Category Archives: Embryonic Stem Cells


Leading innovators in cell therapy for ocular disorders for the … – Pharmaceutical Technology

The pharmaceutical industry continues to be a hotbed of innovation, with activity driven by the evolution of new treatment paradigms, and the gravity of unmet needs, as well as the growing importance of technologies such as pharmacogenomics, digital therapeutics, and artificial intelligence. In the last three years alone, there have been over 633,000 patents filed and granted in the pharmaceutical industry, according to GlobalDatas report on Innovation in Pharmaceuticals: Cell therapy for ocular disorders.

However, not all innovations are equal and nor do they follow a constant upward trend. Instead, their evolution takes the form of an S-shaped curve that reflects their typical lifecycle from early emergence to accelerating adoption, before finally stabilising and reaching maturity.

Identifying where a particular innovation is on this journey, especially those that are in the emerging and accelerating stages, is essential for understanding their current level of adoption and the likely future trajectory and impact they will have.

110 innovations will shape the pharmaceutical industry

According to GlobalDatas Technology Foresights, which plots the S-curve for the pharmaceutical industry using innovation intensity models built on over 756,000 patents, there are 110 innovation areas that will shape the future of the industry.

Within the emerging innovation stage, cell therapy for ocular disorders, coronavirus vaccine components, and DNA polymerase compositions are disruptive technologies that are in the early stages of application and should be tracked closely. Adeno-associated virus vectors, alcohol dehydrogenase compositions, and antibody serum stabilisers are some of the accelerating innovation areas, where adoption has been steadily increasing. Among maturing innovation areas are anti-influenza antibody compositions and anti-interleukin-1, which are now well established in the industry.

Innovation S-curve for the pharmaceutical industry

Cell therapy for ocular disorders is a key innovation area in pharmaceuticals

Stem cells have the capacity to revive degenerated cells or replace cells. Various cell types have been used as the source of therapeutic cells, including human embryonic stem cells (hESCs), induced pluripotent stem cells (iPSCs), and human umbilical tissue-derived cells (hUTCs). The regeneration, proliferation and differentiation potential of stem cells result in therapeutic intervention in different kinds of eye disease, including age-related macular degeneration (AMD), inherited retinal diseases (IRDs), glaucoma, and corneal diseases.

GlobalDatas analysis also uncovers the companies at the forefront of each innovation area and assesses the potential reach and impact of their patenting activity across different applications and geographies. According to GlobalData, there are 30+ companies, spanning technology vendors, established pharmaceutical companies, and up-and-coming start-ups engaged in the development and application of cell therapy for ocular disorders.

Key players in cell therapy for ocular disorders a disruptive innovation in the pharmaceutical industry

Application diversity measures the number of different applications identified for each relevant patent and broadly splits companies into either niche or diversified innovators.

Geographic reach refers to the number of different countries each relevant patent is registered in and reflects the breadth of geographic application intended, ranging from global to local.

Senju Pharmaceutical is the leading patent holder of cell therapies for ocular disorders. The company has filed a number of patents covering various cell therapies for the treatment of ophthalmic disorders. One notable patent is a miR-203 inhibitor for corneal epithelial disorder.

In terms of application diversity, Acro Biomedical is the top company, followed by Daiichi Sankyo, and Mayo Clinic. By means of geographic reach, Intellia Therapeutics holds the top position, while HLB Co Ltd, and Mayo Clinic stand in second and third positions, respectively.

To further understand the key themes and technologies disrupting the pharmaceutical industry, access GlobalDatas latest thematic research report on Pharmaceutical.

Get industry leading news, data and analysis delivered to your inbox

GlobalData, the leading provider of industry intelligence, provided the underlying data, research, and analysis used to produce this article.

GlobalDatas Patent Analytics tracks patent filings and grants from official offices around the world. Textual analysis and official patent classifications are used to group patents into key thematic areas and link them to specific companies across the worlds largest industries.

Originally posted here:
Leading innovators in cell therapy for ocular disorders for the ... - Pharmaceutical Technology

The Future of Fertility Technology, From Technosemen to Uterine … – The MIT Press Reader

How will future generations come to be? There is no straightforward answer.

Fertility technology is an area of intense interest, in which scientists continue to push the boundaries of a human bodys capability to generate the matter that will produce a healthy, living child. It is, unsurprisingly, an area of rapid scientific and technological research so much so that regulatory bodies across the world have difficulty keeping up-to-date with the latest developments in order to regulate their use properly.

