Results

Among the 29 patients. 16 of them were diagnosed with benign diseases, 3 patients were diagnosed with CAEBV and 10 patients were with malignant diseases. 29 blood samples from 29 patients were tested for mNGS. Among all 10 patients with malignant diagnosis, CNV analysis suggested neoplasms in 9 patients. Of all 19 patients with benign or CAEBV diagnosis, 2 patients showed abnormal CNV results. The sensitivity and specificity of CNV analysis for the identification for tumors were 90% and 89.5%, separately.

Conclusions

The application of mNGS could assist in the identification of microbial infection and malignancies in EBV-related diseases. Our results demonstrate that CNV detection through mNGS is faster compared to conventional oncology tests. Moreover, the convenient collection of peripheral blood samples adds to the advantages of this approach.

T‑lymphoblastic lymphoma in a child diagnosed by metagenomic sequencing: A case report

T-lymphoblastic lymphoma (T-LBL) is a rare subtype of non-Hodgkin's lymphoma with a higher incidence in children than adults. T-LBL often presents with multiple lymph node enlargements or mediastinal masses, which can cause local compression symptoms, and is frequently misdiagnosed as an infectious disease at an early stage. By summarizing a recently experienced case of T-LBL in a patient with a suspected infection, with an analysis of clinical features and diagnostic methods, the aim of the present study was to provide more information on the early diagnosis of tumors in patients suspected to have an infection. An 8-year-old boy presented at a local hospital with abdominal pain, chest tightness and shortness of breath for >5 days, and bilateral pleural, abdominal and pericardial effusion were considered. Following hospitalization without significant improvement under treatment with an anti-infection regimen and closed chest cavity drainage, the patient was transferred to another hospital. Once admitted, ultrasound examination indicated a large amount of pericardial and pleural effusion. Pericardiocentesis and closed chest cavity drainage were performed immediately. The initial pericardial drainage, which was bloody in appearance, gradually changed to a pale-yellow fluid. The patient continued to present with a temperature and remained under active anti-infection treatment. With repeated drainage procedures, it was observed that the volume of fluid obtained from the closed chest cavity exhibited an increasing trend. The cytological and tumor marker analysis of the idiopathic effusion specimens detected no abnormalities. Metagenomic next-generation sequencing (mNGS) of the pericardial drainage fluid was performed to identify the infectious pathogen. No pathogen was detected in the specimens, but the copy number variation (CNV) found in multiple chromosomes was highly suggestive of cancer development and progression. Lung imaging revealed no mediastinal lesions or tumors. The fluid from a subsequent closed chest drainage procedure was evaluated by mNGS for diagnostic purposes, and multiple CNVs were again noted, with similar results to those from the pericardial effusion. To determine the tumor type, immunophenotyping of the fluid was performed using flow cytometry and a diagnosis of T-LBL was confirmed. The patient was subsequently transferred to the hematology department for chemotherapy. The present case indicates that mNGS can not only differentiate between infections and tumors but also rapidly determine disease etiology.

Pulmonary infection of Schizophyllum commune diagnosed by metagenomic next- generation sequencing: A case report

RATIONALE

Fungal infection is common and difficult to be diagnosed timely in clinical, for its various kinds and similar manifestations. The rare pulmonary fungal infection such as Schizophyllum commune was one of the harder ones and misdiagnosed in usual.

PATIENT CONCERNS

We report a 32-year-old female which was diagnosed with Metagenomic Next-Generation Sequencing (mNGS). She was hospitalized with the complaint of 4 months and more of repeated cough and expectorating. The chest computer tomography revealed left lower lobe pathological changes, but antibiotics were ineffective. No positive results were found in laboratory tests, including sputum culture and the pathology of lung puncture biopsy.

DIAGNOSES

mNGS of lung biopsy was performed and detected the sequence number of Schizophyllum for 11.

INTERVENTIONS

The patient was treated with voriconazole and itraconazole successively.

OUTCOMES

She recovered to health. There was no recurrence during follow-up.

