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Longitudinal Lower Airway Microbial Signatures of Acute Cellular Rejection in Lung Transplantation

Natalini, Jake G; Wong, Kendrew K; Nelson, Nathaniel C; Wu, Benjamin G; Rudym, Darya; Lesko, Melissa B; Qayum, Seema; Lewis, Tyler C; Wong, Adrian; Chang, Stephanie H; Chan, Justin C Y; Geraci, Travis C; Li, Yonghua; Wang, Chan; Li, Huilin; Pamar, Prerna; Schnier, Joseph; Mahoney, Ian J; Malik, Tahir; Darawshy, Fares; Sulaiman, Imran; Kugler, Matthias C; Singh, Rajbir; Collazo, Destiny E; Chang, Miao; Patel, Shrey; Kyeremateng, Yaa; McCormick, Colin; Barnett, Clea R; Tsay, Jun-Chieh J; Brosnahan, Shari B; Singh, Shivani; Pass, Harvey I; Angel, Luis F; Segal, Leopoldo N
PMID: 38358857
ISSN: 1535-4970
CID: 5633542

Faecal microbial transfer and complex carbohydrates mediate protection against COPD

Budden, Kurtis F; Shukla, Shakti D; Bowerman, Kate L; Vaughan, Annalicia; Gellatly, Shaan L; Wood, David L A; Lachner, Nancy; Idrees, Sobia; Rehman, Saima Firdous; Faiz, Alen; Patel, Vyoma K; Donovan, Chantal; Alemao, Charlotte A; Shen, Sj; Amorim, Nadia; Majumder, Rajib; Vanka, Kanth S; Mason, Jazz; Haw, Tatt Jhong; Tillet, Bree; Fricker, Michael; Keely, Simon; Hansbro, Nicole; Belz, Gabrielle T; Horvat, Jay; Ashhurst, Thomas; van Vreden, Caryn; McGuire, Helen; Fazekas de St Groth, Barbara; King, Nicholas J C; Crossett, Ben; Cordwell, Stuart J; Bonaguro, Lorenzo; Schultze, Joachim L; Hamilton-Williams, Emma E; Mann, Elizabeth; Forster, Samuel C; Cooper, Matthew A; Segal, Leopoldo N; Chotirmall, Sanjay H; Collins, Peter; Bowman, Rayleen; Fong, Kwun M; Yang, Ian A; Wark, Peter A B; Dennis, Paul G; Hugenholtz, Philip; Hansbro, Philip M
OBJECTIVE:Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear. DESIGN/METHODS:mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation. RESULTS:family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes. CONCLUSION/CONCLUSIONS:The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.
PMID: 38331563
ISSN: 1468-3288
CID: 5632452

Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate Chronic Obstructive Pulmonary Disease

Sulaiman, Imran; Wu, Benjamin G; Chung, Matthew; Isaacs, Bradley; Tsay, Jun-Chieh J; Holub, Meredith; Barnett, Clea R; Kwok, Benjamin; Kugler, Matthias C; Natalini, Jake G; Singh, Shivani; Li, Yonghua; Schluger, Rosemary; Carpenito, Joseph; Collazo, Destiny; Perez, Luisanny; Kyeremateng, Yaa; Chang, Miao; Campbell, Christina D; Hansbro, Philip M; Oppenheimer, Beno W; Berger, Kenneth I; Goldring, Roberta M; Koralov, Sergei B; Weiden, Michael D; Xiao, Rui; D'Armiento, Jeanine; Clemente, Jose C; Ghedin, Elodie; Segal, Leopoldo N
PMID: 37677136
ISSN: 1535-4970
CID: 5606572

Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma

Dolgalev, Igor; Zhou, Hua; Murrell, Nina; Le, Hortense; Sakellaropoulos, Theodore; Coudray, Nicolas; Zhu, Kelsey; Vasudevaraja, Varshini; Yeaton, Anna; Goparaju, Chandra; Li, Yonghua; Sulaiman, Imran; Tsay, Jun-Chieh J; Meyn, Peter; Mohamed, Hussein; Sydney, Iris; Shiomi, Tomoe; Ramaswami, Sitharam; Narula, Navneet; Kulicke, Ruth; Davis, Fred P; Stransky, Nicolas; Smolen, Gromoslaw A; Cheng, Wei-Yi; Cai, James; Punekar, Salman; Velcheti, Vamsidhar; Sterman, Daniel H; Poirier, J T; Neel, Ben; Wong, Kwok-Kin; Chiriboga, Luis; Heguy, Adriana; Papagiannakopoulos, Thales; Nadorp, Bettina; Snuderl, Matija; Segal, Leopoldo N; Moreira, Andre L; Pass, Harvey I; Tsirigos, Aristotelis
Approximately 30% of early-stage lung adenocarcinoma patients present with disease progression after successful surgical resection. Despite efforts of mapping the genetic landscape, there has been limited success in discovering predictive biomarkers of disease outcomes. Here we performed a systematic multi-omic assessment of 143 tumors and matched tumor-adjacent, histologically-normal lung tissue with long-term patient follow-up. Through histologic, mutational, and transcriptomic profiling of tumor and adjacent-normal tissue, we identified an inflammatory gene signature in tumor-adjacent tissue as the strongest clinical predictor of disease progression. Single-cell transcriptomic analysis demonstrated the progression-associated inflammatory signature was expressed in both immune and non-immune cells, and cell type-specific profiling in monocytes further improved outcome predictions. Additional analyses of tumor-adjacent transcriptomic data from The Cancer Genome Atlas validated the association of the inflammatory signature with worse outcomes across cancers. Collectively, our study suggests that molecular profiling of tumor-adjacent tissue can identify patients at high risk for disease progression.
PMCID:10632519
PMID: 37938580
ISSN: 2041-1723
CID: 5609852

Microbial Inflammatory Networks in Bronchiectasis Exacerbators With Pseudomonas aeruginosa

Gramegna, Andrea; Narayana, Jayanth Kumar; Amati, Francesco; Stainer, Anna; Wu, Benjamin; Morlacchi, Letizia Corinna; Segal, Leopoldo N; Tsaneva-Atanasova, Krasimira; Marchisio, Paola; Chotirmall, Sanjay H; Blasi, Francesco; Aliberti, Stefano
PMID: 36803648
ISSN: 1931-3543
CID: 5433742

Correcting dysbiosis in the lungs of COPD, one pathogen at a time

Wong, Kendrew K; Segal, Leopoldo N
In this issue of Cell Host & Microbe, Liang et al. demonstrate through genomic analysis of the sputum microbiome from COPD patients and preclinical models that Staphylococcus aureus promotes lung function decline via regulation of homocysteine levels. Homocysteine can promote lung injury by promoting neutrophil apoptosis-to-NETosis shift via AKT1-S100A8/A9 axis.
PMID: 37321178
ISSN: 1934-6069
CID: 5541012

Perceived Hospital Stress, Severe Acute Respiratory Syndrome Coronavirus 2 Activity, and Care Process Temporal Variance During the COVID-19 Pandemic