The following excerpt from the conclusion of Fertility Technology describes some of the methods that scientists and for-profit companies are testing and offering to patients and clients who are willing to try (and to fund, often at great expense) cutting-edge but unproven techniques to raise their chances of having a baby. This excerpt also draws attention to individuals who need extra assistance with conceiving but for financial, health, or ethical reasons do not want to engage with the latest techniques. Some techniques that were available in the 19th century, like artificial insemination, still can work backed by updated forms of medical technologies. There is no lack of attention to this area of scientific and technological development, from prospective parents, from scientists, from sperm and egg banks, from international transit companies, from potential donors, from ethicists and indeed from anyone engaged in questions of how humans will appear in the future.

The health of sperm remains an important area of diagnostic concern. Among a host of other issues, low sperm count, low motility, and sperm antibodies (proteins that damage or kill sperm) are all sources of infertility. Sperm health is difficult to treat, but some workarounds for those with at least some healthy sperm do exist. These include testicular sperm extraction and testicular sperm aspiration, using high-powered needles and delicate microsurgical instruments. Physicians can also perform testicular mapping, where they use fine-needle aspiration to try to find pockets of sperm production in the testes.

In addition to technologies that can help manifest pregnancy, the gametes, or reproductive cells, themselves can be thought of as technologies. This is true of technosemen, or semen that has undergone laboratory manipulation to be suited especially for intra-cytoplasmic sperm injection (ICSI), where a single healthy sperm is injected directly into each mature egg, and IVF, where an egg is combined with sperm in vitro. Researchers Matthew Schmidt and Lisa Jean Moore have called it the new and improved bodily product that semen banks advertise to clients. The methods for technosemen manipulation are various. The swim-up method, for example, involves centrifuging the semen sample, removing the seminal fluid, and placing the remaining sperm pellet in an artificial insemination medium, and then collecting the most active semen, which swim to the top of the solution. Another method is Percoll washing, which involves layering the semen with a cleansing solution and centrifuging it for half an hour.

Washed technosemen is perceived as healthier and more potent than natural, unmanipulated semen.

The ability to manipulate and to choose the best semen affects how clinics view their donors, their donations, and the children who might result from them. For example, in advertising materials for the Danish company Cryos, semen is solely described in light of the technology involved, writes researcher Charlotte Krolkke. Traces of the matter are reworked into sophisticated technology, beautiful children and indeed and not surprisingly happy, healthy, potent donors. This view that semen is a technoscientific product, not a body product, likewise manifests in China, where the countrys Ministry of Health established specific requirements for technosemen under national law from 2001 to 2003. The Ministry requires a concentration standard of 60 million sperm cells per milliliter, which is four times higher than the World Health Organizations criteria for normal male fertility, according to anthropologist Ayo Wahlberg, who published a detailed study of sperm-banking in China. A range of technologies of assurance quantify spermatic quality not only according to sperm per milliliter, but also motility grades, percentages of normal morphology, and milligrams of fructose per milliliter. Then, only the best sperm is used to make the best quality children.

The ability to test spermatic health is a means of managing the effects of environmental pollution on the next generation as well. In cities like Wuhan, one study found, semen donated on days with high levels of air pollution showed lower sperm count and concentration than semen donated on days with lower levels of air pollution. Washed technosemen is perceived as healthier and more potent than natural, unmanipulated semen. (Whether it leads to healthier children is much harder to discern.) Sperm banks can then make claims about the potency of their products, while at the same time making claims as to the naturalness of new reproductive technologies, writes Lisa Jean Moore in her book Sperm Counts. These constructions suggest that new reproductive technologies are not unnatural but rather an improvement upon the inherent unpredictability of natural procreation. In other words, the best semen is not natural; it is processed and refined through technology.

