VBM is supported by NIH grants (R01EY031952, R01EY031360, R01EY030151, and P30EY026877), the Stanford Center for Optic Disc Drusen, and Research to Prevent Blindness, New York, USA. JW and DR are supported by the VitreoRetinal Surgery Foundation, USA. DR is supported by the DARE Fellowship, which is sponsored by the Lundbeck Foundation.

The protocol follows the guidelines of the Institutional Review Board for Human Subjects Research (IRB) at Stanford University, USA.
CAUTION: This protocol is a guide for qualified ophthalmic surgeons. In the context of intraocular malignancies, extraocular tumor seeding in the setting of aqueous humor or vitreous liquid biopsies cannot be ruled out. However, the risk of extraocular extension and orbital involvement is extremely low in transvitreal choroidal tumor biopsy, that is done in safety enhanced manner and with careful entry site consideration6. This protocol does not cover and may be contraindicated in cases of retinoblastoma or tumors with high metastatic risk.
1. Before sample collection
<ol>
	<li>Institutional review board approval
	<ol>
		<li>Obtain the approvals from the local IRB before the start of the experiment and perform sample collection accordingly.</li>
	</ol>
	</li>
	<li>Study population
	<ol>
		<li>Inclusion criteria: Include all patients (ages 0 - 99 years) that undergo intraocular surgery at the institution that will provide an adequate quantity of aqueous humor or vitreous liquid in excess of that required for appropriate diagnostic tests to evaluate the patient&#39;s condition and patients who wish to participate.</li>
		<li>Exclusion criteria: Exclude patients who decline to participate and pregnant women.</li>
	</ol>
	</li>
</ol>