Anesi, George L; Andrews, Adair; Bai, He Julia; Bhatraju, Pavan K; Brett-Major, David M; Broadhurst, M Jana; Campbell, Elizabeth Salvagio; Cobb, J Perren; Gonzalez, Martin; Homami, Sonya; Hypes, Cameron D; Irwin, Amy; Kratochvil, Christopher J; Krolikowski, Kelsey; Kumar, Vishakha K; Landsittel, Douglas P; Lee, Richard A; Liebler, Janice M; Lutrick, Karen; Marts, Lucian T; Mosier, Jarrod M; Mukherjee, Vikramjit; Postelnicu, Radu; Rodina, Valentina; Segal, Leopoldo N; Sevransky, Jonathan E; Spainhour, Christine; Srivastava, Avantika; Uyeki, Timothy M; Wurfel, Mark M; Wyles, David; Evans, Laura
OBJECTIVES:The COVID-19 pandemic threatened standard hospital operations. We sought to understand how this stress was perceived and manifested within individual hospitals and in relation to local viral activity. DESIGN:Prospective weekly hospital stress survey, November 2020-June 2022. SETTING:Society of Critical Care Medicine's Discovery Severe Acute Respiratory Infection-Preparedness multicenter cohort study. SUBJECTS:Thirteen hospitals across seven U.S. health systems. INTERVENTIONS:None. MEASUREMENTS AND MAIN RESULTS:We analyzed 839 hospital-weeks of data over 85 pandemic weeks and five viral surges. Perceived overall hospital, ICU, and emergency department (ED) stress due to severe acute respiratory infection patients during the pandemic were reported by a mean of 43% ( sd , 36%), 32% (30%), and 14% (22%) of hospitals per week, respectively, and perceived care deviations in a mean of 36% (33%). Overall hospital stress was highly correlated with ICU stress (ρ = 0.82; p < 0.0001) but only moderately correlated with ED stress (ρ = 0.52; p < 0.0001). A county increase in 10 severe acute respiratory syndrome coronavirus 2 cases per 100,000 residents was associated with an increase in the odds of overall hospital, ICU, and ED stress by 9% (95% CI, 5-12%), 7% (3-10%), and 4% (2-6%), respectively. During the Delta variant surge, overall hospital stress persisted for a median of 11.5 weeks (interquartile range, 9-14 wk) after local case peak. ICU stress had a similar pattern of resolution (median 11 wk [6-14 wk] after local case peak; p = 0.59) while the resolution of ED stress (median 6 wk [5-6 wk] after local case peak; p = 0.003) was earlier. There was a similar but attenuated pattern during the Omicron BA.1 subvariant surge. CONCLUSIONS:During the COVID-19 pandemic, perceived care deviations were common and potentially avoidable patient harm was rare. Perceived hospital stress persisted for weeks after surges peaked.
PMID: 36790189
ISSN: 1530-0293
CID: 5448062

More than Mycobacterium tuberculosis: site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis

Nyawo, Georgina R; Naidoo, Charissa C; Wu, Benjamin; Sulaiman, Imran; Clemente, Jose C; Li, Yonghua; Minnies, Stephanie; Reeve, Byron W P; Moodley, Suventha; Rautenbach, Cornelia; Wright, Colleen; Singh, Shivani; Whitelaw, Andrew; Schubert, Pawel; Warren, Robin; Segal, Leopoldo; Theron, Grant
BACKGROUND:Lymphadenitis is the most common extrapulmonary tuberculosis (EPTB) manifestation. The microbiome is important to human health but uninvestigated in EPTB. We profiled the site-of-disease lymph node microbiome in tuberculosis lymphadenitis (TBL). METHODS:Fine-needle aspiration biopsies were collected from 158 pretreatment presumptive TBL patients in Cape Town, South Africa. 16S Illumina MiSeq rRNA gene sequencing was done. RESULTS:complex. CONCLUSIONS:-dominated dTBL lymphotypes, which contain taxa potentially targeted by TB treatment, were associated with milder, potentially earlier stage disease. These investigations lay foundations for studying the microbiome's role in lymphatic TB. The long-term clinical significance of these lymphotypes requires prospective validation.
PMCID:9957952
PMID: 36598079
ISSN: 1468-3296
CID: 5441292