Like many areas of medicine, reproductive medicine attracts inventors and entrepreneurs. Some of their solutions may provide valid diagnostic information or improve chances of pregnancy but are not yet tested or approved by medical regulatory bodies. Some can be added to standard IVF treatments or are offered as part of comprehensive fertility medicine packages that may not be necessary for all patients. These add-ons can be problematic, as IVF patients may not be adequately informed about the benefits and risk of IVF add-ons or may not be aware of the paucity of supportive evidence for safety and effectiveness, according to findings from a recent survey. As navigating the world of add-ons may be confusing even for knowledgeable clients, some countries regulatory bodies provide guidance. The UKs Human Fertilisation and Embryology Authority (HFEA) publishes a traffic-light system, which rates add-ons according to available cost implications, risks, and evidence. A green light indicates that a treatment has shown positive results according to at least one randomized control study, an amber light indicates mixed results, and a red light indicates no positive results. Reviews of add-ons available since 2015 show their overall limited benefit and potential unknown harms to patients.

A survey taken in June and July 2020 showed that up to 24 add-ons were available at clinics across Australia, many of which mirrored those available in the UK. They ranged from mild and complementary (aspirin, acupuncture) to loosely linked (melatonin) to highly technological (assisted hatching). Another review of 10 add-ons, from screening hysteroscopy (examination of the uterus under anesthesia) to androgen supplements, found either that they had no effect on implantation or live birth rates or that there was insufficient data to support such a claim. A third review of five add-ons solely for the endometrium (mucus membrane lining the uterus) showed that their effects ranged from unclear (vasodilators such as sildenafil [Viagra] to thicken the endometrium) to harmful (endometrial scratching, which inflames the endometrium and might make the embryo more likely to implant). These reviews caution that profit may motivate clinics to provide costly IVF add-ons with no evidence base.

One of the add-ons that has received the most attention from scholars and fertility medicine specialists is time-lapse imaging, and as such, it is valuable to examine its implications in detail. Time-lapse imaging of embryos from fertilization to three days afterward (for double embryo transfer) to five days afterward (for single embryo transfer) is designed to help embryologists choose the healthiest possible embryo for implantation. Time-lapse imaging technologies, explains Lucy van de Wiel in her exploration of the world of egg freezing, allow for continuous observation by taking photographs every 5 to 20 minutes while the embryos remain in the incubator. . . . By matching the videos with growth patterns of embryos that developed into healthy fetuses, the time-lapse system suggests which embryos are most likely to grow into a baby. The time-lapse systems film the developing embryos and quantify the visual information onto grids, and then clinicians must have specialized training in algorithmic analysis to predict each ones likelihood of turning into a blastocyst, or a fertilized egg. These systems, called EmbryoScope (manufactured by Vitrolife) and Eeva (short for Early Embryo Viability Assessment, manufactured by Merck), depend on past selections to predict future embryo viability. In a May 2019 survey of fertility clinic websites in the United Kingdom, time-lapse imaging costs an average of 478 as a stand-alone treatment and an average of 4,020 as part of a treatment package. The systems themselves cost clinics 75,00080,000.

Reviews caution that profit may motivate clinics to provide costly IVF add-ons with no evidence base.

Time-lapse imaging alters more than just the process of embryo selection. As van de Wiel writes, by matching the embryos cellular growth patterns to previous embryonic populations recorded developmental rhythms, time-lapse technology brings embryonic aging to the forefront in embryo selection. Time-lapse imaging turns embryo selection into a new, data-driven way of seeing using automated pattern recognition and algorithmic predictive analysis. This process not only changes how laboratory technicians and embryologists see and choose embryos for implantation, but it also changes how a prospective parent or parents see their embryos: Ranking means that the woman or couple has a quantified sense of the blastocysts potential for development, researcher Catherine Waldby points out.

HFEA gives time-lapse imaging an amber light, as being undisturbed while they grow may improve the quality of the embryos but theres certainly not enough evidence to show that time-lapse incubation and imaging is effective at improving your chance of having a baby. Before getting a green light from HFEA and other national regulatory agencies, time-lapse imaging needs more proof to support Vitrolifes and Mercks claims that their products improve embryo selection. In general, inventors and suppliers of new add-ons may be pursuing not only patient satisfaction and profit but also the satisfaction of developing an IVF breakthrough technology to improve implantation and live-birth success rates markedly.