<ol start="3">
	<li>Informed consent
	<ol>
		<li>Obtain written informed consent from each patient following the IRB approved protocol.</li>
		<li>Archive the signed consent in a secured database.</li>
		<li>Train involved personnel (surgeons, laboratory technicians, operating room (OR) staff, scientists) as described in this protocol.</li>
		<li>Set up a sample managing database. Use REDCap as a HIPAA-compliant web-based sample database that is designed to support data capture for research studies5. 
		NOTE: This article describes the use of the web-based interface provided by REDCap to design forms, define fields, set up branching logic, and apply data validation rules without the need for extensive programming knowledge. Alternatively, other software, such as standard spreadsheet applications, may also be suitable.</li>
		<li>Ensure the availability of a cooling box, dry ice, syringe for sample collection, and cryovials (see Table of Materials). Use cryovials with barcodes that are permanently etched onto the vials. This eliminates the need to add patient identifiers on the vial and the possibility of losing a label under freezing conditions.</li>
		<li>Notify the surgeon on the case and the lab technician who will help with the sample collection in the OR at least 24 h prior to the scheduled surgery.</li>
	</ol>
	</li>
</ol>
2. Acquisition of surgical specimens in the operating room
<ol>
	<li>Mobile operating room lab interface (MORLI)
	<ol>
		<li>Establish a MORLI in the operating room. MORLI includes a flat lab bench surface, a computer/tablet with a barcode scanner with access to the REDCap database, and a cooling box with dry ice (see Table of Materials). 
		CAUTION: Dry ice is extremely cold. Always wear gloves when handling dry ice, and avoid touching it.</li>
	</ol>
	</li>
	<li>Preparation of sample collection in the OR
	<ol>
		<li>Log in to the computer/tablet on MORLI and open the REDCap database.</li>
		<li>Check that informed consent has been signed by the patient and confirm that with the surgeon. Remind him/her that an undiluted sample is required.</li>
		<li>Wear gloves. Obtain the appropriate number of barcoded cryovials (0.5 mL for aqueous humor and 1.9 mL for vitreous samples) and place them where they are easily accessible.</li>
	</ol>
	</li>
	<li>Collection of aqueous humor liquid biopsies 
	CAUTION: Consider human tissue samples as biohazardous material, which requires appropriate precautions such as a lab coat and gloves to assure the safety of the involved personnel. 
	NOTE: The following steps should only be performed by a trained ophthalmic surgeon. Aqueous humor liquid biopsies can be obtained, for example, at the beginning of cataract surgery, one of the most frequent surgeries worldwide. 
	NOTE: A sterile field is maintained as per standard of care protocols in the operating room. Preoperative procedures related to patient anesthesia follow standard of care steps for anterior chamber and vitreoretinal surgeries.
	<ol>
		<li>Prepare and drape the eye for surgery and place a sterile lid speculum for optimal visualization of the sterile field.</li>
		<li>Use an operating microscope to perform an anterior chamber paracentesis perpendicular to the limbus using a 30-32 G needle connected to a 1 mL syringe. Use a cotton tip or small forceps to stabilize the eye during this procedure. 
		NOTE: Ensure that the needle and the syringe are locked and that there is no pressure in the syringe (by moving the plunger). Ensure that the tip of the needle remains over the peripheral iris in the mid-anterior chamber to avoid damage to intraocular structures. In the case of cataract surgery, the needle to obtain the liquid biopsy can also enter the anterior chamber via one of the paracenteses that are created for the cataract surgery.</li>
		<li>Under direct visualization via the microscope, manually aspirate approximately 100 &#181;L of undiluted aqueous humor using a 1 mL syringe. Move the syringe plunger with the surgeon&#39;s non-dominant hand or by a trained assistant without moving the needle. 
		NOTE: Obtain less than 100 &#181;L of aqueous humor in case the anterior chamber should collapse.</li>
		<li>Carefully remove the needle from the anterior chamber. 
		NOTE: In a phakic eye, keep the needle over the iris to avoid touching the lens. Positive pressure on the globe can increase reflux. Releasing the cotton tip before the needle is withdrawn helps reduce reflux.</li>
		<li>Pull back the plunger and see how the air and the collected fluid are moving.</li>
		<li>Inject the syringe into the cryovial. The extra air clears the syringe&#39;s dead space.</li>
		<li>Use the barcode on the cryovial to scan the sample to the REDCap form on a computer in the operating room (more details in steps 3.1 to 3.9).</li>
		<li>Immediately transfer the cryovial to dry ice in the cooling box.</li>
		<li>Continue with the surgery scheduled for the patient (e.g., a cataract surgery as previously described7 ).</li>
	</ol>
	</li>
	<li>Collection of vitreous liquid biopsies 
	NOTE: The following steps should only be performed by a trained vitreoretinal surgeon. Vitreous liquid biopsies can be obtained at the beginning of a vitrectomy8. Since the goal is to collect an undiluted vitreous sample, the vitrectomy cutter will not be primed with fluid1. 
	NOTE: A sterile field is maintained as per standard of care protocols in the operating room. Preoperative procedures related to patient anesthesia follow the standard of care steps for anterior chamber and vitreoretinal surgeries.
	<ol>
		<li>Prepare and drape the eye for surgery and place a sterile lid speculum for optimal visualization of the sterile field.</li>
		<li>Create sclerotomies with a 23-, 25-, or 27-G trocar cannula, following the standard of care procedures. Insert the infusion cannula and visually confirm the appropriate placement in the vitreous cavity.</li>
		<li>In the vitreous cavity, activate the vitreous cutter without infusion to collect an undiluted vitreous sample. Manually aspirate 0.5 to 1.0 mL of vitreous using a syringe that is connected to the vitreous extrusion cannula1.</li>
		<li>Remove the vitreous cutter from the eye and turn on the fluid infusion.</li>
		<li>Aspirate the remaining fluid within the tubing into the syringe.</li>
		<li>Disconnect the syringe.</li>
		<li>Process the sample as described for an aqueous humor specimen in section 2.3 (step 2.3.5 to step 2.3.9).</li>
	</ol>
	</li>
</ol>
3. Processing of samples in the OR and adding samples to the database
<ol>
	<li>Ask the lab technician to take the prepared cryovial (0.5 mL for aqueous humor and 1.9 mL for vitreous samples) and walk to the surgeon without touching any sterile OR equipment.</li>
	<li>Ask the lab technician to open the cryovial.</li>
	<li>Unload the syringe directly into the cryovial.</li>
	<li>Ask the lab technician to immediately recap the cryovial.</li>
	<li>Ask the lab technician to walk back to the MORLI and immediately transfer the sample onto dry ice in the cooling box (-80 &#730;C). Close the lid of the box.</li>
	<li>Open a new sample collection form. Enter the following information in the respective field of the form: case surgeon, location and date of collection, patient identifier number, and other basic information, such as age, sex, right or left eye, diagnosis, preoperative history (free text), information about the procedure (e.g., type of surgery), as well as information about the samples, such as number of samples collected, type of samples (aqueous humor, vitreous), and other details such as volumes. Add the tube barcode using the barcode scanner.</li>
	<li>Click on Submit/Next.</li>
	<li>Repeat steps 3.1 to 3.7 if any additional samples are collected.</li>
	<li>When all samples are secured, click Save and submit on the REDCap sample collection form. Then log out of the database and the computer/tablet.</li>
</ol>
4. Transferring cryovials to storage
<ol>
	<li>Transport the samples on dry ice in the cooling box from the OR to the lab and place it on a lab bench next to a lab computer.</li>
	<li>Log in to REDCap on the lab computer using your login ID and password.</li>
	<li>Wear gloves. Take one of the collected samples and scan the barcode of the cryovial into the database (more details in section 5). Immediately place the sample back on dry ice.</li>
	<li>Obtain a second container filled with dry ice.</li>
	<li>Obtain a rack for the cryovials from the -80 &#176;C freezer. Place it in the second container on dry ice. 
	NOTE: A 96-format rack will be needed for the 0.5 mL aqueous humor tubes and a 48-format rack for the 1.9 mL vitreous tubes.</li>
	<li>Scan the barcode of the rack to the database (more details in section 5).</li>
	<li>Transfer the sample to the rack.</li>
	<li>Add the position of the vials in the rack to the database (more details in section 5).</li>
	<li>Click Save and submit.</li>
	<li>Transport the rack with the vials on dry ice to the fridge for storage at -80 &#176;C. Add the rack to a specific position in the fridge using a coordinate system. This will later allow to retrieve samples for downstream analysis easily.</li>
</ol>
5. Sample storage form
<ol>
	<li>Complete a storage form for each sample that is collected during the entry form phase. Click on the empty circle or the &#34;+&#34; under Sample Storage to create and open a new storage form.</li>
	<li>Enter the date that this form has been completed under Record Archival Date.</li>
	<li>Scan or type the tube barcode under Specimen Tube Barcode. Immediately place the sample back on dry ice.</li>
	<li>Select whether a sample is transferred out or if the sample is going into internal biorepository storage.</li>
	<li>Verify that written informed consent was obtained from the patient and select the box under Verify Consent Compliance and enter your name under Consent verified by.</li>
	<li>Select a free and suitable location for the cryovial in the rack. Transfer the cryovial at this position into the rack (e.g., position A1). Keep the rack on dry ice.</li>
	<li>In the Location phase, enter the following information: the location of the freezer under Freezer, the shelf number where the sample will be stored under Shelf, the box barcode under Box Barcode, the tube position in the box by row (Tube Position (Row)) and column (Tube Position (Column)). 
	NOTE: Optionally, a box label can also be entered under Box Label, which may facilitate to find the box in the freezer.</li>
	<li>Under the Usage section, enter the following information: the name of the project that the sample is used for (Project Name), the specimen volume in one of the following categories: full, partial, near-empty, or empty (Specimen Volume), and storage notes if applicable under Storage Notes. 
	NOTE: The date, time and user that last accessed the form is auto populated to ensure a chain of custody that can be reviewed and audited as needed.</li>
	<li>Confirm that the form is completed by clicking Complete under Complete?.</li>
	<li>Click Save &#38; Exit Form. This will bring you back to the patient overview.</li>
	<li>For every tube that was collected, generate another sample collection form by clicking on the &#34;+&#34; under Sample Storage. Then repeat steps 5.1 to 5.10.</li>
	<li>Click Save and Exit to complete the form and log out of the database and the computer/tablet.</li>
	<li>Transfer the sample rack (on dry ice) to the fridge at the prespecified position.</li>
</ol>
6. Retrieval of surgical specimens for downstream analysis
NOTE: Specimens are often archived for several years before they are analyzed. The barcoded cryovials and the searchable REDCap database system allow to find and locate each sample easily for downstream analysis.
<ol>
	<li>Identify samples of interest for the experiment by using the search function of the database. This will allow finding e.g., all aqueous humor samples from patients between 20 and 40 years with diabetic retinopathy.</li>
	<li>Obtain the location of the cryovials of interest (freezer, shelf/rack, sample rack, coordinates within the rack). Write them down, print them, or have them available on a mobile computer/tablet to facilitate the finding of the samples in the freezer.</li>
	<li>Mark the samples as used in the database.</li>
	<li>Click Save and Exit to complete the form and log out of REDCap and the computer/tablet.</li>
</ol>

