Spheroid Engineering in Microfluidic Devices

2023-01-01
Tevlek, Atakan
Kecili, Seren
Ozcelik, Ozge S.
Külah, Haluk
Tekin, H. Cumhur
Two-dimensional (2D) cell culture techniques are commonly employed to investigate biophysical and biochemical cellular responses. However, these culture methods, having monolayer cells, lack cell-cell and cell-extracellular matrix interactions, mimicking the cell microenvironment and multicellular organization. Three-dimensional (3D) cell culture methods enable equal transportation of nutrients, gas, and growth factors among cells and their microenvironment. Therefore, 3D cultures show similar cell proliferation, apoptosis, and differentiation properties to in vivo. A spheroid is defined as self-assembled 3D cell aggregates, and it closely mimics a cell microenvironment in vitro thanks to cell-cell/matrix interactions, which enables its use in several important applications in medical and clinical research. To fabricate a spheroid, conventional methods such as liquid overlay, hanging drop, and so forth are available. However, these labor-intensive methods result in low-throughput fabrication and uncontrollable spheroid sizes. On the other hand, microfluidic methods enable inexpensive and rapid fabrication of spheroids with high precision. Furthermore, fabricated spheroids can also be cultured in microfluidic devices for controllable cell perfusion, simulation of fluid shear effects, and mimicking of the microenvironment-like in vivo conditions. This review focuses on recent microfluidic spheroid fabrication techniques and also organ-on-a-chip applications of spheroids, which are used in different disease modeling and drug development studies.

Suggestions

DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles
Hoffmann, Thomas; Marıon, Antoıne; Antes, Iris (Springer Science and Business Media LLC, 2017-02-02)
Background: T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Va/V beta) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly...
Subsequence-based feature map for protein function classification
Sarac, Omer Sinan; Guersoy-Yuezueguellue, Oezge; Atalay, Rengül; Atalay, Mehmet Volkan (2008-04-01)
Automated classification of proteins is indispensable for further in vivo investigation of excessive number of unknown sequences generated by large scale molecular biology techniques. This study describes a discriminative system based on feature space mapping, called subsequence profile map (SPMap) for functional classification of protein sequences. SPMap takes into account the information coming from the subsequences of a protein. A group of protein sequences that belong to the same level of classification...
FTIR spectroscopic characterization of protein structure in aqueous and non-aqueous media
Haris, PI; Severcan, Feride (1999-09-15)
With increasing use of proteins in many different applications, ranging from phramaceuticals to biosensors and biomaterials, there has emerged a need for protein structural characterisation in diverse environments. In many cases it is not sufficient to just have the three-dimensional structure of a protein in H2O or in the crystalline state. Often information on the structural properties of a protein is required in the presence of organic solvents, detergent micelles, phospholipid membranes and so on. Fouri...
CXCL16 influences the nature and specificity of CpG-induced immune activation.
Gürsel, Mayda; Mostowski, HS; Klinman, DM (2006-08-01)
Unmethylated CpG motifs are present at high frequency in bacterial DNA. They provide a danger signal to the mammalian immune system that triggers a protective immune response characterized by the production of Th1 and proinflammatory cytokines and chemokines. Although the recognition of CpG DNA by B cells and plasmacytoid dendritic cells is mediated by TLR 9, these cell types differ in their ability to bind and respond to structurally distinct classes of CpG oligonucleotides. This work establishes that CXCL...
Enzyme prediction with word embedding approach
Akın, Erkan; Atalay, M. Volkan.; Department of Computer Engineering (2019)
Information such as molecular function, biological process, and cellular localization can be inferred from the protein sequence. However, protein sequences vary in length. Therefore, the sequence itself cannot be used directly as a feature vector for pattern recognition and machine learning algorithms since these algorithms require fixed length feature vectors. We describe an approach based on the use of the Word2vec model, more specifically continuous skip-gram model to generate the vector representation o...
Citation Formats
A. Tevlek, S. Kecili, O. S. Ozcelik, H. Külah, and H. C. Tekin, “Spheroid Engineering in Microfluidic Devices,” ACS OMEGA, vol. 8, no. 4, pp. 3630–3649, 2023, Accessed: 00, 2023. [Online]. Available: https://hdl.handle.net/11511/102707.