From The School of Engineering and Applied Science At Yale University And The Karolinska Institute [Karolinska Institutet](SE) Via “phys.org” : “New technology simultaneously maps gene activity and expression”
From The School of Engineering and Applied Science
At
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The Karolinska Institute [Karolinska Institutet](SE)
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3.15.23
Fig. 1: Design and evaluation of spatial epigenome–transcriptome cosequencing with E13 mouse embryo.
a, Schematic workflow. b, Comparison of number of unique fragments and fraction of reads in peaks (FRiP) in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. c, Gene and UMI count distribution in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. Number of pixels in E13, 2,187; in human brain, 2,500; in mouse brain (ATAC), 9,215; in mouse brain (H3K27me3), 9,752; in mouse brain (H3K27ac), 9,370; in mouse brain (H3K4me3), 9,548. Box plots show the median (centre line), the first and third quartiles (box limits) and 1.5× interquartile range (whiskers). d, Spatial distribution and UMAP of all clusters for ATAC, RNA and joint clustering of ATAC and RNA data. Overlay of clusters with the tissue image shows that spatial clusters precisely match anatomic regions. Pixel size, 50 µm; scale bars, 1 mm. e, Spatial mapping of GAS and gene expression for selected marker genes in different clusters for ATAC and RNA in spatial ATAC–RNA-seq. f, Pseudotime analysis from radial glia to postmitotic premature neurons visualized at the spatial level. g, Heatmaps delineating gene expression and GAS for marker genes. h, Dynamic changes in GAS and gene expression across pseudotime.
Fig. 2: Spatial chromatin accessibility and transcriptome co-profiling of P22 mouse brain.
a, Design of microfluidic chips for 100 × 100 barcodes with 20-μm channel size. b, Spatial distribution and UMAP of all clusters for ATAC and RNA in spatial ATAC–RNA-seq of mouse brain. Pixel size, 20 µm; scale bars, 1 mm. c, Integration of ATAC data and scATAC-seq data [30*] from mouse brain. d, Integration of RNA data and scRNA-seq data32 from mouse brain. e, Spatial mapping of GAS and gene expression for selected marker genes in different clusters for ATAC and RNA in spatial ATAC–RNA-seq. A list of abbreviation definitions can be found in Supplementary Table 1.
*Reference in science paper.
For further images see the science paper.
A new study published in Nature [below] reports that a technology known as spatial omics can be used to map simultaneously how genes are switched on and off and how they are expressed in different areas of tissues and organs. This improved technology, developed by researchers at Yale University and Karolinska Institutet, could shed light on the development of tissues, as well as on certain diseases and how to treat them.
Almost all cells in the body have the same set of genes and can in principle become any kind of cell. What distinguishes the cells is how the genes in our DNA are used. In recent years, spatial omics have given us a deeper understanding of how cells read the genome in precise locations in tissues. Now, researchers have further evolved this technology to increase knowledge of how tissues develop and how different diseases arise.
A key part of the study is the researchers’ ability to spatially map simultaneously two crucial components of our genetic makeup, the epigenome and the transcriptome. The epigenome controls the switching mechanisms that turn genes on and off in individual cells, whereas the transcriptome is the result of those gene expressions and what makes each cell unique.
Can detect input and output simultaneously
The epigenome can be thought of as a fuse box. You can flip the switches, but if you can’t see whether the lights are turning on, your information is limited. By spatially mapping both the epigenome and transcriptome, the researchers developed a technology in which both the input (switching on or off a gene) and the output (gene expression) can be detected in the same tissue section. This new technology brings unprecedented insights into gene regulation in precise locations in a tissue.
For this study, the researchers adapted and combined their previously developed techniques to map the epigenome and the transcriptome, and applied these techniques to mouse brains and human brain tissue.
“Now that we can combine the two, we can see both the mechanisms of how the genes are switched on and off, as well as the result,” says Gonçalo Castelo-Branco, professor at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, and one of the corresponding authors. “This has led us to some unexpected observations, which gives us further insights into how these processes are regulated in different tissue areas and contribute to different cell fates.”
