Name: biobanking of human aqueous and vitreous liquid biopsies for molecular analyses
Uploaded: 2023-09-11T14:00:00.000+00:00
Duration: 14 min 54 s
Description: Watch this Scientific Journal Video about Biobanking of Human Aqueous and Vitreous Liquid Biopsies for Molecular Analyses at JoVE.com

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><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&amp;nbsp;</td><td>DS9208-SR4NNU21Z</td><td>Barcode scanner</td></tr><tr><td>Human Glycosylation Antibody Array L3&amp;nbsp;</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.remotexs.ntu.edu.sg/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

Nanyang Technological University

Research

JoVE Journal

Medicine

2.2K Views.  Stanford University. Moleculaire profilering van vloeibare biopsieën uit het menselijk oog kan lokaal verrijkte vloeistoffen vangen die duizenden verschillende moleculen uit zeer gespecialiseerde oculaire weefsels bevatten. Ze maken moleculaire karakterisering van oogziekten bij levende mensen mogelijk en van verdere mogelijkheden om nieuwe diagnostische en therapeutische strategieën te identificeren. Hier hebben we een protocol ontwikkeld voor de gestandaardiseerde verzameling en biobanking van hoogwaardige wa...

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.

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 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 ...

Creation and Maintenance of a Living Biobank - How We Do It

In light of the growing knowledge about the inter-individual properties and heterogeneity of cancers, the emerging field of personalized medicine requires a platform for preclinical research. Over recent years, we have established a biobank of colorectal and pancreatic cancers comprising of primary tumor tissue, normal tissue, sera, isolated peripheral blood lymphocytes (PBL), patient-derived xenografts (PDX), as well as primary and secondary cancer cell lines. Since original tumor tissue is limited and the establishment rate of primary cancer cell lines is still relatively low, PDX allow not only the preservation and extension of the biobank but also the generation of secondary cancer cell lines. Moreover, PDX-models have been proven to be the ideal in vivo model for preclinical drug testing. However, biobanking requires careful preparation, strict guidelines and a well attuned infrastructure. Colectomy, duodenopancreatectomy or resected metastases specimens are collected immediately after resection and transferred to the pathology department. Respecting priority of an unbiased histopathological report, at the discretion of the attending pathologist who carries out the dissections, small tumor pieces and non-tumor tissue are harvested. 
Necrotic parts are discarded and the remaining tumor tissue is cut into small, identical cubes and cryopreserved for later use. Additionally, a small portion of the tumor is minced and strained for primary cancer cell culture. Additionally, blood samples drawn from the patient pre- and postoperatively, are processed to obtain serum and PBLs. For PDX engraftment, the cryopreserved specimens are defrosted and implanted subcutaneously into the flanks of immunodeficient mice. The resulting PDX closely recapitulate the histology of the "donor" tumors and can be either used for subsequent xenografting or cryopreserved for later use. In the following work, we describe the individual steps of creation, maintenance and administration of a large biobank of colorectal and pancreatic cancer. Moreover, we highlight the crucial details and caveats associated with biobanking.

In the following work, we describe the consecutive steps necessary for the establishment of a large biobank of colorectal and pancreatic cancer.

In light of the growing knowledge about the inter-individual properties and heterogeneity of cancers, the emerging field of personalized medicine requires ...

Cancer Research

Aqueous Humor as a Liquid Biopsy for Retinoblastoma: Clear Corneal Paracentesis and Genomic Analysis

There is significant potential clinical utility for the application of a liquid biopsy platform for retinoblastoma, given that direct tumor biopsy is prohibited in these patients. The aqueous humor (AH) forms in a separate compartment from the tumor but is enclosed within the same ocular space. Thus, it is an enriched source of eye-specific tumoral genomic information that can be used as a liquid biopsy or surrogate to tumor biopsy for this disease. This manuscript details a methodology for safely extracting the AH from retinoblastoma eyes via clear corneal paracentesis. Additionally, the steps for genomic analysis, including cell-free DNA isolation and purification, next-generation sequencing, somatic copy number alteration (SCNA) analysis, RB1 single nucleotide variant (SNV) mutation identification, and tumor fraction estimation are presented. The pre-analytical, analytical, and early clinical validity of the AH liquid biopsy platform have been evaluated; however, it is not without limitations. These are largely a consequence of the quantity of cell-free DNA that is required for certain steps of the assay. Compared to other blood-based liquid biopsy platforms currently under investigation for retinoblastoma, an AH-based platform is limited by the volume of biofluid (and thus the quantity of DNA) that can be extracted from the eye; the benefit is that AH is eye-specific. The platform discussed here is unique in that it detects circulating tumor DNA in the AH via two mechanisms (SCNAs and RB1 SNVs), yielding a higher sensitivity for identifying tumoral genomic information. The AH liquid biopsy has the potential for direct clinical application to precision oncology for retinoblastoma patients, with particular importance for patients with bilateral disease as the AH is specific to the tumors in each eye. There is ongoing research with applications of this platform to patients with other ocular tumors as well.