Pleural fluid microbiota as a biomarker for malignancy and prognosis

Kwok, Benjamin; Wu, Benjamin G; Kocak, Ibrahim F; Sulaiman, Imran; Schluger, Rosemary; Li, Yonghua; Anwer, Raheel; Goparaju, Chandra; Ryan, Daniel J; Sagatelian, Marla; Dreier, Matthew S; Murthy, Vivek; Rafeq, Samaan; Michaud, Gaetane C; Sterman, Daniel H; Bessich, Jamie L; Pass, Harvey I; Segal, Leopoldo N; Tsay, Jun-Chieh J
Malignant pleural effusions (MPE) complicate malignancies and portend worse outcomes. MPE is comprised of various components, including immune cells, cancer cells, and cell-free DNA/RNA. There have been investigations into using these components to diagnose and prognosticate MPE. We hypothesize that the microbiome of MPE is unique and may be associated with diagnosis and prognosis. We compared the microbiota of MPE against microbiota of pleural effusions from non-malignant and paramalignant states. We collected a total of 165 pleural fluid samples from 165 subjects; Benign (n = 16), Paramalignant (n = 21), MPE-Lung (n = 57), MPE-Other (n = 22), and Mesothelioma (n = 49). We performed high throughput 16S rRNA gene sequencing on pleural fluid samples and controls. We showed that there are compositional differences among pleural effusions related to non-malignant, paramalignant, and malignant disease. Furthermore, we showed differential enrichment of bacterial taxa within MPE depending on the site of primary malignancy. Pleural fluid of MPE-Lung and Mesothelioma were associated with enrichment with oral and gut bacteria that are commonly thought to be commensals, including Rickettsiella, Ruminococcus, Enterococcus, and Lactobacillales. Mortality in MPE-Lung is associated with enrichment in Methylobacterium, Blattabacterium, and Deinococcus. These observations lay the groundwork for future studies that explore host-microbiome interactions and their influence on carcinogenesis.
PMCID:9908925
PMID: 36755121
ISSN: 2045-2322
CID: 5426932

Angiopoietin-Like4 Is a Novel Marker of COVID-19 Severity

Bhatraju, Pavan K.; Morrell, Eric D.; Stanaway, Ian B.; Sathe, Neha A.; Srivastava, Avantika; Postelnicu, Radu; Green, Richard; Andrews, Adair; Gonzalez, Martin; Kratochvil, Christopher J.; Kumar, Vishakha K.; Hsiang, Tien Ying; Gale, Michael; Anesi, George L.; Wyles, David; Broadhurst, M. Jana; Brett-Major, David; Mukherjee, Vikramjit; Sevransky, Jonathan E.; Landsittel, Douglas; Hung, Chi; Altemeier, William A.; Gharib, Sina A.; Uyeki, Timothy M.; Cobb, J. Perren; Liebler, Janice M.; Crosslin, David R.; Jarvik, Gail P.; Segal, Leopoldo N.; Evans, Laura; Mikacenic, Carmen; Wurfel, Mark M.
IMPORTANCE: Vascular dysfunction and capillary leak are common in critically ill COVID-19 patients, but identification of endothelial pathways involved in COVID-19 pathogenesis has been limited. Angiopoietin-like 4 (ANGPTL4) is a protein secreted in response to hypoxic and nutrient-poor conditions that has a variety of biological effects including vascular injury and capillary leak. OBJECTIVES: To assess the role of ANGPTL4 in COVID-19-related outcomes. DESIGN, SETTING, AND PARTICIPANTS: Two hundred twenty-five COVID-19 ICU patients were enrolled from April 2020 to May 2021 in a prospective, multicenter cohort study from three different medical centers, University of Washington, University of Southern California and New York University. MAIN OUTCOMES AND MEASURES: Plasma ANGPTL4 was measured on days 1, 7, and 14 after ICU admission. We used previously published tissue proteomic data and lung single nucleus RNA (snRNA) sequencing data from specimens collected from COVID-19 patients to determine the tissues and cells that produce ANGPTL4. RESULTS: Higher plasma ANGPTL4 concentrations were significantly associated with worse hospital mortality (adjusted odds ratio per log2increase, 1.53; 95% CI, 1.17-2.00; p = 0.002). Higher ANGPTL4 concentrations were also associated with higher proportions of venous thromboembolism and acute respiratory distress syndrome. Longitudinal ANGPTL4 concentrations were significantly different during the first 2 weeks of hospitalization in patients who subsequently died compared with survivors (p for interaction = 8.1 × 10-5). Proteomics analysis demonstrated abundance of ANGPTL4 in lung tissue compared with other organs in COVID-19. ANGPTL4 single-nuclear RNA gene expression was significantly increased in pulmonary alveolar type 2 epithelial cells and fibroblasts in COVID-19 lung tissue compared with controls. CONCLUSIONS AND RELEVANCE: ANGPTL4 is expressed in pulmonary epithelial cells and fibroblasts and is associated with clinical prognosis in critically ill COVID-19 patients.
SCOPUS:85147151022
ISSN: 2639-8028
CID: 5424302