Another high-technology method currently being developed involves obtaining functional gametes from either human embryonic stem cells or induced pluripotent stem cells, which are derived from skin or blood cells, and the use of mitochondrial DNA from a donor egg to manifest so-called three-parent embryos. For the latter, women with healthy mitochondrial histories are asked to donate their eggs to women with family histories of disease, and the recipients nuclear genetic material is transferred to the healthy egg, explains Waldby. This enables the recipient to conceive a child who is genetically her own, if the terms of genetics are limited to nuclear DNA. The embryo is then the product of three peoples gametes, containing the nuclear DNA of the intending parents and the mitochondrial DNA of an egg donor. The UKs Human Fertilisation and Embryology Act (1990) was amended in 2015 to legalize this procedure, called MDNA transplantation; the United Kingdom is the only country that permits it.

The procedure is intended to help women with mitochondrial disorders often undetectable in preimplantation genetic testing (PGT) avoid passing those disorders onto potential children, and to ensure that those children are their genetic offspring. Unfortunately for the further acceptance of this procedure, one study found, most maternally inherited mitochondrial disorders only develop in adulthood, whereas mitochondrial disorders that severely affect babies are caused, in approximately 80% of cases, by nuclear defects that are inherited from both parents. In other words, replacing mitochondrial DNA alone cannot prevent diseases inherited from both parents, and the procedure helps only in the 20 percent of diseases that are only inherited maternally. The procedure also carries further risks:

[1] the potential side-effects caused by the co-existence of two different types of mitochondria within the embryos cytoplasm, including the possible carry-over of pathogenic mtDNA; [2] the possible defects caused by mismatching the nuclear and mitochondrial genomes, such as metabolic dysfunction and epigenetics effects; and [3] the social and psychological consequences of having been conceived using genetic material from three people.

Access to the procedure is heavily restricted, and disorders can often be found in gametes more easily and cost-efficiently using an older diagnosis method, PGT. The ethical considerations of procedures like IVM and MDNA leave many open questions about their use, especially if more problems with them are identified and more countries legalize them.

Another significant technological step is IVF in persons with transplanted uteri. The first modern attempt at a uterine transplant alone took place in Saudi Arabia in 2000. The first IVF procedure in a transplanted uterus from a live donor that resulted in a live birth happened 14 years later in Gothenburg, Sweden. The first live birth via IVF in a uterine transplant in the United States occurred in 2017, and the IVF-transplant procedure has resulted in 70 uterine transfers with 14 live births worldwide as of June 2021. Uterine transplants have been a focus of reproductive medical attention in the last two decades. If the transplant is successful, the donated uterus is removed after a certain period of time and number of successful IVF pregnancies a number that the patient would determine.

The IVF-transplant procedure has resulted in 70 uterine transfers with 14 live births worldwide as of June 2021.

Uterine transplantation is an intricate procedure, involving immunosuppressant drug regimens, the risk of organ rejection, the possible development of a thrombosis, and other complications. Connecting the blood vessels of the donated uterus to those in the recipients body is particularly tricky. But there are many other steps before the transplant and IVF can begin. On the practical side, there is no uterine donation registry, so in the case of live donation, the person without a uterus must ask a prospective donor for theirs (or the prospective donor must offer). Transplantation from a nondirected (anonymous) living donor or a deceased donor is also possible, though familial donors with identical blood types lower the risk of rejection. For some studies, prospective transplant recipients must secure their own donor. Interviews with 10 uterus-seekers in Sweden described how they reached out to their mothers as well as older sisters or aunts, raising the possibility that they could gestate a child using the same uterus in which they themselves were gestated. The emotional intricacy of asking (and possibly receiving) an organ donation in this situation is obvious.

Familial complexities aside, IVF in uterine transplants sparks the possibility of gestating pregnancies outside the human body completely in artificial wombs (ectogenesis). Research on human ectogenesis is still illegal in the United Kingdom, but animal research has been in progress there since the early 1960s. For humans, writes legal scholar Amel Alghrani, technology that can mimic the functions of the maternal uterus can help save the lives of extremely premature babies born on the cusp of viability. . . . Such technology can also help women who suffer from uterus factor infertility and thus are unable to gestate their own child. Research is underway in Sweden (by the same team that facilitated the first uterine transplant) to create a viable bioengineered uterus, including artificial amniotic fluid and an artificial endometrium. A bioengineered uterus could also be used for part of a pregnancy; for example, gestation could begin in the human womb, with the fetus transferred later to the artificial one. Successful human ectogenesis, whether wholly or partially gestated in an artificial uterus, could open up a new world of possibilities of reproduction.