The aqueous humor is a high-yield liquid biopsy for retinoblastoma, intraocular cancer that cannot be biopsied in vivo due to the risk of extraocular spread. Herein, a method for safely extracting aqueous humor via clear corneal paracentesis and steps for genomic analysis to identify prognostic biomarkers are presented.

There is significant potential clinical utility for the application of a liquid biopsy platform for retinoblastoma, given that direct tumor biopsy is ...

A Standardized Liquid Biopsy Preanalytical Protocol for Downstream Circulating-Free DNA Applications

The term liquid biopsy (LB) refers to molecules such as proteins, DNA, RNA, cells, or extracellular vesicles in blood and other bodily fluids that originate from the primary and/or metastatic tumor. LB has emerged as a mainstay in translational research and has started to become part of clinical oncology practice, providing a minimally invasive alternative to solid biopsy. The LB allows real-time monitoring of a tumor via a minimally invasive sample extraction, such as blood. The applications include early cancer detection, patient follow-up for the detection of disease progression, assessment of minimal residual disease, and potential identification of molecular progression and mechanism of resistance. In order to achieve a reliable analysis of these samples that can be reported in the clinic, the preanalytical procedures should be carefully considered and strictly followed. Sample collection, quality, and storage are crucial steps that determine their usefulness in downstream applications. Here, we present standardized protocols from our liquid biopsy working module for collecting, processing, and storing plasma and serum samples for downstream liquid biopsy analysis based on circulating-free DNA. The protocols presented here require standard equipment and are sufficiently flexible to be applied in most laboratories focused on biological procedures.

The liquid biopsy has revolutionized our approach to oncology translational studies, with sample collection, quality, and storage being crucial steps for its successful clinical application. Here we describe a standardized and validated protocol for downstream circulating-free DNA applications that can be applied in most translational research laboratories.

The term liquid biopsy (LB) refers to molecules such as proteins, DNA, RNA, cells, or extracellular vesicles in blood and other bodily fluids that ...

Biobank for Translational Medicine: Standard Operating Procedures for Optimal Sample Management

Biobanks are key research infrastructures aimed at the collection, storage, processing, and sharing of high-quality human biological samples and associated data for research, diagnosis, and personalized medicine. The Biobank for Translational and Digital Medicine Unit at the European Institute of Oncology (IEO) is a landmark in this field. Biobanks collaborate with clinical divisions, internal and external research groups, and industry, supporting patients' treatment and scientific progress, including innovative diagnostics, biomarker discovery, and clinical trial design. Given the central role of biobanks in modern research, biobanking standard operating procedures (SOPs) should be extremely precise. SOPs and controls by certified specialists ensure the highest quality of samples for the implementation of science-based, diagnostic, prognostic, and therapeutic personalized strategies. However, despite numerous efforts to standardize and harmonize biobanks, these protocols, which follow a strict set of rules, quality controls, and guidelines based on ethical and legal principles, are not easily accessible. This paper presents the biobank standard operating procedures of a large cancer center.

Biobanks are crucial resources for biomedical research and the Biobank for Translational and Digital Medicine Unit at the European Institute of Oncology is a model in this field. Here, we provide a detailed description of biobanks' standard operating procedures for the management of different types of human biological samples.

Biobanks are key research infrastructures aimed at the collection, storage, processing, and sharing of high-quality human biological samples and ...

