Lung Biopsy Tissue Research Articles

Using Minimally Invasive Tissue Sampling and Determination of Cause of Death to Establish Etiologies of Community Respiratory Deaths Among Zambian Infants and Children.

In low-to-middle-income countries, acute lower respiratory infection (ALRI) remains the leading infectious cause of death among infants and children under 5 years old. Case-control studies based on upper respiratory sampling have informed current understandings of ALRI etiologies; in contrast, minimally invasive tissue sampling (MITS) offers a method of directly interrogating lower respiratory tract pathogens to establish etiologic distributions. This study performed in the postmortem setting used MITS and a Determination of Cause of Death (DeCoDe) panel to elucidate the causes of fatal pneumonia in the community in Lusaka, Zambia. For deceased infants and children under age 5 years whose next-of-kin provided consent, a verbal autopsy was obtained and 6 lung tissue biopsies from each case were sent for histopathology and multiplex polymerase chain reaction testing. Subsequently, a multi-disciplinary DeCoDe panel met to review each case, determine if the child died of respiratory causes, construct a causal chain of diagnoses directly leading to the death, and determine if the death was preventable (i.e., if an identifiable intervention would have averted the death). Among 106 deaths, 49 were adjudicated as respiratory deaths, with etiologic causes including Klebsiella pneumoniae (13), Streptococcus pneumoniae (5), and Pneumocystis jirovecii (4), among others. Of note, for 21 respiratory deaths, a causative pathogen could not be identified despite clinical and histopathologic evidence of ALRI. A large majority of all deaths were considered preventable (90/106 or 85%). This study demonstrates the impact of certain respiratory pathogens through direct in situ tissue sampling with supportive pathologic data and presents a useful method of studying the etiologic distribution of fatal ALRIs in settings where many deaths occur in the community.

A novel mouse model of myositis-associated interstitial lung disease was established by using TLR9 agonist combined with muscle homogenate.

Our group previously demonstrated that NETs were involved in interstitial lung diseases (ILD) among patients with idiopathic inflammatory myopathies (IIM) and the experimental autoimmune myositis (EAM) mouse model, and that NETs activated lung fibroblasts through the TLR9-miR7-Smad2 axis. This study aimed to establish a novel mouse model of myositis-associated interstitial lung disease (MAILD) by using a TLR9 agonist (ODN2395). ODN2395 and muscle homogenate were used to induce MAILD in BALB/c mice. MAILD was evaluated using histopathology, immunohistochemistry, serum NETs determination, and myositis-specific antibody profile. Furthermore, TLR9 and IRF3 were examined in a lung biopsy tissue from a dermatomyositis patient with ILD. MAILD mice developed inflammatory myopathy with positive expression of myositis specific antibodies. ILD occurred in all mice of MAILD group. ODN2395 at doses of 5μg, 10μg or 20μg induced ILD, with increasing severity as the dose increased, but 20μg ODN2395 was not recommended due to non-specific damage to lungs. ILD could occur as early as one week after immunization and was most pronounced by the fourth/fifth week. MAILD process was accompanied by NETs infiltration and TLR9 activation. TLR9 activation was demonstrated in the patient with DM-ILD. Serum levels of Cit-H3 were elevated in the MAILD group. Skeletal muscle homogenate and ODN2395 induced neutrophils to form NETs in vitro. Combined with muscle homogenate, ODN2395 induced a novel MAILD mouse model with NETs infiltration and TLR9 activation, which are similar to pathogenesis of IIM-ILD, suggesting that MAILD model could replace EAM model in IIM-ILD research.

Mycobacterium paragordonae pulmonary disease with rapidly growing solitary lesions: a case report and literature review.