Farther in the future is in vitro gametogenesis (IVG), the creation of gametes using pluripotent stem cells (cells that can differentiate into many cell types). If a patient cannot provide gametes for an assisted reproduction treatment, IVG could create gametes from their skin cells. Artificial gametes, writes Alghrani in her book on regulating assisted reproductive technologies, raise one of the most dramatic possibilities that two men (and maybe also two women) could create a baby that is genetically related [to] both of them, in the same way as men and women. Artificial gametes widen procreative possibilities for those unable to reproduce via traditional methods of sexual reproduction. As a result, a couple of any gender could provide all the gametes needed to produce an embryo that is genetically related to both of them.

Of course, child-seekers will continue to use less advanced technologies alongside technologies that require advanced medical assistance and infrastructures. Technologies and methods with historical longevity, such as fertility calendars and home-based insemination, will coexist alongside advances in high-technology methods. Home-based insemination persists especially in countries where access to assisted reproductive technologies is restricted or illegal for some identity groups (usually gay, trans, non-binary, and lesbian individuals). They may find assistance in printed or Internet guides to doing so, which originate in the feminist womens health movements of the 1970s. Lesbian insemination guidebooks have been in print since 1979, and syringes, cannulas, cervical caps or diaphragms, eye droppers, and jars are available to anyone who purchases them from a medical supply store or online.

People who want fertility assistance, but on their own terms, choose methods that do not violate their own boundaries. They develop hybrid-technology practices, as Laura Mamo of the Health Equity Institute calls them, or practices of borrowing from both high- and low-tech methods according to their own health and preferences. Whether its through ovulation timing, smartphone apps, or smart jewelry, individuals and couples have a range of options for charting their own journeys through the fertility landscape as long as they have the time, patience, finances, and good health to do so.

A history of fertility technologies can only hint at the vastly complex ways that the desire for children affects the lives of individuals, couples, communities, and nations. The technologies that make pregnancy possible for some people are a source of disappointment for others. They are means of giving certain embryos a chance to develop as persons in the world, but also a means of keeping other embryos and potential persons out of the world. Fertility technologies are much more than a way to address reproductive health problems or simply a medical procedure to cure a medically described condition, as Sandra P. Gonzlez-Santos reminds us. They are a tool through which people create people. How they will develop next and what kinds of human life will emerge as a result of using them remains to be seen.

Donna J. Drucker is Assistant Director of Scholarship and Research Development at the Columbia University School of Nursing. She is the author of The Classification of Sex: Alfred Kinsey and the Organization of Knowledge, The Machines of Sex Research: Technology and the Politics of Identity, 19451985, Contraception: A Concise History, and Fertility Technology, from which this article is adapted.

Follow this link:
The Future of Fertility Technology, From Technosemen to Uterine ... - The MIT Press Reader

Recent advances in CRISPR-based genome editing technology and … – Military Medical Research

Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096.

Article PubMed Google Scholar

Doudna JA. The promise and challenge of therapeutic genome editing. Nature. 2020;578(7794):22936.

Article CAS PubMed PubMed Central Google Scholar

Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell. 2022;82(2):34888.

Article CAS PubMed PubMed Central Google Scholar

Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014;157(6):126278.

Article CAS PubMed PubMed Central Google Scholar

Komor AC, Badran AH, Liu DR. CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell. 2017;169(3):559.

Article CAS PubMed Google Scholar

Knott GJ, Doudna JA. CRISPR-Cas guides the future of genetic engineering. Science. 2018;361(6405):8669.

Article CAS PubMed PubMed Central Google Scholar

Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, et al. Gene editing and its applications in biomedicine. Sci China Life Sci. 2022;65(4):660700.

Article CAS PubMed PubMed Central Google Scholar

Yang X. Applications of CRISPR-Cas9 mediated genome engineering. Mil Med Res. 2015;2:11.

PubMed PubMed Central Google Scholar

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):81923.

Article CAS PubMed PubMed Central Google Scholar

Liu G, Lin Q, Jin S, Gao C. The CRISPR-Cas toolbox and gene editing technologies. Mol Cell. 2022;82(2):33347.

Article CAS PubMed Google Scholar

Pickar-Oliver A, Gersbach CA. The next generation of CRISPR-Cas technologies and applications. Nat Rev Mol Cell Biol. 2019;20(8):490507.

Article CAS PubMed PubMed Central Google Scholar

Porteus MH. A new class of medicines through DNA editing. N Engl J Med. 2019;380(10):94759.

