Model systems engineering


An important element of target identification and drug development is the need to build realistic pre-clinical models. These models can serve as valuable assays for the accurate prediction of the physiological responses of compounds in the human body or as surrogate test beds for hypothesis testing and target identification.  MGH investigators strive to become a technical and educational hub for the creation of next-generation models that combine the disciplines of material chemistry, cell engineering, micro/nanotechnology, and imaging. These research programs are structured to design, build, validate, and transfer model systems research in a highly collaborative manner with scientists, physicians, and industry.  Read More

Multiplexed molecular models

Chemical reaction between DNA and molecular capture probe wherein a specific region of DNA is targeted based on sequence-specific information

The collection (or library) of biological molecules found in nature is immense and ever growing with the advent of genome sequencing. One of the major limitations of comprehensively studying a library of biomolecules is that traditional technologies of synthesizing molecules from known DNA sequences is too cumbersome and ineffective for pooled screening. Entire libraries composed of all protein-encoding open reading frames (ORFs) cloned in highly flexible vectors will be needed to take full advantage of the information found in any genome sequence. MGH investigators are developing a number of high-throughput cloning methods for the selective isolation and expression of ORFs from any biological sample (cells, tissue, and blood). These methods allow the rapid capture and parallel cloning of thousands of genes at the same time and is cost-effective. The cloned genes can be expressed as a single functional protein library in one shot, constituting an effective gateway from whole genome sequencing efforts to massive parallel screening of full-length proteins for discovery.

Engineered multi-cellular models

Micro-printed tumor-stroma culture spatially deposited and surrounded by stromal cells. Interfacial interactions (inset) can be precisely controlled and monitored to model cell behavior.

Cell-based in vitro assays are an indispensable part of mechanistic studies as well as high-throughput drug discovery/testing. Unfortunately, conventional single cell models present an artificial environment that has limited relevance to in vivo multi-cellular biology.  MGH investigators seek to develop high-throughput cell screening platforms that control multicellular organizations of cells with the use of genetically engineered cells lines and microfluidic environments.  The research has focused on the tumor microenvironment, where we have developed a microengineered tumor-stromal assay (mTSA) in which the composition and spatial organization of cellular components are precisely controlled and probed using micropatterning and microsurgery techniques.  The investigators have also developed tumor cell models in 3-dimensional spheroids and scaffolds with biomaterial structures that further drive the assays towards predictive, human biological responses. These assay systems have proven useful to industrial partners interested in target identification or drug screening.

Implantable tissue microenvironments

3-D biomaterials with user-defined geometry and porosity are made with a template-based synthesis process to replicate tissue anatomy. These biomaterials have been used to create implantable organoids for modeling.

In vivo testing is a necessary step in evaluating the safety and efficacy of a drug before it enters into human testing.  The laboratory focuses on engineering standardized and functional human tissue models that can advance the predictive power of the pre-clinical studies.  In particular, focus has been placed on lymphoid organs such as the bone marrow, thymus,, spleen, and lymph nodes, which are important organs limited in study because of their anatomical inaccessibility, tissue complexity, and lack of relevant pre-clinical models with good experimental throughput.   MGH investigators have developed implantable models with full control of the cells, 3-dimensional scaffold structure, mechanical properties, and porosity of the tissue construct. These implantable models are designed with the opportunity for image-based analysis and minimally invasive sampling that is essential for assay development. Tissue level function has been validated in these implants that are similar to their natural tissue counterparts.

Relevant publications

Lee J, Wang J, Li M, Milwid JM, Dunham J, Vinegoni C, Gorbatov R, Iwamoto Y, Wang F, Shen K, Ebert B, Weissleder R, Yarmush ML, Parekkadan B. Implantable Microenvironments to Attract Hematopoietic Stem/Cancer Cells. Proc Natl Acad Sci U S A. 2012 109(48):19638-43. PubMed PMID: 23150542; PubMed Central PMCID: PMC3511730

Lee J, Wang JB, Bersani F, Parekkadan B. Capture and printing of fixed stromal cell membrane for bioactive display on PDMS surfaces. Langmuir 2013 Aug 27;29(34):10611-6. PubMed PMID: 23927769; PubMed Central PMCID: PMC3789619

Shen K, Lee J, Yarmush ML, Parekkadan B. Microcavity substrates casted from self-assembled microsphere monolayers for spheroid cell culture. Biomed Microdevices. 2014 Aug;16(4):609-15.  PubMed PMID: 24781882

Shen K, Elman JS, Hicks DF, Bohr S, Luk S, Murray R, Iwamoto Y, Pena K, Milwid JM, Wang F, Seker E, Yarmush ML, Toner M, Sgroi D, Parekkadan B. A Micropatterned tumor stromal assay for identifying drugs targeting cancer-stroma interactions.  Nat Commun. 2014 Dec 9;5:5662. PubMed PMID: 25489927; PubMed Central PMCID: PMC4261930

Bersani F, Lee J, Yu M, Morris R, Desai R, Ramaswamy S, Toner M, Haber DA, Parekkadan B. A model of prostate cancer bone metastasis using tumor capturing scaffolds identifies a role for stromal-derived IL-1 beta. Under review at Cancer Research

Lee J, Kohl N, Shanbhag S, Parekkadan B. Scaffold-integrated microchips for end-to-end tumor cell isolation and xenograft formation. Under review at Lab on Chip


Biju Parekkadan, Ph.D.
Massachusetts General Hospital
Center for Engineering in Medicine
51 Blossom St.
Boston, MA 02114

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andrwkirkModel systems engineering