Mycobacterium paragordonae (MPG) is a novel and uncommon nontuberculous mycobacterium (NTM). We describe a case of MPG pulmonary disease (MPGPD) with a single, rapidly growing, pulmonary mass, which has rarely been reported. A chest CT scan of a 66-year-old woman revealed a rapidly growing solitary mass-like lesion in the upper lobe of the right lung, which was not seen in the previous chest CT scan six months ago. H&E-stained section of the CT-guided percutaneous lung tissue biopsy specimen showed chronic inflammatory changes with epithelioid granulomas. Metagenomic next-generation sequencing (mNGS) of lung tissue biopsy specimen identified MPG with a sequence number of 1617 and a confidence level of 99%. Because the subsequent MPG droplet digital PCR (MPG-ddPCR) test of the lung tissue biopsy was positive, she was eventually diagnosed with MPGPD. She was administered a quadruple oral regimen comprising clarithromycin, levofloxacin, rifampicin, and ethambutol according to the ATS/IDSA protocol for Mycobacterium gordonae (MG) infection. The chest CT scans showed a significant reduction in the lesion one month after the treatment and almost complete resolution four months later. MPGPD is a rare NTM infection. The imaging manifestations of MPGPD are diverse and may even show rapid development. mNGS of tissue biopsy can enable prompt diagnosis of MPG infection and is a good alternative to routine NTM microbial testing. The ATS/IDSA protocol for MG infection is an effective treatment for MPG infection.

Bronchoalveolar lavage fluid and lung biopsy tissue metagenomic next-generation sequencing in the diagnosis of pulmonary cryptococcosis.

To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens. In this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. Individuals were classified into PC and non-PC groups according to the diagnostic criteria for PC, and conventional fungal cultures were performed. A serum/BALF cryptococcal antigen (CrAg) test was performed in some patients with PC. The diagnostic efficiencies of three methods for PC (mNGS, conventional culture, and CrAg) were compared. Additionally, two mNGS methods were used in this study: original mNGS (OmNGS, testing time from January 2021 to December 2022) and modified mNGS (MmNGS, testing time from January to December 2023). The diagnostic efficiency of the two mNGS methods on PC was simultaneously compared. Among the 321 patients, 23 (7.2%) had PC and 298 (92.8%) did not. Compared with the composite reference standard for PC diagnosis, the sensitivity, specificity, and accuracy of mNGS for PC were 78.3% (95% confidence interval [CI], 55.8%-91.7%), 98.7% (95% CI, 96.4%-99.6%), and 97.2% (95% CI, 94.7%-98.7%), respectively. The sensitivity of mNGS was similar to that of CrAg (80.0%, 12/15) (P > 0.05). The diagnostic sensitivity of both mNGS and CrAg was higher than that of conventional culture (35.0%, 7/20) (P = 0.006, P = 0.016), and the combined detection of mNGS and CrAg further improved the diagnostic sensitivity of PC (93.3%, 14/15). The area under the receiver operating characteristic curve of mNGS was superior to that of conventional culture (0.885 vs. 0.675). In addition, the diagnostic sensitivity of PC was higher than that of OmNGS (P = 0.046). The sensitivity of mNGS is better than that of conventional culture. The combination of mNGS and CrAg improves the testing sensitivity of Cryptococcus. MmNGS could further improve the detection of Cryptococcus. Conventional PC detection methods are indispensable and mNGS can be used as a rapid and accurate auxiliary diagnostic method for PC.

The RNA Binding Protein Tristetraprolin Contributes to CFTR mRNA Stability in Cystic Fibrosis.

Cystic Fibrosis (CF) is the most common inherited disorder and is characterized by an inflammatory phenotype. Here, we found that in bronchial epithelium reconstituted form lung tissue biopsies from patients with CF, the RNA-binding protein tristetraprolin (TTP), a key regulator of inflammation, is dysregulated in cells that strongly express cytokines and interleukins. TTP activity is regulated by extensive post-translational modifications, particularly phosphorylation. We found that in addition to mRNA downregulation, phosphorylated TTP (which cannot bind to mRNA) accumulated in CF cultures, suggesting that the imbalance in TTP phosphorylation status could contribute to the inflammatory phenotype in CF. We confirmed TTP destabilizing role on IL8 mRNA through its 3'UTR sequence in CF cells. We next demonstrated that TTP phosphorylation is mainly regulated by MK2 through activation of ERK, which also was hyperphosphorylated. TTP is considered a mRNA decay factor with some exception, and we present a new positive role of TTP in CF cultures. We determined that TTP binds to specific ARE motifs on the 3'UTR of mRNA sequences and also, for the first time, to the 3'UTR of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) where TTP binding stabilizes the mRNA level. This study identified new partners that can be targeted in CF and proposes a new way to control CFTR gene expression.