Article CAS PubMed Google Scholar

Yeh CD, Richardson CD, Corn JE. Advances in genome editing through control of DNA repair pathways. Nat Cell Biol. 2019;21(12):146878.

Article CAS PubMed Google Scholar

Clark JF, Dinsmore CJ, Soriano P. A most formidable arsenal: genetic technologies for building a better mouse. Genes Dev. 2020;34(1920):125686.

Article CAS PubMed PubMed Central Google Scholar

Nishiga M, Liu C, Qi LS, Wu JC. The use of new CRISPR tools in cardiovascular research and medicine. Nat Rev Cardiol. 2022;19(8):50521.

Article CAS PubMed Google Scholar

Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):4204.

Article CAS PubMed PubMed Central Google Scholar

Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, et al. Programmable base editing of AT to GC in genomic DNA without DNA cleavage. Nature. 2017;551(7681):46471.

Article CAS PubMed PubMed Central Google Scholar

Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576(7785):14957.

Article CAS PubMed PubMed Central Google Scholar

Watkins WS, Hernandez EJ, Wesolowski S, Bisgrove BW, Sunderland RT, Lin E, et al. De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes. Nat Commun. 2019;10(1):4722.

Article PubMed PubMed Central Google Scholar

Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, Depalma SR, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet. 2017;49(11):1593601.

Article CAS PubMed PubMed Central Google Scholar

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13(11):72236.

Article CAS PubMed PubMed Central Google Scholar

Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, et al. Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR-Cas. Mol Cell. 2019;74(5):936-50.e5.

Article CAS PubMed PubMed Central Google Scholar

Morisaka H, Yoshimi K, Okuzaki Y, Gee P, Kunihiro Y, Sonpho E, et al. CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nat Commun. 2019;10(1):5302.

Article CAS PubMed PubMed Central Google Scholar

Osakabe K, Wada N, Murakami E, Miyashita N, Osakabe Y. Genome editing in mammalian cells using the CRISPR type I-D nuclease. Nucleic Acids Res. 2021;49(11):634763.

Article CAS PubMed PubMed Central Google Scholar

Tan R, Krueger RK, Gramelspacher MJ, Zhou X, Xiao Y, Ke A, et al. Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems. Mol Cell. 2022;82(4):852-67.e5.

Article CAS PubMed PubMed Central Google Scholar

Liu TY, Doudna JA. Chemistry of class 1 CRISPR-Cas effectors: binding, editing, and regulation. J Biol Chem. 2020;295(42):1447387.

Article CAS PubMed PubMed Central Google Scholar

Altae-Tran H, Kannan S, Demircioglu FE, Oshiro R, Nety SP, Mckay LJ, et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science. 2021;374(6563):5765.

Article CAS PubMed PubMed Central Google Scholar

Karvelis T, Druteika G, Bigelyte G, Budre K, Zedaveinyte R, Silanskas A, et al. Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature. 2021;599(7886):6926.

Article CAS PubMed PubMed Central Google Scholar

Schuler G, Hu C, Ke A. Structural basis for RNA-guided DNA cleavage by IscB-RNA and mechanistic comparison with Cas9. Science. 2022;376(6600):147681.

Article CAS PubMed Google Scholar

Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 2015;520(7546):18691.

Article CAS PubMed PubMed Central Google Scholar

Hou Z, Zhang Y, Propson NE, Howden SE, Chu LF, Sontheimer EJ, et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A. 2013;110(39):156449.

Article CAS PubMed PubMed Central Google Scholar

Kim E, Koo T, Park SW, Kim D, Kim K, Cho HY, et al. In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nat Commun. 2017;8:14500.

Article CAS PubMed PubMed Central Google Scholar

Edraki A, Mir A, Ibraheim R, Gainetdinov I, Yoon Y, Song CQ, et al. A compact, high-accuracy Cas9 with a dinucleotide PAM for in vivo genome editing. Mol Cell. 2019;73(4):714-26 e4.

Article CAS PubMed Google Scholar

Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature. 2019;566(7743):21823.

Article CAS PubMed PubMed Central Google Scholar

Kim DY, Lee JM, Moon SB, Chin HJ, Park S, Lim Y, et al. Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus. Nat Biotechnol. 2022;40(1):94102.