<ol>
	<li>Mishra, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intraoperative+complications+with+vitreous+biopsy+for+molecular+proteomics.">Intraoperative complications with vitreous biopsy for molecular proteomics.</a> Ophthalmic Surgeries, Lasers Imaging Retina. 54 (1), 32-36 (2023).</li><li>Velez, G., Bassuk, A. G., Colgan, D., Tsang, S. H., Mahajan, V. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Therapeutic+drug+repositioning+using+personalized+proteomics+of+liquid+biopsies.">Therapeutic drug repositioning using personalized proteomics of liquid biopsies.</a> JCI Insight. 2 (24), (2017).</li><li>Velez, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Liquid+biopsy+proteomics+of+uveal+melanoma+reveals+biomarkers+associated+with+metastatic+risk.">Liquid biopsy proteomics of uveal melanoma reveals biomarkers associated with metastatic risk.</a> Molecular Cancer. 20 (1), 39 (2021).</li><li>Wert, K. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolite+therapy+guided+by+liquid+biopsy+proteomics+delays+retinal+neurodegeneration.">Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration.</a> EBioMedicine. 52, 102636 (2020).</li><li>Harris, P. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+REDCap+consortium:+Building+an+international+community+of+software+platform+partners.">The REDCap consortium: Building an international community of software platform partners.</a> Journal of Biomedical Informatics. 95, 103208 (2019).</li><li>Finn, A. P., Materin, M. A., Mruthyunjaya, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Choroidal+tumor+biopsy:+A+review+of+the+current+state+and+a+glance+into+future+techniques.">Choroidal tumor biopsy: A review of the current state and a glance into future techniques.</a> Retina. 38 Suppl 1, S79-S87 (2018).</li><li>Tarantola, R. M., Graff, J. M., Somani, R., Mahajan, V. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temporal+approach+for+small-gauge+pars+plana+vitrectomy+combined+with+anterior+segment+surgery.">Temporal approach for small-gauge pars plana vitrectomy combined with anterior segment surgery.</a> Retina. 32 (8), 1614-1623 (2012).</li><li>Mahajan, V. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sutureless+triplanar+sclerotomy+for+23-gauge+vitrectomy.">Sutureless triplanar sclerotomy for 23-gauge vitrectomy.</a> Archives in Ophthalmology. 129 (5), 585-590 (2011).</li><li>Mitchell, B. L., Yasui, Y., Li, C. I., Fitzpatrick, A. L., Lampe, P. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+freeze-thaw+cycles+and+storage+time+on+plasma+samples+used+in+mass+spectrometry+based+biomarker+discovery+projects.">Impact of freeze-thaw cycles and storage time on plasma samples used in mass spectrometry based biomarker discovery projects.</a> Cancer Informatics. 1 (1), 98-104 (2005).</li><li>Velez, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+insight+into+the+pathogenesis+of+CAPN5-vitreoretinopathy.">Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy.</a> Science Reports. 9 (1), 7608 (2019).</li><li>Montgomery, M. R., Hull, E. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alterations+in+the+glycome+after+HDAC+inhibition+impact+oncogenic+potential+in+epigenetically+plastic+SW13+cells.">Alterations in the glycome after HDAC inhibition impact oncogenic potential in epigenetically plastic SW13 cells.</a> BMC Cancer. 19 (1), 79 (2019).</li><li>Okamoto, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+serum+metabolomics+pathways+and+patterns+between+patients+with+major+depressive+disorder+with+and+without+type+2+diabetes+mellitus:+An+exploratory+study.">Comparison of serum metabolomics pathways and patterns between patients with major depressive disorder with and without type 2 diabetes mellitus: An exploratory study.</a> Journal of Integrated Neuroscience. 22 (1), 13 (2023).</li><li>Pang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MetaboAnalyst+5.0:+narrowing+the+gap+between+raw+spectra+and+functional+insights.">MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.</a> Nucleic Acids Research. 49 (W1), W388-W396 (2021).</li><li>Wolf, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Human+Eye+Transcriptome+Atlas:+A+searchable+comparative+transcriptome+database+for+healthy+and+diseased+human+eye+tissue.">The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue.</a> Genomics. 114 (2), 110286 (2022).</li><li>Seok, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genomic+responses+in+mouse+models+poorly+mimic+human+inflammatory+diseases.">Genomic responses in mouse models poorly mimic human inflammatory diseases.</a> Proceedings of the National Academy of Sciences U. S. A. 110 (9), 3507-3512 (2013).</li><li>Wolf, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+transcriptome+analysis+of+human+and+murine+choroidal+neovascularization+identifies+fibroblast+growth+factor+inducible-14+as+phylogenetically+conserved+mediator+of+neovascular+age-related+macular+degeneration.">Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration.</a> Biochimca et Biophysica Acta Molecular Basis of Diseases. 1868 (4), 166340 (2022).</li><li>Dowden, H., Munro, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trends+in+clinical+success+rates+and+therapeutic+focus.">Trends in clinical success rates and therapeutic focus.</a> Nature Reviews Drug Discovery. 18 (7), 495-496 (2019).</li><li>Li, H. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterizing+DNA+methylation+signatures+of+retinoblastoma+using+aqueous+humor+liquid+biopsy.">Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy.</a> Nature Communication. 13 (1), 5523 (2022).</li><li>Velez, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Personalized+proteomics+for+precision+health:+identifying+biomarkers+of+vitreoretinal+disease.">Personalized proteomics for precision health: identifying biomarkers of vitreoretinal disease.</a> Translational Vision Science and Technology. 7 (5), 12 (2018).</li><li>Skeie, J. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+biorepository+for+ophthalmic+surgical+specimens.">A biorepository for ophthalmic surgical specimens.</a> Proteomics Clin Applications. 8 (3-4), 209-217 (2014).</li><li>Rinsky, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+the+aqueous+humor+proteome+in+patients+with+age-related+macular+degeneration.">Analysis of the aqueous humor proteome in patients with age-related macular degeneration.</a> Investigative Ophthalmology and Visual Science. 62 (10), 18 (2021).</li></ol>

