The world’s first mouse “perturbation map” decodes gene function

“The human genome has long been sequenced, but its function is still hidden, which seriously hinders the diagnosis and treatment of diseases.” Chi Tian, a professor at the School of Life Sciences at ShanghaiTech University, said, “The important task of biomedicine in the 21st century is to decode the ‘mysterious book’ of the human genome. ”

On July 22, Chi Tian’s team published a paper online in Cell, reporting a new mouse gene targeting technology, iMAP, and quickly identified the basic functions of 90 genes in 39 tissues, constructing the world’s first mouse miniature “perturbation map”. This gene decoding technology provides a powerful weapon for cracking the code of the human genome.


iMAP principle Courtesy of the interviewee

Revolutionary iMAP

“iMAP blends Cre-loxP and CRISPR-Cas9 technologies.” Chi Tian said, “Through drug induction, 100 genes can be knocked out throughout the mouse body, but each cell can only randomly knock out one, thus transforming mice into mosaic organisms.” ”

Wild-type animals have the same genome for each cell, and chimeras are made up of cells carrying different genomes. iMAP chimeras can be used to quickly map the basic functions of 100 target genes in various cells throughout the body, and can also derive 100 traditional single gene knockout strains through simple mating and reproduction, thereby greatly reducing the preparation cost of the latter.

As a proof of concept, Chi Tian’s team examined the effects of 90 gene knockouts on the survival, expansion, or cell differentiation of 39 organs/tissues/cells, and mapped the world’s first “perturbation map.” Although this atlas is only a prototype of the whole genome atlas, it has provided a wealth of valuable information that is difficult to obtain easily with other techniques, and has laid the foundation for depicting the whole genome atlas.

At present, Aviv Regev, a leader in single-cell biology, has launched the “Single Cell Perturbation Atlas Project” with Chi Tian, preparing to unite multiple laboratories around the world to use iMAP to map the perturbation maps of all 20,000 protein-coding genes in mice in tissues throughout the body at the single-cell level.

“This atlas will be an important milestone in the history of biomedical research – after that, exploring the basic functions of any gene in mice will be as simple as finding a gene sequence, rather than spending years of painstaking effort.” Chi Tian said.

The atlas will be a watershed in biomedical research, and in addition to identifying the function of protein-coding genes, iMAP can also be used to decode any other sequences in the genome, explore “old drugs for new uses” and screen drug targets. iMAP also has the potential to be extended to other model organisms; Some rice experts have planned to use iMAP to improve rice varieties. A congratulatory letter from an internationally renowned immunologist at Yale University to Chi Tian’s team predicted that “iMAP will change many fields.”

Eight years of science “marathon”

iMAP is powerful, but behind its birth is a scientific “marathon” that has lasted for eight years and has been the efforts of six students.

Chi Tian was still at Yale In 2014, when CRISPR gene editing technology was available and Chi Tian was familiar with Cre-loxP. He had a whim and tried to fuse the two technologies, but his colleagues weren’t optimistic. “Some people are dismissive, some people call crazy, most of them are suspicious.” Chi Tian recalled, “This is not surprising, because iMAP is too new, it is 0 to 1, and there is no mainstream technology that can be directly benchmarked.” Just like the concept of PCR after the embryonic, even after the initial results came out, it is still coldly received within Cetus, which seems incredible, but it is not difficult to understand. ”

The development process of iMAP is full of hardships and twists and turns. “We stepped on a lot of pits, and some of them were weird.” In order to prevent peers from repeating the mistakes of the past, some of these failed experiments were published in preprints two years ago. Through the efforts of Ravinder Kaundal (postdoctoral fellow at Yale University) and Chen Yuxin, Mao Shaoshuai, and Liu Bo (2014, 2015, and 2016 graduate students of the School of Life Sciences of Shanghai University of Science and Technology, respectively), when Jing Zhengyu, a doctoral student of the class of 2018, joined the research group, the dawn finally dawned, but the road was still bumpy. “There is very little literature to refer to in our research work, and we encountered various difficulties during the research period, but fortunately we succeeded in the end.” Jing Zhengyu recalled.

Liu Bo, a 2016 doctoral student who graduated this year and led Jing Zhengyu and Zhang Xiaoming, a 2019 doctoral student, said, “The success of the project is inseparable from Mr. Chi’s overall planning and careful planning, and it is also inseparable from the unity and hard work of the members of the laboratory. “In addition to the students being very powerful, the strong support of the school also makes Chi Tian’s research very successful.”

“I started several other high-stakes projects like iMAP at Yale, but they all died for financial reasons. Shanghai HKUST encouraged professors to have the courage to sit on the cold bench, and Nobel Laureate James Rothman also said that Shanghai HKUST was suitable for me. Chi Tian added, “Therefore, I instruct students that the topic must be done to the end, and the paper will not be published unless it is published.” ”

The iMAP development process is “high mountains and long pits”, but the review process is quite smooth. The paper was submitted on February 15 this year, received feedback on March 10, completed the experiment at the end of the month, and the paper was “accepted in principle” on May 12 and officially accepted on June 21. In the more than a month from the “acceptance in principle” of the paper to the formal acceptance, the team repeatedly revised and polished the paper at the request of the journal editor, trying to clearly show the revolutionary side of iMAP.

“The editor is very dedicated and self-written to rewrite the article, which is very rare.” Chi Tian said. The editorial board also invited Aviv Regev to write a Preview for iMAP to be published at the same time as the paper, but due to time conflicts, it was finally decided to write a long review of the article, which will be published in November this year.


Chi Tian (back row, third from right) team Courtesy of the interviewee

To “be able to sit on the cold bench”

“Waiting for the flowers to bloom sometimes, don’t envy the results of others, I believe that the premise of every flower blooming is that you have planted the seeds in advance.” Liu Bo shared his scientific research insights in this way.

In the challenging life of scientific research, Jing Zhengyu summed up his doctoral career: “Not only did I learn how to solve a problem, but I found that scientific research itself is really a very interesting thing!” Although the process is always accompanied by many failures and setbacks, there is always something to be gained after maintaining passion and investing enough time. ”

For Zhang Xiaoming, the process of experimentation is more important than the results, “solving problems, constantly simplifying the process, and establishing a new system… In the process, I feel the improvement of my ability, which is what I have been pursuing.”

“The sword blade comes out of the grinding, and the plum blossom fragrance comes from the bitter cold.” Chen Yuxin very much misses the time when the team worked together to overcome scientific research problems – Teacher Chi Tian’s adventurous spirit and exploration spirit, the research team was not afraid of difficulties, and worked together, which eventually contributed to the birth of iMAP. “In addition, I have a big gain: how to face failure after failure without losing confidence; How to find the way to the dawn and proactively solve problems in the face of constant failure, while still living and working with hope. Chen Yuxin said.

“Did Iron Man, can afford to sit on the cold bench.” Chi Tian quoted Jiang Mianheng, president of Shanghai University of Science and Technology, as saying to the new students of the first batch of graduate students of Shanghai University of Science and Technology, “Eight years of one sword proves that we can ‘sit on the cold bench’.” Shanghai University of Science and Technology has excellent double gene, so we also have the hope of ‘doing Iron Man’, sword fighting the disease, and benefiting mankind.” (Source: China Science Daily, Zhang Shuanghu, Huang Xin)

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