Endobronchial ultrasound-guided transbronchial fine needle aspiration: synopsis and prospects

Despite the high informativeness of minimally invasive methods for assessing respiratory system, lung tissue biopsy is often required to verify the diagnosis. Conventional methods include surgical biopsy, which considered as the gold standard but is associated with significant complications and mortality, and transbronchial biopsy, a less invasive but substantially less informative method. The most informative and novel approach is endobronchial ultrasoundguided transbronchial fine needle aspiration (EBUS-TBNA), which significantly surpasses forceps biopsy. Here I focus on EBUS-TBNA, highlighting its capabilities, the future prospects, expedient technical solutions in certain of its modification and the lack thereof in others, and approaches for the standardization.

Development of novel broad-range pan-genus PCR assays for the detection of Tropheryma species.

Introduction. Tropheryma whipplei is responsible for the classical Whipple's disease. Recently, a new Tropheryma species was described in a Belgian immunocompromised patient with pleuritis.Gap Statement. There is currently no specific molecular diagnostic test detecting other Tropheryma species than Tropheryma whipplei.Aim. To develop and validate two broad-range pan-Tropheryma genus PCRs detecting both T. whipplei and new Tropheryma species.Methodology. From shotgun sequencing data of the lung tissue biopsy of the Belgian subject, we designed two PCRs targeting the 23S rRNA and rnpB genes. Prospectively, requests for T. whipplei PCR were tested with T. whipplei-specific PCRs and the two Tropheryma broad-range PCRs from January 2019 to November 2022.Results. In total, 2605 samples were tested using both the pan-Tropheryma 23S rRNA PCR and the T. whipplei-specific PCR. In addition, 833 of the 2605 samples were also tested using the pan-Tropheryma rnpB PCRs. Sensitivity was 78.8% and 79.7% for 23S rRNA and rnpB PCRs, as compared with the species-specific T. whipplei PCR. Specificity was 99.9% and 99.7% for the 23S rRNA and the rnpB PCRs, respectively. We identified a patient whose bronchoalveolar lavage tested positive with the two broad-range PCRs with >105 copies ml-1. Specific T. whipplei PCRs were negative. Known for panuveitis, this 49-year-old male presented with an eye inflammation recurrence, and a CT scan showed multiple mediastino-hilar necrotic adenopathies. Doxycyclin (1 year), hydroxychloroquin (1 year) and co-trimoxazol (1 month) treatments led to a favourable outcome.Conclusion. Specific T. whipplei PCR exhibited better sensitivity than the pan-Tropheryma PCRs. However, both broad-range pan-Tropheryma PCRs demonstrated excellent specificity and were pivotal to identifying a new probable case of Tropheryma infection due to another species-level lineage.

Pulmonary benign metastasizing leiomyoma presenting as acute hypoxemic respiratory failure: a case report

Pulmonary benign metastasizing leiomyoma is an uncommon condition, predominantly affecting women of childbearing age with a history of uterine smooth muscle tumors and uterine leiomyoma surgery for uterine leiomyoma. The progression of PBML is often unpredictable and depends on the extent of lung involvement. Generally, most patients remain asymptomatic, but a minority may experience coughing, wheezing, or shortness of breath, which are frequently misdiagnosed as pneumonia. consequently, this presents significant challenges in both treatment and nursing care before diagnosis. This paper reports the case of a 35-year-old woman primarily diagnosed with acute hypoxic respiratory failure who was transferred from the emergency room to the intensive care unit. The initial computed tomography scan of the patient’s lungs indicated diffuse interstitial pneumonia, but the sequencing of the alveolar lavage fluid pathogen macro did not detect any bacteria, fungi, or viruses. Moreover, the patient remained in a persistent hypoxic state before the definitive diagnosis. Therefore, our focus was on maintaining the airway patency of the patient, using prone ventilation, inhaling nitric oxide, monitoring electrical impedance tomography, and preventing ventilator-associated pneumonia to improve oxygenation, while awaiting immunohistochemical staining of the patient’s biopsied lung tissue. This would help us clarify the diagnosis and treat it based on etiology. After meticulous treatment and nursing care, the patient was weaned off the ventilator after 26 days and transferred to the respiratory ward after 40 days. This case study may serve as a reference for clinical practice and assist patients suffering from PBML.