The authors have nothing to disclose.

Surgical specimens from patients allow direct molecular characterization of disease in living humans2,3,4,14, and may help overcome the limitations of cell and animal disease models that do not fully recapitulate human disease15,16. Molecular analysis of human tissue could improve the selection of new drug targets and may contribute to a higher success rate of clinical trials and drug approval17. In addition, this approach offers the potential for personalized medicine, as the obtained tissue retains the unique genomic, epigenomic, metabolomic, glycomic, and proteomic fingerprint of each individual2,18,19.
High and consistent sample quality is fundamental for all molecular analysis applications. Previous studies have shown that immediate freezing after sample retrieval and avoiding repeated freeze/thaw cycles are critical for high sample qualities9,20. Long-term storage over several years at -70 &#176;C did not significantly affect the integrity of the proteomic profile9. A standardized protocol is an important foundation to reduce bias and improve the comparability of scientific data, especially when several people (surgeons, technicians, and others) or different institutions are involved in the sampling process. Apart from the sample quality, the annotation of samples is another important factor that requires standardization to allow the correlation of molecular findings with clinical data. Our protocol relies on three essential principles to accomplish this: 1) a standardized sampling procedure for aqueous humor and vitreous liquid biopsies by an ophthalmic surgeon, 2) the immediate processing and snap-freezing of samples in the OR by laboratory personnel, and 3) a metadata annotation of each sample in a web-based database that allows researchers to quickly find samples for later experiments.
In addition to vitreous specimens20, this workflow also establishes the standardized collection of aqueous humor liquid biopsies for molecular analysis. The aqueous humor is a highly accessible, complex fluid in the anterior chamber of the eye that does not only reflect ocular diseases of the anterior but also of the posterior segment of the eye, including retinal disease18,21. Along with the fact that a high number of aqueous humor samples could be collected e.g., during cataract surgery, one of the most frequently performed surgery worldwide, these features make it an interesting source for liquid biopsies from the human eye. The standardized metadata annotation of each sample established in this workflow could also allow the correlation of proteome data with prospective clinical follow-up data. This provides the exciting opportunity to identify new prognostic biomarkers which may help to estimate the prognosis for future patients.
However, molecular analysis of human surgical specimens also has important limitations. For example, complex experimental manipulations are often only possible in animal and cell models. A solution may be to compare the molecular profile of animal or cell models with that of human disease. This strategy can identify overlapping protein biomarkers and therapeutic targets that can be validated in animals or cell models to identify the most promising candidates that correlate with human disease and are likely to succeed in clinical trials4,16.
In conclusion, our workflow establishes a practical interface between the OR and the research laboratory that allows standardized and high-throughput collection, annotation, and storing of high-quality surgical specimens for molecular downstream analysis, providing a valuable foundation for future translational research.