Advancing the field of personalized medicine
The work could bring researchers closer to understanding potential genetic targets for drug therapy, and help advance the field of personalized medicine.
“In the future with this technology, we will be able to really understand in every single patient how those cancer-promoting genes and tumor suppressor genes are being regulated by the epigenetic mechanisms,” says Rong Fan, professor at Yale University and last author of the paper. “The whole epigenetic therapeutics field is just emerging, but I think our technology can potentially empower epigenetic drug discovery.”
See the full article here .
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The Karolinska Institute [Karolinska Institutet](SE) sometimes known as the (Royal) Caroline Institute in English is a research-led medical university in Solna within the Stockholm urban area of Sweden. The Karolinska Institute is consistently ranked amongst the world’s best medical schools, ranking 6th worldwide for medicine in 2021. The Nobel Assembly at the Karolinska Institute awards the Nobel Prize in Physiology or Medicine. The assembly consists of fifty professors from various medical disciplines at the university.
The Karolinska Institute was founded in 1810 on the island of Kungsholmen on the west side of Stockholm; the main campus was relocated decades later to Solna, just outside Stockholm. A second campus was established more recently in Flemingsberg, Huddinge, south of Stockholm.
The Karolinska Institute is Sweden’s third oldest medical school, after Uppsala University[Uppsala universitet](SE) (founded in 1477) and The Lund University [Lunds universitet](SE) (founded in 1666). It is one of Sweden’s largest centres for training and research, accounting for 30% of the medical training and more than 40% of all academic medical and life science research conducted in Sweden.
The Karolinska University Hospital, located in Solna and Huddinge, is associated with the university as a research and teaching hospital. Together they form an academic health science centre. While most of the medical programs are taught in Swedish, the bulk of the PhD projects are conducted in English. The institute’s name is a reference to the Caroleans.
Yale School of Engineering and Applied Science Daniel L Malone Engineering Center
The Yale School of Engineering & Applied Science is the engineering school of Yale University. When the first professor of civil engineering was hired in 1852, a Yale School of Engineering was established within the Yale Scientific School, and in 1932 the engineering faculty organized as a separate, constituent school of the university. The school currently offers undergraduate and graduate classes and degrees in electrical engineering, chemical engineering, computer science, applied physics, environmental engineering, biomedical engineering, and mechanical engineering and materials science.
Yale University is a private Ivy League research university in New Haven, Connecticut. Founded in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and one of the nine Colonial Colleges chartered before the American Revolution. The Collegiate School was renamed Yale College in 1718 to honor the school’s largest private benefactor for the first century of its existence, Elihu Yale. Yale University is consistently ranked as one of the top universities and is considered one of the most prestigious in the nation.
Chartered by Connecticut Colony, the Collegiate School was established in 1701 by clergy to educate Congregational ministers before moving to New Haven in 1716. Originally restricted to theology and sacred languages, the curriculum began to incorporate humanities and sciences by the time of the American Revolution. In the 19th century, the college expanded into graduate and professional instruction, awarding the first PhD in the United States in 1861 and organizing as a university in 1887. Yale’s faculty and student populations grew after 1890 with rapid expansion of the physical campus and scientific research.
Yale is organized into fourteen constituent schools: the original undergraduate college, the Yale Graduate School of Arts and Sciences and twelve professional schools. While the university is governed by the Yale Corporation, each school’s faculty oversees its curriculum and degree programs. In addition to a central campus in downtown New Haven, the university owns athletic facilities in western New Haven, a campus in West Haven, Connecticut, and forests and nature preserves throughout New England. As of June 2020, the university’s endowment was valued at $31.1 billion, the second largest of any educational institution. The Yale University Library, serving all constituent schools, holds more than 15 million volumes and is the third-largest academic library in the United States. Students compete in intercollegiate sports as the Yale Bulldogs in the NCAA Division I – Ivy League.
As of October 2020, 65 Nobel laureates, five Fields Medalists, four Abel Prize laureates, and three Turing award winners have been affiliated with Yale University. In addition, Yale has graduated many notable alumni, including five U.S. Presidents, 19 U.S. Supreme Court Justices, 31 living billionaires, and many heads of state. Hundreds of members of Congress and many U.S. diplomats, 78 MacArthur Fellows, 252 Rhodes Scholars, 123 Marshall Scholars, and nine Mitchell Scholars have been affiliated with the university.
