February 1, 2023

STAMPScreen Pipeline: Taking the Guesswork Out of Genetic Engineering

Frustration is the mom of creation
Chatterjee and Christian Kramme, a co-first author of the paper, were irritated. The two scientists were attempting to check out the hereditary foundations of different aspects of biology– like resistance, fertility, and aging– by integrating the strengths of digital approaches (believe algorithms) and genetic modification (think gene sequencing). But they kept encountering issues with the numerous tools and procedures they were utilizing, which are prevalent in science labs.
The algorithms that supposed to sift through an organisms genes to recognize those with a substantial impact on an offered biological procedure might tell when a genes expression pattern altered, but didnt provide any insight into the cause of that change. When they desired to check a list of prospect genes in living cells, it wasnt instantly clear what kind of experiment they need to run. And a lot of the tools readily available to place genes into cells and evaluate them were expensive, time-consuming, and inflexible.
Co-first author of the paper, Christian Kramme, at his bench at the Wyss Institute. Credit: Wyss Institute at Harvard University
” I was using methods understood as Golden Gate and Gateway to clone genes into vectors for screening experiments, and it took me months and countless dollars to clone 50 genes. And utilizing Gateway, I couldnt physically barcode the genes to recognize which one entered which vector, which was a vital requirement for my downstream sequencing-based experimental design. We figured there had to be a much better way to do this type of research, and when we could not discover one, we took on the difficulty of creating it ourselves,” said Kramme, who is a college student at the Wyss Institute and HMS,
Kramme partnered with co-first author and fellow Church laboratory member Alexandru Plesa, who was experiencing identical frustrations making gene vectors for his project. Kramme, Plesa, and Chatterjee then set to work detailing what would be required to make an end-to-end platform for genetic screening that would work for all of their tasks, which varied from protein engineering to fertility and aging.
From bits to the bench
To improve the earliest phase of hereditary research– recognizing genes of interest to study– the team created two brand-new algorithms to help satisfy the need for computational tools that can draw out and examine info from the significantly large datasets that are being generated through next-generation sequencing (NGS). The first algorithm takes the basic information about a genes expression level and integrates it with information about the state of the cell, along with information about which proteins are understood to communicate with the gene. The algorithm provides a high score to genes that are extremely connected to other genes and whose activity is associated with large, cell-level changes. The 2nd algorithm supplies more high-level insight by generating networks to represent the dynamic modifications in gene expression throughout cell-type distinction and after that applying midpoint measures, such as Googles PageRank algorithm, to rank the essential regulators of the process.
MegaGate, a novel method for cloning target genes of interest into vectors, is far more effective at producing successful gene-bearing vectors (left) than other existing methods like Gateway (ideal). Credit: Wyss Institute at Harvard University
” The computational part of hereditary research studies resembles a Jenga video game: if each block in the tower represents a gene, were looking for the genes that make up the base of the Jenga tower, the ones that hold the entire thing up. The majority of algorithms can just inform you which genes are in the same row as each other, but ours permit you to house in on how far up or down the tower they are, so you can rapidly recognize the ones that have the biggest impact on the cell state in question,” stated Chatterjee.
When the target genes have actually been recognized, the STAMPScreen procedure moves from the laptop to the lab, where experiments are carried out to interfere with those genes in cells and see what effect that perturbation has on the cell. The team of scientists methodically examined multiple gene perturbation tools including complementary DNA (cDNA) and numerous variations of CRISPR in human induced pluripotent stem cells (hiPSCs), the very first known head-to-head comparisons carried out completely in this highly flexible yet tough cell type.
They then developed a new tool that allows CRISPR and cDNA to be used within the same cell to unlock synergies between the 2 techniques. For example, CRISPR can be utilized to shut off expression of all isoforms of a gene, and cDNA can be utilized to sequentially express each isoform separately, allowing more nuanced genetic studies and significantly reducing background expression of off-target genes.
Scanning library barcodes
Generally, gene fragments are inserted into bacterial plasmids (circular pieces of DNA) utilizing methods that work well for small pieces of DNA, but are cumbersome to use when inserting larger genes. Numerous of the existing approaches likewise rely on a method called Gateway, which utilizes a procedure called lambda phage recombination and the production of a contaminant to eliminate off any germs that did not get a plasmid with the gene of interest.
Meganuclease recognition series do not appear in the genes of any known organism, thus guaranteeing that the enzyme will not unintentionally cut the placed gene itself during cloning. Any plasmids that do not effectively receive the gene of interest, nevertheless, keep these recognition series and are cut to pieces when a meganuclease is included, leaving only a pure swimming pool of plasmids containing the inserted gene.
“MegaGate not only fixes much of the issues that we kept running into with older cloning techniques, it is also compatible with lots of existing gene libraries like the TFome and hORFeome. You can basically take Gateway and meganucleases off the rack, put them together with a library of genes and a library of barcoded location vectors, and 2 hours later on you have your barcoded genes of interest. Weve cloned almost 1,500 genes with it, and have yet to have a failure,” said Plesa, who is a college student at the Wyss Institute and HMS.
Lastly, the scientists showed that their barcoded vectors might be effectively inserted into living hiPSCs, and swimming pools of cells could be evaluated utilizing NGS to identify which delivered genes were being revealed by the pool. They likewise effectively utilized a variety of approaches, including RNA-Seq, TAR-Seq, and Barcode-Seq, to read both the hereditary barcodes and the entire transcriptomes of hiPSCs, making it possible for researchers to use whichever tool they are most knowledgeable about.
The group prepares for that STAMPScreen could show helpful for a wide array of research studies, including path and gene regulatory network studies, distinction factor screening, drug and complex pathway characterizations, and anomaly modeling. STAMPScreen is likewise modular, permitting researchers to incorporate various parts of it into their own workflows.
“Theres a gold mine of details housed in openly available hereditary datasets, but that information will only be comprehended if we utilize the right tools and techniques to analyze it. STAMPScreen will help scientists get to eureka moments faster and speed up the speed of innovation in genetic engineering,” stated senior author George Church, Ph.D., a Wyss Core Faculty member who is also a Professor of Genetics at HMS and Professor of Health Sciences and Technology at Harvard and MIT.
“At the Wyss Institute we aim for impactful moonshot solutions to pressing problems, however we understand that to get to the moon, we have to very first build a rocket. This job is an excellent example of how our neighborhood innovates on-the-fly to make it possible for clinical advancements that will alter the world for the better,” said Wyss Founding Director Don Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at HMS and the Vascular Biology Program at Boston Childrens Hospital, as well as Professor of Bioengineering at Harvard John A. Paulson School of Engineering and Applied Sciences.
Referral: “An Integrated Pipeline for Mammalian Genetic Screening” 27 September 2021, Cell Reports Methods.
Additional authors of the paper consist of Helen Wang, Bennett Wolf, Merrick Smela, Xiaoge Guo, Ph.D., and Richie Kohman, Ph.D. from the Wyss Institute and HMS.

