@article {2070, title = {Liquid Biopsy Proteomics in Ophthalmology.}, journal = {J Proteome Res}, volume = {23}, year = {2024}, month = {2024 Feb 02}, pages = {511-522}, abstract = {

Minimally invasive liquid biopsies from the eye capture locally enriched fluids that contain thousands of proteins from highly specialized ocular cell types, presenting a promising alternative to solid tissue biopsies. The advantages of liquid biopsies include sampling the eye without causing irreversible functional damage, potentially better reflecting tissue heterogeneity, collecting samples in an outpatient setting, monitoring therapeutic response with sequential sampling, and even allowing examination of disease mechanisms at the cell level in living humans, an approach that we refer to as TEMPO (Tracing Expression of Multiple Protein Origins). Liquid biopsy proteomics has the potential to transform molecular diagnostics and prognostics and to assess disease mechanisms and personalized therapeutic strategies in individual patients. This review addresses opportunities, challenges, and future directions of high-resolution liquid biopsy proteomics in ophthalmology, with particular emphasis on the large-scale collection of high-quality samples, cutting edge proteomics technology, and artificial intelligence-supported data analysis.

}, keywords = {Artificial Intelligence, Biopsy, Humans, Liquid Biopsy, Ophthalmology, Proteins, Proteomics}, issn = {1535-3907}, doi = {10.1021/acs.jproteome.3c00756}, author = {Wolf, Julian and Franco, Joel A and Yip, Rui and Dabaja, Mohamed Ziad and Velez, Gabriel and Liu, Fei and Bassuk, Alexander G and Mruthyunjaya, Prithvi and Dufour, Antoine and Mahajan, Vinit B} } @article {2037, title = {Intraoperative Complications With Vitreous Biopsy for Molecular Proteomics.}, journal = {Ophthalmic Surg Lasers Imaging Retina}, volume = {54}, year = {2023}, month = {2023 Jan}, pages = {32-36}, abstract = {

OBJECTIVE: To study the incidence of intraoperative complications while collecting a vitreous sample for proteomic biomarker analyses during small-gauge pars plana vitrectomy (PPV).

METHODS: A retrospective case series was assembled from the surgical logs and charts of patients who underwent 23-, 25-, and 27-gauge PPV along with an undiluted vitreous biopsy. Primary surgical indication and detailed operative reports were reviewed. Complications specific to vitreous biopsy were assessed while complications related to vitrectomy in general without biopsy were not tabulated.

RESULTS: In 1190 eyes that underwent vitreous biopsy, the most common indications for PPV were rhegmatogenous retinal detachment (24.2\%), epiretinal membrane (ERM) (21.7\%), vitreous hemorrhage (11.0\%), uveitis (8.3\%), and macular hole (7.5\%). An adequate sample of 0.5 cc to 1.0 cc was obtained in all cases. There was one sclerotomy break associated with biopsy, but no instances of lens touch, retinal contusion, retinal detachment, or intraocular hemorrhage.

CONCLUSIONS: Undiluted vitreous biopsy obtained at the time of small-gauge vitrectomy is a generally safe procedure and may be considered for collection of samples for proteomic analysis. .

}, keywords = {Biopsy, Humans, Intraoperative Complications, Postoperative Complications, Proteomics, Retinal Detachment, Retrospective Studies, Vitrectomy}, issn = {2325-8179}, doi = {10.3928/23258160-20221214-02}, author = {Mishra, Kapil and Velez, Gabriel and Chemudupati, Teja and Tang, Peter H and Mruthyunjaya, Prithvi and Sanislo, Steven R and Mahajan, Vinit B} } @article {2058, title = {Liquid-biopsy proteomics combined with AI identifies cellular drivers of eye aging and disease in~vivo.}, journal = {Cell}, volume = {186}, year = {2023}, month = {2023 Oct 26}, pages = {4868-4884.e12}, abstract = {

Single-cell analysis in living humans is essential for understanding disease mechanisms, but it is impractical in non-regenerative organs, such as the eye and brain, because tissue biopsies would cause serious damage. We resolve this problem by integrating proteomics of liquid biopsies with single-cell transcriptomics from all known ocular cell types to trace the cellular origin of 5,953 proteins detected in the aqueous humor. We identified hundreds of cell-specific protein markers, including for individual retinal cell types. Surprisingly, our results reveal that retinal degeneration occurs in Parkinson\&$\#$39;s disease, and the cells driving diabetic retinopathy switch with disease stage. Finally, we developed artificial intelligence (AI) models to assess individual cellular aging and found that many eye diseases not associated with chronological age undergo accelerated molecular aging of disease-specific cell types. Our approach, which can be applied to other organ systems, has the potential to transform molecular diagnostics and prognostics while uncovering new cellular disease and aging mechanisms.

}, keywords = {Aging, Artificial Intelligence, Biopsy, Humans, Liquid Biopsy, Proteomics}, issn = {1097-4172}, doi = {10.1016/j.cell.2023.09.012}, author = {Wolf, Julian and Rasmussen, Ditte K and Sun, Young Joo and Vu, Jennifer T and Wang, Elena and Espinosa, Camilo and Bigini, Fabio and Chang, Robert T and Montague, Artis A and Tang, Peter H and Mruthyunjaya, Prithvi and Aghaeepour, Nima and Dufour, Antoine and Bassuk, Alexander G and Mahajan, Vinit B} } @article {129, title = {Proteomic analysis of vitreous biopsy techniques.}, journal = {Retina}, volume = {32}, year = {2012}, month = {2012 Nov-Dec}, pages = {2141-9}, abstract = {

PURPOSE: To compare vitreous biopsy methods using analysis platforms used in proteomics biomarker discovery.

METHODS: Vitreous biopsies from 10 eyes were collected sequentially using a 23-gauge needle and a 23-gauge vitreous cutter instrument. Paired specimens were evaluated by UV absorbance spectroscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and liquid chromatography tandem mass spectrometry (LC-MS/MS).

RESULTS: The total protein concentration obtained with a needle and vitrectomy instrument biopsy averaged 1.10 mg/mL (standard error of the mean = 0.35) and 1.13 mg/mL (standard error of the mean = 0.25), respectively. In eight eyes with low or medium viscidity, there was a very high correlation (R = 0.934) between the biopsy methods. When data from 2 eyes with high viscidity vitreous were included, the correlation was reduced (R = 0.704). The molecular weight protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of paired needle and vitreous cutter samples were similar, except for a minority of pairs with single band intensity variance. Using LC-MS/MS, equivalent peptides were identified with similar frequencies (R \≥ 0.90) in paired samples.

CONCLUSION: Proteins and peptides collected from vitreous needle biopsies are nearly equivalent to those obtained from a vitreous cutter instrument. This study suggests both techniques may be used for most proteomic and biomarker discovery studies of vitreoretinal diseases, although a minority of proteins and peptides may differ in concentration.

}, keywords = {Adolescent, Aged, Biological Markers, Biopsy, Chromatography, Liquid, Electrophoresis, Polyacrylamide Gel, Eye Diseases, Eye Proteins, Female, Humans, Male, Middle Aged, Proteomics, Spectrophotometry, Ultraviolet, Tandem Mass Spectrometry, Vitrectomy, Vitreous Body, Young Adult}, author = {Skeie, Jessica M and Brown, Eric N and Martinez, Harryl D and Russell, Stephen R and Birkholz, Emily S and Folk, James C and Boldt, H Culver and Gehrs, Karen M and Stone, Edwin M and Wright, Michael E and Mahajan, Vinit B} }