Research
Yale is a member of the Association of American Universities (AAU) and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation, Yale spent $990 million on research and development in 2018, ranking it 15th in the nation.
Yale’s faculty include 61 members of the National Academy of Sciences , 7 members of the National Academy of Engineering and 49 members of the American Academy of Arts and Sciences. The college is, after normalization for institution size, the tenth-largest baccalaureate source of doctoral degree recipients in the United States, and the largest such source within the Ivy League.
Yale’s English and Comparative Literature departments were part of the New Criticism movement. Of the New Critics, Robert Penn Warren, W.K. Wimsatt, and Cleanth Brooks were all Yale faculty. Later, the Yale Comparative literature department became a center of American deconstruction. Jacques Derrida, the father of deconstruction, taught at the Department of Comparative Literature from the late seventies to mid-1980s. Several other Yale faculty members were also associated with deconstruction, forming the so-called “Yale School”. These included Paul de Man who taught in the Departments of Comparative Literature and French, J. Hillis Miller, Geoffrey Hartman (both taught in the Departments of English and Comparative Literature), and Harold Bloom (English), whose theoretical position was always somewhat specific, and who ultimately took a very different path from the rest of this group. Yale’s history department has also originated important intellectual trends. Historians C. Vann Woodward and David Brion Davis are credited with beginning in the 1960s and 1970s an important stream of southern historians; likewise, David Montgomery, a labor historian, advised many of the current generation of labor historians in the country. Yale’s Music School and Department fostered the growth of Music Theory in the latter half of the 20th century. The Journal of Music Theory was founded there in 1957; Allen Forte and David Lewin were influential teachers and scholars.
In addition to eminent faculty members, Yale research relies heavily on the presence of roughly 1200 Postdocs from various national and international origin working in the multiple laboratories in the sciences, social sciences, humanities, and professional schools of the university. The university progressively recognized this working force with the recent creation of the Office for Postdoctoral Affairs and the Yale Postdoctoral Association.
Notable alumni
Over its history, Yale has produced many distinguished alumni in a variety of fields, ranging from the public to private sector. According to 2020 data, around 71% of undergraduates join the workforce, while the next largest majority of 16.6% go on to attend graduate or professional schools. Yale graduates have been recipients of 252 Rhodes Scholarships, 123 Marshall Scholarships, 67 Truman Scholarships, 21 Churchill Scholarships, and 9 Mitchell Scholarships. The university is also the second largest producer of Fulbright Scholars, with a total of 1,199 in its history and has produced 89 MacArthur Fellows. The U.S. Department of State Bureau of Educational and Cultural Affairs ranked Yale fifth among research institutions producing the most 2020–2021 Fulbright Scholars. Additionally, 31 living billionaires are Yale alumni.
At Yale, one of the most popular undergraduate majors among Juniors and Seniors is political science, with many students going on to serve careers in government and politics. Former presidents who attended Yale for undergrad include William Howard Taft, George H. W. Bush, and George W. Bush while former presidents Gerald Ford and Bill Clinton attended Yale Law School. Former vice-president and influential antebellum era politician John C. Calhoun also graduated from Yale. Former world leaders include Italian prime minister Mario Monti, Turkish prime minister Tansu Çiller, Mexican president Ernesto Zedillo, German president Karl Carstens, Philippine president José Paciano Laurel, Latvian president Valdis Zatlers, Taiwanese premier Jiang Yi-huah, and Malawian president Peter Mutharika, among others. Prominent royals who graduated are Crown Princess Victoria of Sweden, and Olympia Bonaparte, Princess Napoléon.