Allergic bronchopulmonary aspergillosis with low serum IgE: a case report

Here, we reported a case of delayed diagnosis of allergic bronchopulmonary aspergillosis (ABPA) with low serum IgE and normal Aspergillus fumigatus-specific IgE levels. During the course of the disease, the patient (female, 55 years old) had imaging manifestation of mass shadow and significant elevation of carcinoembryonic antigen, leading to suspicion of a lung tumor. Later, transbronchial lung biopsy tissue culture showed Aspergillus fumigatus. Combined with the history, clinical characteristics and imaging, she was diagnosed with allergic bronchopulmonary aspergillosis combined with invasive pulmonary aspergillosis. As the diagnostic criteria for ABPA do not cover all patients with ABPA, in rare cases where immunological evidence is insufficient, a combination of clinical and imaging features is required for early diagnosis and treatment.

Design, infectability, and transcriptomic analysis of transregionally differentiated and scalable lung organoids derived from adult bronchial cells.

The lung is a primary target for many lethal respiratory viruses, leading to significant global mortality. Current organoid models fail to completely mimic the cellular diversity and intricate tubular and branching structures of the human lung. Lung organoids derived from adult primary cells have so far only included cells from the input cell region, proximal or distal. Existing models are expensive. They often require cells from invasive deep lung tissue biopsies. The present study aimed to address these limitations. The lung organoids obtained using an original protocol exhibited transregional differentiation and were derived from relatively more accessible primary cells from the trachea/bronchi. Immortal bronchial cell lines were also used to simplify organoid fabrication and improve its scalability. The lung organoids are formed starting from bronchial cells with fibroblasts feeder cells in an alginate hydrogel coated with base membrane zone proteins. Characterizations were performed using bulk RNA sequencing and tandem mass tags. The resulting organoids express markers of different lung regions and mimic to some extent the tubular and branching morphology of the lung. The proteomic profile of organoid from primary cells and from cell lines was found to evolve towards that of mature lung tissue. Upregulated genes were mostly related to the respiratory system, tube development, and various aspects of respiratory viral infections. Infection with SARS-CoV-2 and influenza H1N1 was successful and did not require organoid disassembly. The organoids matured within 21 days and did not require complex or expensive culture methods. Transregionally differentiated lung organoid may find applications for the study of emerging or re-emerging viral infections and fostering the development of novel in-vitro therapeutic strategies.

A single-center, retrospective study of hospitalized patients with lower respiratory tract infections: clinical assessment of metagenomic next-generation sequencing and identification of risk factors in patients

IntroductionLower respiratory tract infections(LRTIs) in adults are complicated by diverse pathogens that challenge traditional detection methods, which are often slow and insensitive. Metagenomic next-generation sequencing (mNGS) offers a comprehensive, high-throughput, and unbiased approach to pathogen identification. This retrospective study evaluates the diagnostic efficacy of mNGS compared to conventional microbiological testing (CMT) in LRTIs, aiming to enhance detection accuracy and enable early clinical prediction.MethodsIn our retrospective single-center analysis, 451 patients with suspected LRTIs underwent mNGS testing from July 2020 to July 2023. We assessed the pathogen spectrum and compared the diagnostic efficacy of mNGS to CMT, with clinical comprehensive diagnosis serving as the reference standard. The study analyzed mNGS performance in lung tissue biopsies and bronchoalveolar lavage fluid (BALF) from cases suspected of lung infection. Patients were stratified into two groups based on clinical outcomes (improvement or mortality), and we compared clinical data and conventional laboratory indices between groups. A predictive model and nomogram for the prognosis of LRTIs were constructed using univariate followed by multivariate logistic regression, with model predictive accuracy evaluated by the area under the ROC curve (AUC).Results(1) Comparative Analysis of mNGS versus CMT: In a comprehensive analysis of 510 specimens, where 59 cases were concurrently collected from lung tissue biopsies and BALF, the study highlights the diagnostic superiority of mNGS over CMT. Specifically, mNGS demonstrated significantly higher sensitivity and specificity in BALF samples (82.86% vs. 44.42% and 52.00% vs. 21.05%, respectively, p < 0.001) alongside greater positive and negative predictive values (96.71% vs. 79.55% and 15.12% vs. 5.19%, respectively, p < 0.01). Additionally, when comparing simultaneous testing of lung tissue biopsies and BALF, mNGS showed enhanced sensitivity in BALF (84.21% vs. 57.41%), whereas lung tissues offered higher specificity (80.00% vs. 50.00%). (2) Analysis of Infectious Species in Patients from This Study: The study also notes a concerning incidence of lung abscesses and identifies Epstein-Barr virus (EBV), Fusobacterium nucleatum, Mycoplasma pneumoniae, Chlamydia psittaci, and Haemophilus influenzae as the most common pathogens, with Klebsiella pneumoniae emerging as the predominant bacterial culprit. Among herpes viruses, EBV and herpes virus 7 (HHV-7) were most frequently detected, with HHV-7 more prevalent in immunocompromised individuals. (3) Risk Factors for Adverse Prognosis and a Mortality Risk Prediction Model in Patients with LRTIs: We identified key risk factors for poor prognosis in lower respiratory tract infection patients, with significant findings including delayed time to mNGS testing, low lymphocyte percentage, presence of chronic lung disease, multiple comorbidities, false-negative CMT results, and positive herpesvirus affecting patient outcomes. We also developed a nomogram model with good consistency and high accuracy (AUC of 0.825) for predicting mortality risk in these patients, offering a valuable clinical tool for assessing prognosis.ConclusionThe study underscores mNGS as a superior tool for lower respiratory tract infection diagnosis, exhibiting higher sensitivity and specificity than traditional methods.