Molecular profiling of liquid biopsies from the human eye can capture locally enriched fluids containing molecules such as DNA, RNA, proteins, glycans, and metabolites from highly specialized ocular tissues. Liquid biopsies from the vitreous in the posterior chamber of the human eye proved to be a generally safe procedure1. They allow molecular characterization of ocular diseases in living humans and offer the potential to identify novel diagnostic and therapeutic strategies2,3,4. The aqueous humor in the anterior chamber of the eye has even higher surgical accessibility and could be obtained in large numbers, e.g., during cataract surgery, which is one of the most frequently performed surgeries. However, no standardized protocol for the collection, annotation, and biobanking of human aqueous humor and vitreous liquid biopsies for molecular downstream analyses, including proteomics, metabolomics, and glycomics, is available until now.
Here, we developed a protocol for the collection and biobanking of high-quality liquid biopsies for molecular analyses from patients undergoing eye surgery. A Mobile Operating Room Lab Interface (MORLI) enables a researcher to immediately snap-freeze the collected samples in barcoded cryovials on dry ice at -80 &#730;C in the operating room (OR). This procedure ensures a high and consistent sample quality for downstream molecular analysis. In addition to excellent sample quality, accurate annotation of samples in a biobank is critical. Using a web-based HIPAA (Health Insurance Portability and Accountability Act)-compliant REDCap (research electronic data capture) database5, our workflow allows storage of detailed metadata for each sample, including age, sex, disease, disease stage, sample type, and unique features of the surgery. This will allow accurate future searching capacity, e.g., for samples from a specific disease or a particular group of patients. In addition, the exact location of each sample in the freezer is archived using a cartesian grid system, which enables efficient sample retrieval for downstream experiments. We show examples of DNA, protein, glycan, and metabolite analyses.
Our workflow represents a practical and effective connection between the OR and the research laboratory and provides a valuable foundation for translational research.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.5ml Tri-coded Tube, 96-format, External Thread</td>
			<td>Azenta Life Sciences, Burlington, MA 01803, USA</td>
			<td>68-0703-12</td>
			<td>used for aqueous humor samples</td>
		</tr>
		<tr>
			<td>1 mL syringe</td>
			<td>surgical grade, whatever available in hospital</td>
			<td>-</td>
			<td>for aqueous humor biopsies</td>
		</tr>
		<tr>
			<td>1.9ml Tri-coded Tube, 48-format, External Thread</td>
			<td>Azenta Life Sciences, Burlington, MA 01803, USA</td>
			<td>65-7643</td>
			<td>used for vitreous samples</td>
		</tr>
		<tr>
			<td>3 mL syringe</td>
			<td>surgical grade, whatever available in hospital</td>
			<td>-</td>
			<td>for vitreous biopsies</td>
		</tr>
		<tr>
			<td>30-32-gauge needle</td>
			<td>surgical grade, whatever available in hospital</td>
			<td>-</td>
			<td>for aqueous humor biopsies</td>
		</tr>
		<tr>
			<td>Capillary electrophoresis coupled with Fourier transformed mass spectrometry (CE-FTMS)</td>
			<td>Human Metabolome Technologies, Inc., Tsuruoka, Japan</td>
			<td>-</td>
			<td>-</td>
		</tr>
		<tr>
			<td>Constellation vitrectomy system with 23-, 25-, or 27-gauge trocar cannula system</td>
			<td>Alcon Laboratories Inc, Fort Worth, TX, USA</td>
			<td>-</td>
			<td>for vitreous biopsies</td>
		</tr>
		<tr>
			<td>Cooling box</td>
			<td>Standard styrofoam box, whatever available in lab</td>
			<td>-</td>
			<td>-</td>
		</tr>
		<tr>
			<td>Dry ice</td>
			<td>Whatever available in lab</td>
			<td>-</td>
			<td>-</td>
		</tr>
		<tr>
			<td>Handsfree Standard Range Scanner Kit with Shielded USB Cable</td>
			<td>Zebra Symbol&#160;</td>
			<td>DS9208-SR4NNU21Z</td>
			<td>Barcode scanner</td>
		</tr>
		<tr>
			<td>Human Glycosylation Antibody Array L3&#160;</td>
			<td>RayBiotech, Peachtree Corners, GA, USA</td>
			<td>GAH-GCM-L3</td>
			<td>-</td>
		</tr>
		<tr>
			<td>Mac mini</td>
			<td>Apple Inc., Cupertino, CA 95014, USA</td>
			<td>-</td>
			<td>-</td>
		</tr>
		<tr>
			<td>MetaboAnalyst software</td>
			<td>Pang et al., 2021, PMID: 34019663</td>
			<td>-</td>
			<td>-</td>
		</tr>
		<tr>
			<td>Rack for 0.5ml tubes, 96-Format</td>
			<td>Azenta Life Sciences, Burlington, MA 01803, USA</td>
			<td>66-51026</td>
			<td>for aqueous humor samples</td>
		</tr>
		<tr>
			<td>Rack for 1.9ml tubes, 48-Format</td>
			<td>Azenta Life Sciences, Burlington, MA 01803, USA</td>
			<td>65-9451</td>
			<td>for vitreous samples</td>
		</tr>
		<tr>
			<td>REDCap browser-based sample database</td>
			<td>REDCap Consortium, Vanderbilt University, https://www.project-redcap.org</td>
			<td>-</td>
			<td>-</td>
		</tr>
	</tbody>
</table>

biobanking of human aqueous and vitreous liquid biopsies for molecular analyses

A critical challenge in translational research is establishing a viable and efficient interface between patient care in the operating room (OR) and the research laboratory. Here, we developed a protocol for acquiring high-quality liquid biopsies for molecular analyses from the aqueous humor and the vitreous from patients undergoing eye surgery. In this workflow, a Mobile Operating Room Lab Interface (MORLI) cart equipped with a computer, a barcode scanner, and lab instruments, including onboard cold storage, is used to obtain and archive human biological samples. A web-based data privacy-compliant database enables annotating each sample over its lifetime, and a cartesian coordinate system allows tracking each barcoded specimen in storage, enabling quick and accurate retrieval of samples for downstream analyses. Molecular characterization of human tissue samples not only serves as a diagnostic tool (e.g., to distinguish between infectious endophthalmitis and other non-infectious intraocular inflammation) but also represents an important component of translational research, allowing the identification of new drug targets, development of new diagnostic tools, and personalized therapeutics.

The collected liquid biopsy specimens can be subjected to a variety of molecular analyses, including the analysis of DNA, proteins, glycans, and metabolites. It has been shown before that long-term storage over several years at -70 &#176;C did not significantly affect the integrity of the proteomic profile9. The REDCap database enables simple and quick retrieval of samples. The database can be searched for samples from a specific group of patients, e.g., all patients with diabetic retinopathy. The database will then provide the barcodes of the tubes and the positions in storage. Until now, we have collected and archived more than 1,000 liquid biopsies. The database allowed us to quickly find the samples for downstream analyses3,10 and helped to perform the following experiments.
A 17-year-old female presented with retinal and optic nerve inflammation. She was immunocompromised, and there was a concern for infection. Aqueous humor was collected from her right eye and sent for DNA PCR analysis. The results were positive for Cytomegalovirus and negative for Herpes simplex virus and toxoplasmosis. These findings illustrate that aqueous humor liquid biopsies can help to distinguish infectious from non-infectious forms of intraocular inflammation, which is critical to select the appropriate therapy.
Liquid chromatography-mass spectrometry enables an unbiased and semi-quantitative analysis of the proteome. In a liquid biopsy from the vitreous of a patient undergoing vitrectomy, the technique was able to identify 484 unique proteins, including Complement C3 (C3), Opticin (OPTC), and Collagen Type II Alpha 1 (COL2A1) (Figure 1A).
Three vitreous liquid biopsies were analyzed using a glycoproteomics multiplex ELISA (see Table of Materials)11. The assay detected the glycosylation profiles of 500 human proteins, capturing a variety of biological pathways, such as metabolism, immune response, cell adhesion, and actin organization (Figure 1B).
A metabolomics screen using capillary electrophoresis coupled with Fourier transformed mass spectrometry12 (see Table of Materials) identified 292 different metabolites in three aqueous humor liquid biopsy samples. A pathway analysis (see Table of Materials)13 identified a variety of metabolic pathways, including amino acid metabolism, urea cycle and carnitine synthesis (Figure 1C).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/65804/65804fig01.jpg" /> 
Figure 1: Representative results. (A) Proteomics analysis of human vitreous humor using liquid chromatography and tandem mass spectrometry (LC-MS/MS) identified 484 unique proteins in a single liquid biopsy. Protein levels are shown and ranked based on spectral counts. Representative proteins are highlighted in blue. (B)&#160;A glycoproteomics multiplex ELISA detected glycosylation levels of 500 unique proteins in three vitreous liquid biopsies. A STRING protein interaction analysis identified clusters of protein interactions (clusters with at least 10 proteins are shown). The most significantly enriched pathway is shown for each cluster. (C) Metabolomics analysis using mass spectrometry identified 292 different metabolites in three aqueous humor liquid biopsies. Each point represents one sample. The height of the bar corresponds to the mean number of metabolites, the error bar represents the standard deviation. The right panel shows significantly enriched pathways. The number of detected metabolites (numerator) as well as the total number of metabolites in each pathway (denominator) are shown. <a href="https://www.jove.com/files/ftp_upload/65804/65804fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Biobanking of Human Aqueous and Vitreous Liquid Biopsies for Molecular Analyses at JoVE.com