Yale alumni have had considerable presence in U.S. government in all three branches. On the U.S. Supreme Court, 19 justices have been Yale alumni, including current Associate Justices Sonia Sotomayor, Samuel Alito, Clarence Thomas, and Brett Kavanaugh. Numerous Yale alumni have been U.S. Senators, including current Senators Michael Bennet, Richard Blumenthal, Cory Booker, Sherrod Brown, Chris Coons, Amy Klobuchar, Ben Sasse, and Sheldon Whitehouse. Current and former cabinet members include Secretaries of State John Kerry, Hillary Clinton, Cyrus Vance, and Dean Acheson; U.S. Secretaries of the Treasury Oliver Wolcott, Robert Rubin, Nicholas F. Brady, Steven Mnuchin, and Janet Yellen; U.S. Attorneys General Nicholas Katzenbach, John Ashcroft, and Edward H. Levi; and many others. Peace Corps founder and American diplomat Sargent Shriver and public official and urban planner Robert Moses are Yale alumni.
Yale has produced numerous award-winning authors and influential writers, like Nobel Prize in Literature laureate Sinclair Lewis and Pulitzer Prize winners Stephen Vincent Benét, Thornton Wilder, Doug Wright, and David McCullough. Academy Award winning actors, actresses, and directors include Jodie Foster, Paul Newman, Meryl Streep, Elia Kazan, George Roy Hill, Lupita Nyong’o, Oliver Stone, and Frances McDormand. Alumni from Yale have also made notable contributions to both music and the arts. Leading American composer from the 20th century Charles Ives, Broadway composer Cole Porter, Grammy award winner David Lang, and award-winning jazz pianist and composer Vijay Iyer all hail from Yale. Hugo Boss Prize winner Matthew Barney, famed American sculptor Richard Serra, President Barack Obama presidential portrait painter Kehinde Wiley, MacArthur Fellow and contemporary artist Sarah Sze, Pulitzer Prize winning cartoonist Garry Trudeau, and National Medal of Arts photorealist painter Chuck Close all graduated from Yale. Additional alumni include architect and Presidential Medal of Freedom winner Maya Lin, Pritzker Prize winner Norman Foster, and Gateway Arch designer Eero Saarinen. Journalists and pundits include Dick Cavett, Chris Cuomo, Anderson Cooper, William F. Buckley, Jr., and Fareed Zakaria.
In business, Yale has had numerous alumni and former students go on to become founders of influential business, like William Boeing (Boeing, United Airlines), Briton Hadden and Henry Luce (Time Magazine), Stephen A. Schwarzman (Blackstone Group), Frederick W. Smith (FedEx), Juan Trippe (Pan Am), Harold Stanley (Morgan Stanley), Bing Gordon (Electronic Arts), and Ben Silbermann (Pinterest). Other business people from Yale include former chairman and CEO of Sears Holdings Edward Lampert, former Time Warner president Jeffrey Bewkes, former PepsiCo chairperson and CEO Indra Nooyi, sports agent Donald Dell, and investor/philanthropist Sir John Templeton,
Yale alumni distinguished in academia include literary critic and historian Henry Louis Gates, economists Irving Fischer, Mahbub ul Haq, and Nobel Prize laureate Paul Krugman; Nobel Prize in Physics laureates Ernest Lawrence and Murray Gell-Mann; Fields Medalist John G. Thompson; Human Genome Project leader and National Institutes of Health director Francis S. Collins; brain surgery pioneer Harvey Cushing; pioneering computer scientist Grace Hopper; influential mathematician and chemist Josiah Willard Gibbs; National Women’s Hall of Fame inductee and biochemist Florence B. Seibert; Turing Award recipient Ron Rivest; inventors Samuel F.B. Morse and Eli Whitney; Nobel Prize in Chemistry laureate John B. Goodenough; lexicographer Noah Webster; and theologians Jonathan Edwards and Reinhold Niebuhr.
In the sporting arena, Yale alumni include baseball players Ron Darling and Craig Breslow and baseball executives Theo Epstein and George Weiss; football players Calvin Hill, Gary Fenick, Amos Alonzo Stagg, and “the Father of American Football” Walter Camp; ice hockey players Chris Higgins and Olympian Helen Resor; Olympic figure skaters Sarah Hughes and Nathan Chen; nine-time U.S. Squash men’s champion Julian Illingworth; Olympic swimmer Don Schollander; Olympic rowers Josh West and Rusty Wailes; Olympic sailor Stuart McNay; Olympic runner Frank Shorter; and others.
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