Performance of rapid on-site evaluation of touch imprints of bronchoscopic biopsies or lung tissue biopsies for the diagnosis of invasive pulmonary filamentous fungi infections in non-neutropenic patients.

The diagnosis of invasive pulmonary fungal disease depends on histopathology and mycological culture; there are few studies on touch imprints of bronchoscopic biopsies or lung tissue biopsies for the diagnosis of pulmonary filamentous fungi infections. The purpose of the present study was to explore the detection accuracy of rapid on-site evaluation of touch imprints of bronchoscopic biopsies or lung tissue biopsies for the filamentous fungi, and it aims to provide a basis for initiating antifungal therapy before obtaining microbiological evidence. We retrospectively analyzed the diagnosis and treatment of 44 non-neutropenic patients with invasive pulmonary filamentous fungi confirmed by glactomannan assay, histopathology, and culture from February 2017 to December 2023. The diagnostic positive rate and sensitivity of rapid on-site evaluation for these filamentous fungi identification, including diagnostic turnaround time, were calculated. Compared with the final diagnosis, the sensitivity of rapid on-site evaluation was 81.8%, and the sensitivity of histopathology, culture of bronchoalveolar lavage fluid, and glactomannan assay of bronchoalveolar lavage fluid was 86.4%, 52.3%, and 68.2%, respectively. The average turnaround time of detecting filamentous fungi by rapid on-site evaluation was 0.17 ± 0.03 hours, which was significantly faster than histopathology, glactomannan assay, and mycological culture. A total of 29 (76.3%) patients received earlier antifungal therapy based on ROSE diagnosis and demonstrated clinical improvement. Rapid on-site evaluation showed good sensitivity and accuracy that can be comparable to histopathology in identification of pulmonary filamentous fungi. Importantly, it contributed to the triage of biopsies for further microbial culture or molecular detection based on the preliminary diagnosis, and the decision on early antifungal therapy before microbiological evidence is available.

Is there a role for lung or bronchial biopsies for the diagnosis of mycobacterial pulmonary disease in patients with bronchiectasis?

BackgroundWorkup of bronchiectasis patients mandates microbiological characterization often being sought via Bronchoscopy. However, whether to perform bronchial or lung biopsies, is unknown, especially for the diagnosis of NTM pulmonary disease. We aimed to assess the current practice and yield of the different bronchoscopic procedures in this setting. MethodsData from an adult cohort with bronchiectasis referred for bronchoscopy for microbiologic sampling was reviewed, including demographics, etiology, imaging and results of the different bronchoscopic procedures performed. Results127 subjects were analyzed (mean age 61, 56% female). BAL culture was positive in 44%. Frequent pathogens were Hemophilus Influenza (20%), pseudomonas aeruginosa (8%) and Staphylococcus aureus (7%). NTM and tuberculosis were found in 6% and 1.5% respectively. BAL cytology was sent in 125 procedures, EBB was performed in 51 patients (40%) and TBLB in 38 patients (30%). BAL cytology and both EBB and TBB (including tissue cultures) had no benefit over BAL with respect to microbiological diagnosis, including identification of mycobacterial disease. ConclusionsIn adult subjects with Non-CF bronchiectasis requiring bronchoscopy for microbiological characterization, BAL cytology and lung tissue biopsies were frequently performed but were of minimal additional benefit over BAL culture (including for mycobacterial pulmonary disease), and are most likely futile.

