Blood-based Transcriptomic and Proteomic Biomarkers of Emphysema

Suryadevara, Rahul; Gregory, Andrew; Lu, Robin; Xu, Zhonghui; Masoomi, Aria; Lutz, Sharon M.; Berman, Seth; Yun, Jeong H.; Saferali, Aabida; Ryu, Min Hyung; Moll, Matthew; Sin, Don D.; Hersh, Craig P.; Silverman, Edwin K.; Dy, Jennifer; Pratte, Katherine A.; Bowler, Russell P.; Castaldi, Peter J.; Boueiz, Adel; Crapo, James D.; Silverman, Edwin K.; Make, Barry J.; Regan, Elizabeth A.; Beaty, Terri H.; Castaldi, Peter J.; Cho, Michael H.; DeMeo, Dawn L.; Boueiz, Adel; Foreman, Marilyn G.; Ghosh, Auyon; Hayden, Lystra P.; Hersh, Craig P.; Hetmanski, Jacqueline; Hobbs, Brian D.; Hokanson, John E.; Kim, Wonji; Laird, Nan; Lange, Christoph; Lutz, Sharon M.; McDonald, Merry-Lynn; Prokopenko, Dmitry; Moll, Matthew; Morrow, Jarrett; Qiao, Dandi; Regan, Elizabeth A.; Saferali, Aabida; Sakornsakolpat, Phuwanat; Silverman, Edwin K.; Wan, Emily S.; Yun, Jeong; Centeno, Juan Pablo; Charbonnier, Jean-Paul; Coxson, Harvey O.; Galban, Craig J.; Han, MeiLan K.; Hoffman, Eric A.; Humphries, Stephen; Jacobson, Francine L.; Judy, Philip F.; Kazerooni, Ella A.; Kluiber, Alex; Lynch, David A.; Nardelli, Pietro; Newell, Jr., John D.; Notary, Aleena; Oh, Andrea; Regan, Elizabeth A.; Ross, James C.; Estepar, Raul San Jose; Schroeder, Joyce; Sieren, Jered; Stoel, Berend C.; Tschirren, Juerg; Van Beek, Edwin; van Ginneken, Bram; van Rikxoort, Eva; Sanchez Ferrero, Gonzalo Vegas; Veitel, Lucas; Washko, George R.; Wilson, Carla G.; Jensen, Robert; Everett, Douglas; Crooks, Jim; Pratte, Katherine; Strand, Matt; Wilson, Carla G.; Hokanson, John E.; Austin, Erin; Kinney, Gregory; Lutz, Sharon M.; Young, Kendra A.; Bhatt, Surya P.; Bon, Jessica; Diaz, Alejandro A.; Han, MeiLan K.; Make, Barry; Murray, Susan; Regan, Elizabeth; Soler, Xavier; Wilson, Carla G.; Bowler, Russell P.; Kechris, Katerina; Kashani, Farnoush Banaei; Curtis, Jeffrey L.; Pernicano, Perry G.; Hanania, Nicola; Atik, Mustafa; Boriek, Aladin; Guntupalli, Kalpatha; Guy, Elizabeth; Parulekar, Amit; DeMeo, Dawn L.; Hersh, Craig; Jacobson, Francine L.; Washko, George; Graham Barr, R.; Austin, John; D’Souza, Belinda; Thomashow, Byron; MacIntyre, Neil; Page McAdams, H.; Washington, Lacey; McEvoy, Charlene; Tashjian, Joseph; Wise, Robert; Brown, Robert; Hansel, Nadia N.; Horton, Karen; Lambert, Allison; Putcha, Nirupama; Casaburi, Richard; Adami, Alessandra; Budoff, Matthew; Fischer, Hans; Porszasz, Janos; Rossiter, Harry; Stringer, William; Sharafkhaneh, Amir; Lan, Charlie; Wendt, Christine; Bell, Brian; Kunisaki, Ken M.; Flenaugh, Eric L.; Gebrekristos, Hirut; Ponce, Mario; Terpenning, Silanath; Westney, Gloria; Bowler, Russell; Lynch, David A.; Rosiello, Richard; Pace, David; Criner, Gerard; Ciccolella, David; Cordova, Francis; Dass, Chandra; D’Alonzo, Gilbert; Desai, Parag; Jacobs, Michael; Kelsen, Steven; Kim, Victor; James Mamary, A.; Marchetti, Nathaniel; Satti, Aditi; Shenoy, Kartik; Steiner, Robert M.; Swift, Alex; Swift, Irene; Vega-Sanchez, Maria Elena; Dransfield, Mark; Bailey, William; Bhatt, Surya P.; Iyer, Anand; Nath, Hrudaya; Michael Wells, J.; Conrad, Douglas; Soler, Xavier; Yen, Andrew; Comellas, Alejandro P.; Hoth, Karin F.; Newell, John; Thompson, Brad; Han, MeiLan K.; Kazerooni, Ella; Labaki, Wassim; Galban, Craig; Vummidi, Dharshan; Billings, Joanne; Begnaud, Abbie; Allen, Tadashi; Sciurba, Frank; Bon, Jessica; Chandra, Divay; Weissfeld, Joel; Anzueto, Antonio; Adams, Sandra; Maselli-Caceres, Diego; Ruiz, Mario E.; Singh, Harjinder

doi:10.1164/rccm.202301-0067oc

Cited by 3 publications

(1 citation statement)

References 74 publications

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“…Regarding the peripheral blood transcriptome, to date, there are no published works in bronchiectasis, whereas evidence is increasing in COPD [ 88 – 91 ]. Recently, a COPD study showing integrated blood transcriptome and proteome analyses revealed key blood-based biomarkers of emphysema to enhance its prediction [ 92 ].…”

Section: From Pathophysiology To Multiomicsmentioning

confidence: 99%

Pathophysiology and genomics of bronchiectasis

Perea,

Faner,

Chalmers

et al. 2024

Eur Respir Rev

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Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30–40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.

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Section: From Pathophysiology To Multiomicsmentioning

confidence: 99%

Pathophysiology and genomics of bronchiectasis

Perea,

Faner,

Chalmers

et al. 2024

Eur Respir Rev

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A Means to an End(othelium): Using Peripheral Blood Mononuclear Cell 'Omics to Peer into the Pulmonary Vasculature

Chiles

2024

Annals ATS

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Multi Omics Applications in Biological Systems

Gutierrez Reyes,

Alejo-Jacuinde,

Perez Sanchez

et al. 2024

CIMB

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Traditional methodologies often fall short in addressing the complexity of biological systems. In this regard, system biology omics have brought invaluable tools for conducting comprehensive analysis. Current sequencing capabilities have revolutionized genetics and genomics studies, as well as the characterization of transcriptional profiling and dynamics of several species and sample types. Biological systems experience complex biochemical processes involving thousands of molecules. These processes occur at different levels that can be studied using mass spectrometry-based (MS-based) analysis, enabling high-throughput proteomics, glycoproteomics, glycomics, metabolomics, and lipidomics analysis. Here, we present the most up-to-date techniques utilized in the completion of omics analysis. Additionally, we include some interesting examples of the applicability of multi omics to a variety of biological systems.

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Blood-based Transcriptomic and Proteomic Biomarkers of Emphysema

Abstract: doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.

Cited by 3 publications

References 74 publications

Pathophysiology and genomics of bronchiectasis

Pathophysiology and genomics of bronchiectasis

A Means to an End(othelium): Using Peripheral Blood Mononuclear Cell 'Omics to Peer into the Pulmonary Vasculature

Multi Omics Applications in Biological Systems

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