Protocol for Prostatectomy Specimen Mapping and Dissection

Enhancing Prostate Tumor Biobanking Reliability with Improved Sampling Technique and Histological Characterization

Acquiring fresh and well-characterized tumor tissue samples is critical for conducting high-quality &#34;omics&#34; studies. However, it can be particularly challenging in the context of prostate cancer (PC) due to the unique nature of this organ and the high heterogeneity associated with this tumor. On the other hand, histopathologically characterizing samples before their storage without causing significant tissue alterations is also an intriguing challenge. In this context, we present a new method for acquiring, mapping, characterizing, and micro-dissecting resected prostate tissue based on anatomopathological criteria.
Unlike previously published protocols, this method reduces the time required for histopathological analysis of the prostate specimen without compromising its structure, which is crucial for assessing surgical margins. Furthermore, it enables the delineation and micro-macro dissection of fresh prostate tissue samples, with a focus on histological tumor areas defined by pathological criteria such as Gleason score, precursor lesions (high-grade prostatic intraepithelial neoplasia - PIN), and inflammatory lesions (prostatitis). These samples are then stored in a Biobank for subsequent research analyses.

Author Spotlight: Advancing Prostate Cancer Research Through Improved Tissue Sampling and Biobanking

This protocol describes a method for facilitating the collection of samples from radical prostatectomy specimens. The goal is to map, characterize, and micro-macro dissect tissue samples from the specimens based on anatomopathological criteria before storing them in a Biobank.

Acquiring fresh and well-characterized tumor tissue samples is critical for conducting high-quality &#34;omics&#34; studies. However, it can be ...

Diagnosis of Vitreoretinal Lymphoma Using Cell-Free DNA

Cell-Free DNA Extraction of Vitreous and Aqueous Humor Specimens for Diagnosis and Monitoring of Vitreoretinal Lymphoma

Vitreoretinal lymphoma (VRL) represents an aggressive lymphoma, often categorized as primary central nervous system diffuse large B-cell lymphoma. To diagnose VRL, specimens such as vitreous humor and, more recently, aqueous humor are collected. Diagnostic testing for VRL on these specimens includes cytology, flow cytometry, and molecular testing. However, both cytopathology and flow cytometry, along with molecular testing using cellular DNA, necessitate intact whole cells. The challenge lies in the fact that vitreous and aqueous humor typically have low cellularity, and many cells get destroyed during collection, storage, and processing. Moreover, these specimens pose additional difficulties for molecular testing due to the high viscosity of vitreous humor and the low volume of both vitreous and aqueous humor. This study proposes a method for extracting cell-free DNA from vitreous and aqueous specimens. This approach complements the extraction of cellular DNA or allows the cellular component of these specimens to be utilized for other diagnostic methods, including cytology and flow cytometry.

Author Spotlight: Advancing VRL Diagnosis Using Cell-Free DNA Extraction from Vitreous Humor 

A procedure to extract cell-free DNA from vitreous and aqueous humor to perform molecular studies for diagnosing vitreoretinal lymphoma is established here. The method offers the ability to concurrently extract DNA from the cellular component of the sample or to reserve it for ancillary testing.

Vitreoretinal lymphoma (VRL) represents an aggressive lymphoma, often categorized as primary central nervous system diffuse large B-cell lymphoma. To ...

Establishment of a Clinic-based Biorepository

The incidence of skin cancer (e.g., squamous cell carcinoma, basal cell carcinoma, and melanoma) has been increasing over the past several years. It is expected that there will be a parallel demand for cutaneous tumor samples for biomedical research studies. Tissue availability, however, is limited due the cost of establishing a biorepository and the lack of protocols available for obtaining clinical samples that do not interfere with clinical operations. A protocol was established to collect and process cutaneous tumor and associated blood and saliva samples that has minimal impact on routine clinical procedures on the date of a Mohs surgery. Tumor samples are collected and processed from patients undergoing their first layer of Mohs surgery for biopsy-proven cutaneous malignancies by the Mohs histotechnologist. Adjacent normal tissue is collected at the time of surgical closure. Additional samples that may be collected are whole-blood and buccal swabs. By utilizing tissue samples that are normally discarded, a biorepository was generated that offers several key advantages by being based in the clinic versus the laboratory setting. These include a wide range of collected samples; access to de-identified patient records, including pathology reports; and, for the typical donor, access to additional samples during follow-up visits.

Cutaneous tumors are often discarded following Mohs micrographic surgery. A protocol is described here that enables clinical support staff to effectively process and store cutaneous tumor (e.g., squamous cell carcinoma, basal cell carcinoma, and melanoma) samples for downstream laboratory applications without interfering with clinical operations.

The incidence of skin cancer (e.g., squamous cell carcinoma, basal cell carcinoma, and melanoma) has been increasing over the past several years. It is ...

Biobanking of Human Aqueous and Vitreous Liquid Biopsies for Molecular Analyses

Samenvatting

Meer video's verkennen

Hoofdstukken in deze video