Динамика выявления РНК вируса SARS-CoV-2 у пациентов и сотрудников ФГБУ «НМИЦ гематологии» Минздрава России в первые 2 года пандемии новой коронавирусной инфекции COVID-19

Background. COVID-19 required fundamental changes in healthcare management, also in medical care for oncological and hematological patients. Visits to healthcare organizations were minimized, 75 % of doctor appointments were converted to telemedicine consultations. The solutions aimed at preventing further spread of COVID-19 included establishing of observational units, distinguishing between patient and employee flows, regular SARS-CoV-2 RNA testing, reducing hospital stays and transferring patients with positive COVID-19 tests to the remodeled hospitals specializing in the novel coronavirus infection, as well as providing only emergency medical treatment and, as far as feasible, converting systemic chemotherapy to per os treatment, etc.&#x0D; Aim. To assess SARS-CoV-2 RNA detection dynamics at the National Research Center for Hematology from April 2020 to January 2022 during the implementation of epidemic control measures.&#x0D; Materials &amp; Methods. The study was based on SARS-CoV-2 RNA testing of naso- and oropharyngeal samples obtained from patients and employees of the National Research Center for Hematology (hereafter referred to as Center). Besides, bronchoalveolar lavage fluid, lung tissue biopsies, and sputum were examined for SARS-CoV-2 RNA. The study was performed at the Center’s Virusology Department with the use of Sintol reagent kit “ПЦР-РВ-2019-nCov”.&#x0D; Results. The study was based on 107,470 tests: 58,141 (54 %) of employees and 45,126 (46 %) of patients; 35,508 (33 %) of men and 71,962 (67 %) of women. In 1318 cases SARS-CoV-2 RNA was detected which accounted for 1.15 % of total test number. In the groups of employees/patients, virus detection rate was 1.42 %/1.09 % (p &lt; 0.001), and in male/female groups it was 1.3 %/1.2 %, respectively (p = 0.154). The rate of infection in the groups of tumor and non-tumor hematological patients, as proved by SARS-CoV-2 RNA testing, was 1.24 % and 0.92 %, respectively (p = 0.147). In employees and patients of the Center, a wave-like virus detection rate was observed. The largest number of infections was registered in April-June 2020 (79 patients and 170 employees), October-December 2020 (126 patients and 190 employees), and January 2022 (59 patients and 203 employees), which corresponded to the first, second, and fifth COVID-19 waves in Russia.&#x0D; Conclusion. The analysis of data obtained at the National Research Center for Hematology demonstrated a wave-like SARS-CoV-2 RNA detection rate in employees and patients of the Center, which corresponded to the general trend in Russia. The SARS-CoV-2 RNA detection rate did not depend on sex of subjects under study and was not significantly different in the groups of tumor and non-tumor hematological patients. Although the patients in hematological hospital are more exposed to the risk of severe infectious complications, they showed laboratory markers for COVID-19 less frequently than the Center employees.

Digital methylation-specific PCR: New applications for liquid biopsy.

Epigenetic analysis is a fundamental part of understanding pathophysiological processes with potential applications in diagnosis, prognosis, and assessment of disease susceptibility. Epigenetic changes have been widely studied in chronic obstructive pulmonary disease (COPD), but currently, there is no molecular marker used to improve the treatment of patients. Furthermore, this progressive disease is a risk factor for the development of more severe COVID-19. Methylation-specific polymerase chain reaction (MSP-PCR) plays an important role in the analysis of DNA methylation profiles, and it is one of the most widely used techniques. In this context, the combination of MSP-PCR with emerging PCR technologies, such as digital PCR (dPCR), results in more accurate analyses of the DNA methylation profile of the genes under study. In this study, we propose the application of the MSP-dPCR technique to evaluate the methylation profile of the ADAM33 gene from saliva samples and lung tissue biopsies of patients with COPD and COVID-19. MSP-dPCR generated a measurable prediction of gene methylation rate, with the potential application of this combined technology for diagnostic and prognostic purposes. It has also proven to be a powerful tool for liquid biopsy applications.

Histologic Characteristics and Clinical Courses of Primary Viral Pneumonia Other than COVID-19.