LESSONS

mNGS as a diagnostic method could quickly detect pathogens through the processing of fragment, synthesis, comparison, and analysis of sample genes. It is suitable for detecting especially rare and polymicrobial infections. To our best knowledge, infection of Schizophyllum commune have not been reported in English literature with diagnostic method of mNGS.

A multicenter-retrospective cohort study of chromosome instability in lung cancer: clinical characteristics and prognosis of patients harboring chromosomal instability detected by metagenomic next-generation sequencing

Background

The usefulness of metagenomic next-generation sequencing (mNGS) in identifying the prognosis of lung cancer with chromosomal instability (CIN) remains unclear. We aimed to analyze clinical characteristics and prognosis of patients in patients harboring CIN.

Methods

This retrospective cohort study included 668 patients diagnosed with suspected pulmonary infection or lung cancer whose samples underwent mNGS detection from January 2021 to January 2022. Difference between clinical characteristics were calculated by the Student's t-test and the chi-square test. The subjects were followed-up from registered to September 2022. Survival curves were analyzed by the Kaplan-Meier method.

Results

Of 619 bronchoalveolar lavage fluid (BALF) samples collected by bronchoscopy, 30 CIN-positive samples were confirmed as malignant on histopathology, with a sensitivity of 61.22%, a specificity of 99.65%, and an 83.17% accuracy [cut-off values were established by the receiver operating characteristic (ROC) area under the curve (AUC) =0.804]. In 42 patients with lung cancer, mNGS detected 24 patients as CIN-positive and 18 as CIN-negative. There were no differences between two groups including ages, pathologic types, stage and metastases. In 25 cases, we detected 523 chromosomal copy number variants (CNVs) with forms including duplication (dup), deletion (del), mosaic (mos), and whole chromosome amplification or loss. A total of 243 duplication variants and 192 deletion variants occurred in all chromosomes. Duplications occurred in most chromosomes except for Chr9 and Chr13, in which CNV tended to delete. The median overall survival (OS) in patients with Chr5p15 duplication was 32.4 months [95% confidence interval (CI), 10.35-54.45 months]. The median OS differed significantly between the 5p15dup+ group and the combined group (32.4 vs. 8.63 months, P=0.049). In 29 patients with unresected lung cancer, the median OS of 18 cases in the CIN-positive group was 32.4 months (95% CI, 14.2-50.6 months) and the median OS of 11 cases in the CIN-negative group was 35.63 months (95% CI, 21.64-49.62 months; Wilcoxon, P=0.227).

Conclusions

Various forms of CIN detected by mNGS may predict prognosis of patients with lung cancer differentially. CIN with duplication or deletion deserves further study to guide clinical treatment.

Recent Advances and Ongoing Challenges in the Diagnosis of Culture Negative Endophthalmitis

BACKGROUND

Culture negative (CN) but presumed infectious endophthalmitis poses a huge diagnostic challenge in terms of clinical management. This article outlines the current state of knowledge of infectious endophthalmitis with negative cultures and summarizes the recommendations for the work up of this condition along with providing a simple algorithm, by putting into context the recent concerns about over-diagnosing endophthalmitis.

METHODS

We searched the PubMed and Scopus databases for large hospital based studies on diagnosis of endophthalmitis, with emphasis on culture-negative infections in October 2021. Only clinical studies written in English were included. Basic science studies, letters to the editor and case reports on endophthalmitis were excluded.

RESULTS

Twenty studies were included in this study. The prevalence of CN endophthalmitis ranged from 40% to 70%. Recent advances in PCR along with high throughput sequencing have helped identify the etiological agent in most cases but these technologies are not easily available, requires advanced bioinformatic analysis and are not cost effective. Role of other inflammatory and relatively low-cost biomarkers in diagnosing a presumed infection is yet to be validated clinically but hold promise in helping ophthalmologists identify the causative agent.

CONCLUSIONS

CN endophthalmitis is a relatively frequent finding and should not be labelled as sterile endophthalmitis. Recent advances provide a new perspective for ophthalmologist in diagnosis of presumed infectious endophthalmitis and further studies are needed to confirm their utility in clinical settings.