Biobanking of Human Aqueous and Vitreous Liquid Biopsies for Molecular Analyses

This protocol presents an integrated biorepository platform for the standardized collection, annotation, and biobanking of high-quality human aqueous humor and vitreous liquid biopsies for molecular downstream analyses, including proteomics, metabolomics, and glycomics.

A critical challenge in translational research is establishing a viable and efficient interface between patient care in the operating room (OR) and the ...

biobanking-human-aqueous-vitreous-liquid-biopsies-for-molecular

Research

JoVE Journal

Medicine

2.2K Views.  Stanford University. This protocol presents an integrated biorepository platform for the standardized collection, annotation, and biobanking of high-quality human aqueous humor and vitreous liquid biopsies for molecular downstream analyses, including proteomics, metabolomics, and glycomics.

Video: Biobanking of Human Aqueous and Vitreous Liquid Biopsies for Molecular Analyses

Dissection of Human Vitreous Body Elements for Proteomic Analysis

The vitreous is an optically clear, collagenous extracellular matrix that fills the inside of the eye and overlies the retina. 1,2 Abnormal interactions between vitreous substructures and the retina underlie several vitreoretinal diseases, including retinal tear and detachment, macular pucker, macular hole, age-related macular degeneration, vitreomacular traction, proliferative vitreoretinopathy, proliferative diabetic retinopathy, and inherited vitreoretinopathies. 1,2 The molecular composition of the vitreous substructures is not known. Since the vitreous body is transparent with limited surgical access, it has been difficult to study its substructures at the molecular level. We developed a method to separate and preserve these tissues for proteomic and biochemical analysis. The dissection technique in this experimental video shows how to isolate vitreous base, anterior hyaloid, vitreous core, and vitreous cortex from postmortem human eyes. One-dimensional SDS-PAGE analyses of each vitreous component showed that our dissection technique resulted in four unique protein profiles corresponding to each substructure of the human vitreous body. Identification of differentially compartmentalized proteins will reveal candidate molecules underlying various vitreoretinal diseases.

This video shows an effective technique for differentiating and dissecting the various semi-transparent structures of the human vitreous body in post mortem eyes.

The vitreous is an optically clear, collagenous extracellular matrix that fills the inside of the eye and overlies the retina. 1,2 Abnormal interactions ...

Isolation of Mouse Respiratory Epithelial Cells and Exposure to Experimental Cigarette Smoke at Air Liquid Interface

Pulmonary epithelial cells can be isolated from the respiratory tract of mice and cultured at air-liquid interface (ALI) as a model of differentiated respiratory epithelium. A protocol is described for isolating and exposing these cells to mainstream cigarette smoke (CS), in order to study epithelial cell responses to CS exposure. The protocol consists of three parts: the isolation of airway epithelial cells from mouse trachea, the culturing of these cells at air-liquid interface (ALI) as fully differentiated epithelial cells, and the delivery of calibrated mainstream CS to these cells in culture. The ALI culture system allows the culture of respiratory epithelia under conditions that more closely resemble their physiological setting than ordinary liquid culture systems. The study of molecular and lung cellular responses to CS exposure is a critical component of understanding the impact of environmental air pollution on human health. Research findings in this area may ultimately contribute towards understanding the etiology of chronic obstructive pulmonary disease (COPD), and other tobacco-related diseases, which represent major global health problems.

Pulmonary epithelial cells can be isolated from the respiratory tract of mice and cultured at air-liquid interface as a model of differentiated respiratory epithelium. A protocol is described for isolating, culturing and exposing these cells to mainstream cigarette smoke, in order to study molecular responses to this environmental toxin.

Pulmonary epithelial cells can be isolated from the respiratory tract of mice and cultured at air-liquid interface (ALI) as a model of differentiated ...

Cell Population Analyses During Skin Carcinogenesis

Cancer development is a multiple-step process involving many cell types including cancer precursor cells, immune cells, fibroblasts and endothelial cells. Each type of cells undergoes signaling and functional changes during carcinogenesis. The current challenge for many cancer researchers is to dissect these changes in each cell type during the multiple-step process in vivo. In the last few years, the authors have developed a set of procedures to isolate different cell populations during skin cancer development using K14creER/R26-SmoM2YFP mice. The procedure is divided into 6 parts: 1) generating appropriate mice for the study (K14creER+ and R26-SmoM2YFP+ mice in this protocol); 2) inducing SmoM2YFP expression in mouse skin; 3) preparing mouse skin biopsies; 4) isolating epidermis from skin; 5) preparing single cells from epidermis; 6) labeling single cell populations for flow cytometry analysis. Generation of sufficient number of mice with the right genotype is the limiting step in this protocol, which may take up to two months. The rest of steps take a few hours to a few days. Within this protocol, we also include a section for troubleshooting. Although we focus on skin cancer, this protocol may be modified to apply for other animal models of human diseases.