Todays genetic engineers have a myriad of resources at their disposal: an ever-increasing number of massive datasets readily available online, highly precise gene editing tools like CRISPR, and inexpensive gene sequencing techniques. The STAMPScreen workflow is an integrated pipeline that permits scientists to quickly and quickly evaluate an experimental database for potential genes of interest (1 ), choose which screening tool to use (2 ), develop a screening library (3 ), and utilize next-generation sequencing to screen genes in vivo (4 ).” I was using techniques understood as Golden Gate and Gateway to clone genes into vectors for evaluating experiments, and it took me months and thousands of dollars to clone 50 genes. The very first algorithm takes the basic data about a genes expression level and combines it with information about the state of the cell, as well as information about which proteins are understood to communicate with the gene. Typically, gene fragments are inserted into bacterial plasmids (circular pieces of DNA) utilizing methods that work well for small pieces of DNA, but are cumbersome to use when placing bigger genes.

Mammalian cells that have been successfully genetically crafted utilizing the STAMPScreen method. Credit: Wyss Institute at Harvard University
STAMPScreen Pipeline Helps Streamline Genetic Studies in Mammalian Cells
Todays hereditary engineers have a plethora of resources at their disposal: an ever-increasing variety of enormous datasets available online, extremely exact gene modifying tools like CRISPR, and inexpensive gene sequencing approaches. The expansion of brand-new technologies has not come with a clear roadmap to help researchers figure out which genes to target, which tools to use, and how to interpret their outcomes. A group of scientists and engineers at Harvards Wyss Institute for Biologically Inspired Engineering, Harvard Medical School (HMS), and the MIT Media Lab decided to make one.
The Wyss team has developed an integrated pipeline for performing genetic screening research studies, encompassing every step of the procedure from identifying target genes of interest to cloning and evaluating them rapidly and efficiently. The protocol, called Sequencing-based Target Ascertainment and Modular Perturbation Screening (STAMPScreen), is described in Cell Reports Methods, and the associated open-source algorithms are available on GitHub.
The STAMPScreen workflow is an integrated pipeline that enables researchers to quickly and easily evaluate a speculative database for prospective genes of interest (1 ), choose which screening tool to use (2 ), produce a screening library (3 ), and use next-generation sequencing to screen genes in vivo (4 ). The specific actions can likewise be used in other workflows. Credit: Wyss Institute at Harvard University
” STAMPScreen is a structured workflow that makes it simple for scientists to identify genes of interest and carry out genetic screens without having to guess which tool to utilize or what experiments to perform to get the outcomes they want,” said corresponding author Pranam Chatterjee, Ph.D., a previous college student at the MIT Media Lab who is now the Carlos M. Varsavsky Research Fellow at HMS and the Wyss Institute. “It is totally compatible with numerous existing systems and databases, and we hope that many scientists are able to make the most of STAMPScreen to conserve themselves time and improve the quality of their outcomes.”

By Wyss Institute for Biologically Inspired Engineering at Harvard
September 27, 2021

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