Diagnosis of lung squamous cell carcinoma based on metagenomic Next-Generation Sequencing

Background

The clinical treatment of patients suspected of pulmonary infections often rely on empirical antibiotics. However, preliminary diagnoses were based on clinical manifestations and conventional microbiological tests, which could later be proved wrong. In this case, we presented a patient whose initial diagnosis was lung abscess, but antibiotic treatments had no effect, and metagenomic Next-Generation Sequencing (mNGS) indicated presence of neoplasm.

Case presentation

A 62-year-old female was diagnosed with lung abscess at three different health facilities. However, mNGS of bronchoalveolar lavage fluid did not support pulmonary infections. Rather, the copy number variation analysis using host DNA sequences suggested neoplasm. Using H&E staining and immunohistochemistry of lung biopsy, the patient was eventually diagnosed with lung squamous cell carcinoma.

Conclusions

mNGS not only detects pathogens and helps diagnose infectious diseases, but also has potential in detecting neoplasm via host chromosomal copy number analysis. This might be beneficial for febrile patients with unknown or complex etiology, especially when infectious diseases were initially suspected but empirical antibiotic regimen failed.

Diffuse Large B-Cell Lymphoma of the Mandible Diagnosed by Metagenomic Sequencing: A Case Report

Introduction: Non-Hodgkin lymphoma (NHL) has a much higher incidence rate than Hodgkin lymphoma. Approximately 40% NHL occurs in extranodal tissues or organs, and its clinical manifestations are often nonspecific. Primary bone NHL involving the mandible is an uncommon NHL that is characterized by fever, gum swelling and toothache. Therefore, it is often misdiagnosed as oral diseases.

Case Presentation: A 52-year-old female had recurrent fever for more than 1 month, with numbness in her left jaw and toothache. PET/CT showed an uptake area in the left mandible, suggesting microbial infections. However, antibacterial, and antiviral treatment were ineffective. Furthermore, metagenomic sequencing of plasma reported no pathogens, but instead showed significant copy number variations of multiple chromosomes, which highly suggested the existence of tumor. Finally, diffuse large B-cell lymphoma (DLBCL) was diagnosed by mandibular biopsy, and the patient was transferred to Hematology department for chemotherapy.

Conclusion: mNGS not only assists rapid etiological diagnosis, but also helps rule out infection and diagnose malignant neoplasm.

Metagenomic next-generation sequencing to identify pathogens and cancer in lung biopsy tissue

BACKGROUND

Lung biopsy tissue samples can be used for infection detection and cancer diagnosis. Metagenomic next-generation sequencing (mNGS) has the potential to further improve diagnosis.

METHODS

From July 2018 to May 2020, lung biopsy samples of 133 patients with suspected pulmonary infection or abnormal imaging findings were collected and subjected to clinical microbiological testing, Illumina and Nanopore sequencing to identify pathogens. The neural networks were pretrained by extracting features of human reads from 2,095 metagenomic next-generation sequencing results, and the human reads of lung biopsy samples were entered into the validated pipeline to predict the risk of cancer.

FINDINGS

Based on the pathogen-cancer detection pipeline, the Illumina platform showed 77·6% sensitivity and 97·6% specificity compared to the composite reference standard for infection diagnosis. However, the Nanopore platform showed 34·7% sensitivity and 98·7% specificity. mNGS identified more fungi, which was confirmed by subsequent pathological examination. M. tuberculosis complex was weakly detected. For cancer detection, compared with histology, the Illumina platform showed 83·7% sensitivity and 97·6% specificity, diagnosing an additional 36 cancer patients, of whom half had abnormal imaging findings (pulmonary shadow, space-occupying lesions, or nodules).

INTERPRETATION

For the first time, we have established a pipeline to simultaneously detect pathogens and cancer based on Illumina sequencing of lung biopsy tissue. This pipeline efficiently diagnosed cancer in patients with abnormal imaging findings.

FUNDING

This work was supported by the National Key Research and Development Program of China and National Natural Science Foundation of China.