MPAPASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

Welsh, Joshua; Killingsworth, Bryce; Kepley, Julia; Traynor, Tim; Cook, S. D.; Savage, Jason E.; Marte, Jenn; Lee, Min-Jung; Maeng, Hoyoung; Pleet, Michelle L.; Magaña, Setty M.; Görgens, André; Maire, Cécile L.; Lamszus, Katrin; Merino, María J.; Linehan, Marston; Greten, Tim F.; Cooks, Tomer; Harris, Curtis C.; Apolo, Andrea B.; Abdel-Mageed, Asim B.; Ivanov, Alexander R.; Trepel, Jane B.; Roth, Matthew E.; Tkach, Mercedes; Milosavljevic, Aleksandar; Théry, Clotilde; LeBlanc, Amy K.; Berzofsky, Jay A.; Ruppin, Eytan; Aldape, Kenneth; Camphausen, Kevin; Gulley, James L.; Ghiran, Ionita; Jacobson, Steve; Jones, Jennifer C.

doi:10.1016/j.crmeth.2021.100136

Cited by 13 publications

(24 citation statements)

References 24 publications

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“…Proteins from cells or EVs are detected with fluorescence using fluorophore-tagged Abs bound to the target. Flow cytometry is ideal for a multiplexed and high-throughput analysis based on its ability to examine multiple protein markers on thousands of cells per second . However, bulk EV flow cytometry faces challenges of swarm detection.…”

Section: Digital Ev Assaysmentioning

confidence: 99%

“…Ab cross-reactivity can limit the scaling of multiplexing and, thus, assay performance may read out inaccurate or even false conclusions. Moreover, nonspecific Ab binding to other targets is a large hurdle that requires optimizing protocols . Aptamers and nanobodies are functional alternatives to Abs and are better suited for ultrasensitive EV detection since their sensing range matches the nanoscale size of EVs (Figure A, right).…”

Section: Future Design Opportunities For Digital Ev Assaysmentioning

confidence: 99%

“…Flow cytometry is ideal for a multiplexed and high-throughput analysis based on its ability to examine multiple protein markers on thousands of cells per second. 71 However, bulk EV flow cytometry faces challenges of swarm detection. Conventional flow cytometry optics and fluidics are configured for microscale particles (i.e., single cells) and not optimized for nanoscale EVs.…”

Section: Digital Ev Assaysmentioning

confidence: 99%

“…Moreover, nonspecific Ab binding to other targets is a large hurdle that requires optimizing protocols. 71 Aptamers and nanobodies are functional alternatives to Abs and are better suited for ultrasensitive EV detection since their sensing range matches the nanoscale size of EVs (Figure 3A, right). Aptamers.…”

Section: Future Design Opportunities For Digital Ev Assaysmentioning

confidence: 99%

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Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles

Morales

2022

ACS Nano

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Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.

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Section: Digital Ev Assaysmentioning

confidence: 99%

Section: Future Design Opportunities For Digital Ev Assaysmentioning

confidence: 99%

Section: Digital Ev Assaysmentioning

confidence: 99%

Section: Future Design Opportunities For Digital Ev Assaysmentioning

confidence: 99%

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Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles

Morales

2022

ACS Nano

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“…Jones's group has developed single-EV methods for labeling and sorting EVs via flow cytometry 101,102. In addition, new software tools provide more accurate methods to characterize single EVs, via FCM pass , or EV repertoires via MPA pass 103,104. A third software, RPS pass , provides more…”

mentioning

confidence: 99%

Exosomes, microvesicles, and other extracellular vesicles—a Keystone Symposia report

Cable¹,

Witwer

Coffey

et al. 2023

Annals of the New York Academy of Sciences

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Extracellular vesicles (EVs) are small, lipid‐bilayer‐bound particles released by cells that can contain important bioactive molecules, including lipids, RNAs, and proteins. Once released in the extracellular environment, EVs can act as messengers locally as well as to distant tissues to coordinate tissue homeostasis and systemic responses. There is a growing interest in not only understanding the physiology of EVs as signaling particles but also leveraging them as minimally invasive diagnostic and prognostic biomarkers (e.g., they can be found in biofluids) and drug‐delivery vehicles. On October 30–November 2, 2022, researchers in the EV field convened for the Keystone symposium “Exosomes, Microvesicles, and Other Extracellular Vesicles” to discuss developing standardized language and methodology, new data on the basic biology of EVs and potential clinical utility, as well as novel technologies to isolate and characterize EVs.

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Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Welsh,

Goberdhan,

O'Driscoll

et al. 2024

J of Extracellular Vesicle

Self Cite

731

163

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Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year‐on‐year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non‐vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its ‘Minimal Information for Studies of Extracellular Vesicles’, which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.

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MPAPASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

Cited by 13 publications

References 24 publications

Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles

Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles

Exosomes, microvesicles, and other extracellular vesicles—a Keystone Symposia report

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

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