Carcinogenesis is a process involving interactions between cancer cells and the cancer microenvironment. To dissect the molecular events, one needs to isolate different cell populations at different stages during cancer development. Using a mouse model for basal cell carcinoma, we describe a protocol for cell analyses during carcinogenesis.

Cancer development is  a multiple-step process involving many cell types including cancer precursor  cells, immune cells, fibroblasts and endothelial ...

Three-dimensional Imaging of Nociceptive Intraepidermal Nerve Fibers in Human Skin Biopsies

A punch biopsy of the skin is commonly used to quantify intraepidermal nerve fiber densities (IENFD) for the diagnosis of peripheral polyneuropathy 1,2. At present, it is common practice to collect 3 mm skin biopsies from the distal leg (DL) and the proximal thigh (PT) for the evaluation of length-dependent polyneuropathies 3. However, due to the multidirectional nature of IENFs, it is challenging to examine overlapping nerve structures through the analysis of two-dimensional (2D) imaging. Alternatively, three-dimensional (3D) imaging could provide a better solution for this dilemma.
In the current report, we present methods for applying 3D imaging to study painful neuropathy (PN). In order to identify IENFs, skin samples are processed for immunofluorescent analysis of protein gene product 9.5 (PGP), a pan neuronal marker. At present, it is standard practice to diagnose small fiber neuropathies using IENFD determined by PGP immunohistochemistry using brightfield microscopy 4. In the current study, we applied double immunofluorescent analysis to identify total IENFD, using PGP, and nociceptive IENF, through the use of antibodies that recognize tropomyosin-receptor-kinase A (Trk A), the high affinity receptor for nerve growth factor 5. The advantages of co-staining IENF with PGP and Trk A antibodies benefits the study of PN by clearly staining PGP-positive, nociceptive fibers. These fluorescent signals can be quantified to determine nociceptive IENFD and morphological changes of IENF associated with PN. The fluorescent images are acquired by confocal microscopy and processed for 3D analysis. 3D-imaging provides rotational abilities to further analyze morphological changes associated with PN. Taken together, fluorescent co-staining, confocal imaging, and 3D analysis clearly benefit the study of PN.

In order to study the changes of nociceptive intraepidermal nerve fibers (IENFs) in painful neuropathies (PN), we developed protocols that could directly examine three-dimensional morphological changes observed in nociceptive IENFs. Three-dimensional analysis of IENFs has the potential to evaluate the morphological changes of IENF in PN.

A punch biopsy of the skin is commonly used to quantify intraepidermal nerve fiber densities (IENFD) for the diagnosis of peripheral polyneuropathy 1,2. ...

An Orthotopic Murine Model of Human Prostate Cancer Metastasis

Our laboratory has developed a novel orthotopic implantation model of human prostate cancer (PCa). As PCa death is not due to the primary tumor, but rather the formation of distinct metastasis, the ability to effectively model this progression pre-clinically is of high value. In this model, cells are directly implanted into the ventral lobe of the prostate in Balb/c athymic mice, and allowed to progress for 4-6 weeks. At experiment termination, several distinct endpoints can be measured, such as size and molecular characterization of the primary tumor, the presence and quantification of circulating tumor cells in the blood and bone marrow, and formation of metastasis to the lung. In addition to a variety of endpoints, this model provides a picture of a cells ability to invade and escape the primary organ, enter and survive in the circulatory system, and implant and grow in a secondary site. This model has been used effectively to measure metastatic response to both changes in protein expression as well as to response to small molecule therapeutics, in a short turnaround time.

This orthotopic model of human prostate cancer allows for quantification of tumor size, circulating tumor cells, and formation of distinct metastasis to the lung. As cells must escape the primary organ, enter the blood stream, and implant into a secondary site, this model effectively recapitulates the scenario in humans.

Our laboratory has developed a novel orthotopic implantation model of  human prostate cancer (PCa). As PCa death is not due to the primary tumor, but  ...

Enrichment for Chemoresistant Ovarian Cancer Stem Cells from Human Cell Lines

Cancer stem cells (CSCs) are defined as a subset of slow cycling and undifferentiated cells that divide asymmetrically to generate highly proliferative, invasive, and chemoresistant tumor cells. Therefore, CSCs are an attractive population of cells to target therapeutically. CSCs are predicted to contribute to a number of types of malignancies including those in the blood, brain, lung, gastrointestinal tract, prostate, and ovary. Isolating and enriching a tumor cell population for CSCs will enable researchers to study the properties, genetics, and therapeutic response of CSCs. We generated a protocol that reproducibly enriches for ovarian cancer CSCs from ovarian cancer cell lines (SKOV3 and OVCA429). Cell lines are treated with 20 &#181;M cisplatin for 3 days. Surviving cells are isolated and cultured in a serum-free stem cell media containing cytokines and growth factors. We demonstrate an enrichment of these purified CSCs by analyzing the isolated cells for known stem cell markers Oct4, Nanog, and Prom1 (CD133) and cell surface expression of CD177 and CD133. The CSCs exhibit increased chemoresistance. This method for isolation of CSCs is a useful tool for studying the role of CSCs in chemoresistance and tumor relapse.

Cancer stem cells (CSCs) are&#160;implicated in tumor relapse due to chemoresistance. We have optimized a protocol for selection and expansion of CSCs from ovarian cancer cell lines. By treating cells with the chemotherapeutic cisplatin and culturing&#160;in a stem cell promoting media we enrich for non-adherent CSC cultures.

Cancer stem cells (CSCs) are defined as a subset of slow cycling and undifferentiated cells that divide asymmetrically to generate highly proliferative, ...