Objective To clarify both the histologic changes in primary viral pneumonia other than COVID-19 and whether patients with severe lung injury (SLI) on biopsy specimens progress to severe respiratory insufficiency. Methods Patients with primary viral pneumonia other than COVID-19, who underwent lung tissue biopsy, were retrospectively studied. Patients Forty-three patients (41 living patients and 2 autopsied cases) were included in the study. Results Nine patients had SLI, whereas most of patients who recovered from primary viral pneumonia showed a nonspecific epithelial injury pattern. One patient underwent a biopsy under mechanical ventilation. Two of 8 (25.0%) patients on ambient air or low-flow oxygen therapy progressed to a severe respiratory condition and then to death, while only 1 (3.1%) of 32 patients without SLI progressed to a severe respiratory condition and death (p=0.096). The proportion of patients who required O2 treatment for ≥2 weeks was higher in patients with SLI than in those without SLI (p=0.033). The 2 autopsy cases showed a typical pattern of diffuse alveolar damage, with both showing hyaline membranes. Non-specific histologic findings were present in 32 patients without SLI. Conclusion Some patients with SLI progressed to severe respiratory insufficiency, whereas those without SLI rarely progressed to severe respiratory insufficiency or death. The frequency of patients progressing to a severe respiratory condition or death did not differ significantly between those with and without SLI. The proportion of patients who required longer O2 treatment was higher in SLI group than in those without SLI.

Pathological features and diagnostic significance of lung biopsy in occupational lung diseases

Objective: To investigate the clinicopathological characteristics of occupational lung diseases, to reduce the missed diagnoses and misdiagnoses of the diseases and to help standardize the diagnosis and treatment of these patients. Methods: A total of 4 813 lung biopsy specimens (including 1 935 consultation cases) collected at the Department of Pathology, Nanjing Drum Tower Hospital, Nanjing, China from January 1st, 2017 to December 31th, 2019 were retrospectively analyzed. Among them, 126 cases of occupational lung diseases were confirmed with clinical-radiological-pathological diagnosis. Special staining, PCR and scanning electron microscopy were also used to rule out the major differential diagnoses. Results: The 126 patients with occupational lung diseases included 102 males and 24 females. All of them had a history of exposure to occupational risk factor(s). Morphologically, 68.3% (86/126) of the cases mainly showed pulmonary fibrotic nodules, dust plaque formation or carbon end deposition in pulmonary parenchyma. 16.7% (21/126) of the cases mainly showed welding smoke particle deposition in the alveolar cavity and lung interstitium while 15.1% (19/126) of the cases showed granulomas with fibrous tissue hyperplasia, alveolar protein deposition or giant cell interstitial pneumonia. The qualitative and semi-quantitative analyses of residual dust components in the lung under scanning electron microscope were helpful for the diagnosis of welder's pneumoconiosis and hard metal lung disease. Conclusions: The morphological characteristics of lung biopsy tissue are important reference basis for the clinicopathological diagnosis and differential diagnosis of occupational lung diseases. Recognizing the characteristic morphology and proper use of auxiliary examination are the key to an accurate diagnosis of occupational lung diseases on biopsy specimens.

HTA challenges for personalized medicine: the case of liquid biopsy for lung cancer

Abstract Background Personalized medicine and related health technologies are growing rapidly. In this context, health technology assessment methodologies must be prepared and adapted. Evaluating liquid biopsy (LB) for the diagnosis, treatment indication and prognosis of lung cancer is an example of the challenges in the personalized medicine assessment. Methods A systematic review and metanalysis based on EUnetHTA CoreModel. Review question: What is the effectiveness of LB for the diagnosis, therapeutic adequacy and prognosis of lung cancer versus tissue biopsy? The Covidence software was used for the systematic review and MetaDiSC software for the meta-analysis. The quality of the included systematic reviews was assessed with AMSTAR-2 and the quality of the clinical studies with QUADAS-II. Results 69 systematic reviews corresponding to different therapeutic purposes: 12 for treatment adequacy, 47 for diagnosis and 13 for prognosis. Also 24 clinical trials were included. The omics alterations analysed were: punctual mutations in EGFR, BRAF, KRAS and ALK, methylation patterns, lncRNA expression, detection of circulating tumour cells, quantification of circulating DNA, NGS analysis of point mutations, miRNA expression and analysis of exosome content. Conclusions Use of LB tests at different disease stages and need of individual validation for the biomolecules and mutations analysed, are the main challenges. An evaluation framework that includes the specificities of these technologies is necessary for their proper assessment. Key messages • Liquid biopsy may be an alternative to tissue biopsy. The evaluation of the biomolecules analysed should be disaggregated. • The particularities of personalised medicine technologies require assessment methodologies adapted to them.

