Biology subjects

Zvirblyte, J.

Publications and source records attributed to Zvirblyte, J..

3 recordsLinked to original sources

bioRxiv2025

High-throughput single cell -omics using semi-permeable capsules

Biological systems are inherently complex and heterogeneous. Deciphering this complexity increasingly relies on high-throughput analytical methods and tools that efficiently probe the cellular phenotype and genotype. While recent advancements have enabled various single-cell -omics assays, their broader applications are inherently limited by the challenge of efficiently conducting multi-step biochemical assays while retaining various biological analytes. Extending on our previous work (1) here we present a versatile technology based on semi-permeable capsules (SPCs), tailored for a variety of high-throughput nucleic acid assays, including digital PCR, genome sequencing, single-cell RNA-sequencing (scRNA-Seq) and FACS-based isolation of individual transcriptomes based on nucleic acid marker of interest. Being biocompatible, the SPCs support single-cell cultivation and clonal expansion over long periods of time - a fundamental limitation of droplet microfluidics systems. Using SPCs we perform scRNA-Seq on white blood cells from patients with hematopoietic disorders and demonstrate that capsule-based sequencing approach (CapSeq) offers superior transcript capture, even for the most challenging cell types. By applying CapSeq on acute myeloid leukemia (AML) samples, we uncover notable changes in transcriptomes of mature granulocytes and monocytes associated with blast and progenitor cell phenotypes. Accurate representation of the entirety of the cellular heterogeneity of clinical samples, driving new insights into the malfunctioning of the innate immune system, and ability to clonally expand individual cells over long periods of time, positions SPC technology as customizable, highly sensitive and broadly applicable tool for easy-to-use, scalable single-cell -omics applications.

genomics↗

bioRxiv2023

inDrops-2: a flexible, versatile and cost-efficient droplet microfluidics approach for high-throughput scRNA-seq of fresh and preserved clinical samples

The development of a large variety of single-cell analytical techniques has empowered researchers to explore diverse biological questions at the level of individual cells. Among these, droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly prevalent owing to their high-throughput capabilities and reduced reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, the relatively high cost impose limitations for profiling large numbers of samples. Moreover, as the scope and scale of single cell sequencing methods keeps expanding, the possibility to accommodate diverse molecular biology workflows and inexpensively profile multiple biospecimens simultaneously becomes highly relevant. Herein, we present inDrops-2: an open-source scRNA-seq platform designed to profile fresh or preserved clinical samples with a sensitivity matching that of state-of-the-art commercial systems, yet at a few folds lower cost. Using inDrops-2, we conducted a comparative analysis of two prominent scRNA-seq protocols - those based on exponential and linear amplification of cDNA - and provide useful insights about the pros and cons inherited to each approach. We showcase the utility of inDrops-2 by simultaneously profiling 18 human lung carcinoma samples, all in one run, following cell preservation, long-term storage and multiplexing, to obtain a multiregional cellular profile of tumor microenvironment. The scalability, experimental flexibility and cost-efficiency offered by inDrops-2 should make it appealing for various single-cell transcriptomic studies.

molecular biology↗

bioRxiv2023

Single-cell transcriptional profiling of clear cell renal cell carcinoma reveals an invasive tumor vasculature phenotype

Clear cell renal cell carcinoma (ccRCC) is the most prevalent form of renal cancer, accounting for over 75% of cases. The asymptomatic nature of the disease contributes to late-stage diagnoses and poor survival. Highly vascularized and immune infiltrated microenvironment are prominent features of ccRCC, yet the interplay between vasculature and immune cells, disease progression and response to therapy remains poorly understood. Using droplet-based single-cell RNA sequencing we profiled 50,236 transcriptomes from paired tumor and healthy adjacent kidney tissues. Our analysis revealed significant heterogeneity and inter-patient variability of the tumor microenvironment. Notably, we discovered a previously uncharacterized vasculature subpopulation associated with epithelial-mesenchymal transition. The cell-cell communication analysis revealed multiple modes of immunosuppressive interactions within the tumor microenvironment, including clinically relevant interactions between tumor vasculature and stromal cells with immune cells. The upregulation of the genes involved in these interactions was associated with worse survival in the TCGA KIRC cohort. Our findings demonstrate the role of tumor vasculature and stromal cell populations in shaping the ccRCC microenvironment and uncover a subpopulation of cells within the tumor vasculature that is associated with an invasive phenotype.

cancer biology↗