Human Dupuytren's Ex Vivo Culture for the Study of Myofibroblasts and Extracellular Matrix Interactions

Organ fibrosis or &#8220;scarring&#8221; is known to account for a high death toll due to the extensive amount of disorders and organs affected (from cirrhosis to cardiovascular diseases). There is no effective treatment and the in vitro tools available do not mimic the in vivo situation rendering the progress of the out of control wound healing process still enigmatic.
To date, 2D and 3D cultures of fibroblasts derived from DD patients are the main experimental models available. Primary cell cultures have many limitations; the fibroblasts derived from DD are altered by the culture conditions, lack cellular context and interactions, which are crucial for the development of fibrosis and weakly represent the derived tissue. Real-time PCR analysis of fibroblasts derived from control and DD samples show that little difference is detectable. 3D cultures of fibroblasts include addition of extracellular matrix that alters the native conditions of these cells. 
As a way to characterize the fibrotic, proliferative properties of these resection specimens we have developed a 3D culture system, using intact human resections of the nodule part of the cord. The system is based on transwell plates with an attached nitrocellulose membrane that allows contact of the tissue with the medium but not with the plastic, thus, preventing the alteration of the tissue. No collagen gel or other extracellular matrix protein substrate is required. The tissue resection specimens maintain their viability and proliferative properties for 7 days. This is the first &#8220;organ&#8221; culture system that allows human resection specimens from DD patients to be grown ex vivo and functionally tested, recapitulating the in vivo situation.

Human Dupuytren&#039;s Ex Vivo Culture for the Study of Myofibroblasts and Extracellular Matrix Interactions

Dupuytren&#8217;s disease (DD) is a fibroproliferative disease of the palm of the hand. Here, we present a protocol to culture resection specimens from DD in a three-dimensional (3D) culture system. Such short-term culture system allows preservation of the 3D structure and molecular properties of the fibrotic tissue.

Organ fibrosis or &#8220;scarring&#8221; is known to account for a high death toll due to the extensive amount of disorders and organs affected (from ...

Whole Vitreous Humor Dissection for Vitreodynamic Analysis

The authors propose an effective technique to isolate whole, intact vitreous core and cortex from post mortem enucleated porcine eyes. While previous studies have shown the results of such dissections, the detailed steps have not been described, precluding researchers outside the field from replicating their methods. Other studies harvest vitreous either through aspiration, which does not maintain the vitreous structure anatomy, or through partial dissection, which only isolates the vitreous core. The proposed method isolates the whole vitreous body, with the vitreous core and cortex intact, while maintaining vitreous anatomy and structural integrity. In this method, a full thickness scleral flap in an enucleated porcine eye is first created and through this, the choroid tissue can be separated from the sclera. The scleral flap is then expanded and the choroid is completely separated from the sclera. Finally the choroid-retina tissue is peeled off the vitreous to leave an isolated intact vitreous body. The proposed vitreous dissection technique can be used to study physical properties of the vitreous humor. In particular, this method has significance for experimental studies involving drug delivery, vitreo-retinal oxygen transport, and intraocular convection.

The goal of this protocol is to show an effective technique to isolate whole, intact vitreous core and cortex from post mortem enucleated porcine eyes.

The authors propose an effective technique to isolate whole, intact vitreous core and cortex from post mortem enucleated porcine eyes. While previous ...

Induction of Accelerated Atherosclerosis in Mice: The "Wire-Injury" Model

Atherosclerosis is a proliferative fibro-inflammatory disease developing in the arterial wall, inducing a deficient blood flow or a lack of blood flow. Moreover, by rupture of the defective vascular wall, atherosclerosis induces occlusive thrombus formation, which represents the main cause of myocardial infarction or stroke and the most frequent cause of death. Despite the advances in the cardiovascular field, many questions remain unanswered, and additional basic research is essential to improve our understanding of the molecular mechanisms during atherosclerosis and its effects. Due to limited clinical studies, there is a need for representative animal models recreating atherosclerotic conditions such as neointima formation after stent implantation, balloon angioplasty, or endarterectomy. Since the mouse presents many advantages and is the most frequently used model for studying molecular processes, the current study proposes an invasive procedure of endothelial denudation, also known as the wire-injury model, which is representative of the human condition of neointima formation in arteries after revascularization procedures.

Induction of Accelerated Atherosclerosis in Mice: The &quot;Wire-Injury&quot; Model

This study describes an invasive procedure for the induction of accelerated atherosclerosis in mice. In comparison to other methods using electric- or cryo-induced injury, mechanical-induced injury mimics the human condition of restenosis after revascularization therapies and is ideal for the study of the molecular mechanisms involved.

Atherosclerosis is a proliferative fibro-inflammatory disease developing in the arterial wall, inducing a deficient blood flow or a lack of blood flow. ...

In Vitro and In Vivo Detection of Mitophagy in Human Cells, C. Elegans, and Mice

Mitochondria are the powerhouses of cells and produce cellular energy in the form of ATP. Mitochondrial dysfunction contributes to biological aging and a wide variety of disorders including metabolic diseases, premature aging syndromes, and neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Maintenance of mitochondrial health depends on mitochondrial biogenesis and the efficient clearance of dysfunctional mitochondria through mitophagy. Experimental methods to accurately detect autophagy/mitophagy, especially in animal models, have been challenging to develop. Recent progress towards the understanding of the molecular mechanisms of mitophagy has enabled the development of novel mitophagy detection techniques. Here, we introduce several versatile techniques to monitor mitophagy in human cells, Caenorhabditis elegans (e.g., Rosella and DCT-1/ LGG-1 strains), and mice (mt-Keima). A combination of these mitophagy detection techniques, including cross-species evaluation, will improve the accuracy of mitophagy measurements and lead to a better understanding of the role of mitophagy in health and disease.

In Vitro and In Vivo Detection of Mitophagy in Human Cells, C. Elegans, and Mice

Mitophagy, the process of clearing damaged mitochondria, is necessary for mitochondrial homeostasis and health maintenance. This article presents some of the latest mitophagy detection methods in human cells, Caenorhabditis elegans, and mice.

Mitochondria are the powerhouses of cells and produce cellular energy in the form of ATP. Mitochondrial dysfunction contributes to biological aging and a ...