Identification of regional variation in gene expression and inflammatory proteins in donor lung tissue and ex vivo lung perfusate

ObjectiveDiagnosing lung injury is a challenge in lung transplantation. It has been unclear if a single biopsy specimen is truly representative of the entire organ. Our objective was to investigate lung inflammatory biomarkers using human lung tissue biopsies and ex vivo lung perfusion perfusate. MethodsEight human donor lungs declined for transplantation were air inflated, flash frozen, and partitioned from apex to base. Biopsies were then sampled throughout the lung. Perfusate was sampled from 4 lung lobes in 8 additional donor lungs subjected to ex vivo lung perfusion. The levels of interleukin-6, interleukin-8, interleukin-10, and interleukin-1β were measured using quantitative reverse transcription polymerase chain reaction from lung biopsies and enzyme-linked immunosorbent assay from ex vivo lung perfusion perfusate. ResultsThe median intra-biopsy equal-variance P value was .50 for messenger RNA biomarkers in tissue biopsies. The median intra-biopsy coefficient of variance was 18%. In donors with no apparent focal injuries, the biopsies in each donor showed no difference in various lung slices, with a coefficient of variance of 20%. The exception was biopsies from the lingula and injured focal areas that demonstrated larger differences. Cytokines in ex vivo lung perfusion perfusate showed minimal variation among different lobes (coefficient of variance = 4.9%). ConclusionsCytokine gene expression in lung biopsies was consistent, and the biopsy analysis reflects the whole lung, except when specimens were collected from the lingula or an area of focal injury. Ex vivo lung perfusion perfusate also provides a representative measurement of lung inflammation from the draining lobe. These results will reassure clinicians that a lung biopsy or an ex vivo lung perfusion perfusate sample can be used to inform donor lung selection.

Ways of transformation of typical X-ray signs of community acquired pneumonia of viral etiology (COVID-19) according to radiomics data

For 3 years since the announcement of the coronavirus disease (COVID-19) pandemic, doctors around the world have been studying the complications caused by different strains of SARS-CoV-2. To study the structure of the lung parenchyma in patients with a complicated course of community acquired viral pneumonia of COVID-19 and different ways of transformation, the most informative is the digital software processing of computed tomography (CT) images of the chest organs (CT).&#x0D; Objective — to investigate the ways of transformation of typical radiological signs in patients with community-acquired pneumonia of viral etiology (COVID-19) and the possibility of their transformation into bronchioloalveolar cancer (BAC) by the radiomics method.&#x0D; Materials and methods. Chest CT data in the dynamics of 112 patients with a complicated course of community-acquired viral pneumonia COVID-19 were analyzed. Chest CT was performed on an Aquilion TSX-101A Tochiba scanner (Japan) with subsequent digital software processing of CT images using the Dragonfly program from Obyect Research Systems (ORS), Montreal, Canada. The diagnosis of BAC was made based on the data of the pathomorphological examination. Transbronchial biopsy of lung tissue was performed during diagnostic fibrobronchoscopy.&#x0D; Results and discussion. As a result of the analysis of possible ways of transformation of typical X-ray changes of COVID-19 community-acquired pneumonia, we identified 3 main ways. In 71 (64.0 %) subjects, according to the chest CT scan, there was gradual resorption of pathological changes and recovery of the lung parenchyma. In 35 (31.2 %) patients, the formation of signs of «vanishing lung syndrome» was detected. 5 (4.5 %) patients were diagnosed with BAC according to the CT scan and pathomorphological examination. Digital software processing of chest CT in dynamics allows to track the process of transformation of the lung parenchyma structure in patients with a complicated course of COVID-19 community-acquired viral pneumonia into BAC and in some cases to confirm the secondary nature of the oncological process.&#x0D; Conclusions. Digital software processing of the chest CT data is a highly informative research method that clearly reflects the morphological structure of the lung parenchyma and allows diagnosis and differential diagnosis of diseases.