Article CAS PubMed Google Scholar

Wu Z, Zhang Y, Yu H, Pan D, Wang Y, Wang Y, et al. Programmed genome editing by a miniature CRISPR-Cas12f nuclease. Nat Chem Biol. 2021;17(11):11328.

Article CAS PubMed Google Scholar

Xu X, Chemparathy A, Zeng L, Kempton HR, Shang S, Nakamura M, et al. Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing. Mol Cell. 2021;81(20):4333-45.e4

Article CAS PubMed Google Scholar

Pausch P, Al-Shayeb B, Bisom-Rapp E, Tsuchida CA, Li Z, Cress BF, et al. CRISPR-Cas from huge phages is a hypercompact genome editor. Science. 2020;369(6501):3337.

Article CAS PubMed PubMed Central Google Scholar

Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, et al. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell. 2022;185(24):4574-86.e16.

Article CAS PubMed Google Scholar

Collias D, Beisel CL. CRISPR technologies and the search for the PAM-free nuclease. Nat Commun. 2021;12(1):555.

Article CAS PubMed PubMed Central Google Scholar

Miller SM, Wang T, Randolph PB, Arbab M, Shen MW, Huang TP, et al. Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nat Biotechnol. 2020;38(4):47181.

Article CAS PubMed PubMed Central Google Scholar

Walton RT, Christie KA, Whittaker MN, Kleinstiver BP. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020;368(6488):2906.

Article CAS PubMed PubMed Central Google Scholar

Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, et al. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019;37(3):27682.

Article CAS PubMed PubMed Central Google Scholar

Tth E, Varga , Kulcsr PI, Kocsis-Jutka V, Krausz SL, Nyeste A, et al. Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases. Nucleic Acids Res. 2020;48(7):372233.

Article PubMed PubMed Central Google Scholar

Chatterjee P, Jakimo N, Lee J, Amrani N, Rodriguez T, Koseki SRT, et al. An engineered ScCas9 with broad PAM range and high specificity and activity. Nat Biotechnol. 2020;38(10):11548.

Article CAS PubMed Google Scholar

Chatterjee P, Lee J, Nip L, Koseki SRT, Tysinger E, Sontheimer EJ, et al. A Cas9 with PAM recognition for adenine dinucleotides. Nat Commun. 2020;11(1):2474.

Article CAS PubMed PubMed Central Google Scholar

Ma D, Xu Z, Zhang Z, Chen X, Zeng X, Zhang Y, et al. Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information. Nat Commun. 2019;10(1):560.

Article CAS PubMed PubMed Central Google Scholar

Liu RM, Liang LL, Freed E, Chang H, Oh E, Liu ZY, et al. Synthetic chimeric nucleases function for efficient genome editing. Nat Commun. 2019;10(1):5524.

Article CAS PubMed PubMed Central Google Scholar

Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science. 2016;351(6268):848.

Article CAS PubMed Google Scholar

Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature. 2016;529(7587):4905.

Article CAS PubMed PubMed Central Google Scholar

Read more:
Recent advances in CRISPR-based genome editing technology and ... - Military Medical Research

Iron & the brain: Where and when neurodevelopmental disabilities … – URMC

Study finds possible cellular origin for impairments associated with gestational iron deficiency

The cells that make up the human brain begin developing long before the physical shape of the brain has formed. This early organizing of a network of cells plays a major role in brain health throughout the course of a lifetime. Numerous studies have found that mothers with low iron levels during pregnancy have a higher risk of giving birth to a child that develops cognitive impairments like autism, attention deficit syndrome, and learning disabilities. However, iron deficiency is still prevalent in pregnant mothers and young children.

The mechanisms by which gestational iron deficiency (GID) contributes to cognitive impairment are not fully understood.The laboratory of Margot Mayer- Proschel, PhD, a professor ofBiomedical GeneticsandNeuroscienceat theUniversity of Rochester Medical Center, was the first todemonstrated that the brains of animals born to iron-deficient mice react abnormally to excitatory brain stimuli, and that iron supplements giving at birth does not restore functional impairment that appears later in life. Most recently, her lab has made a significant progress in the quest to find the cellular origin of the impairment and have identified a new embryonic neuronal progenitor cell target for GID. This study was recently published in the journalDevelopment.

We are very excited by this finding, Mayer-Proschel said, who was awarded a$2 million grant from the National Institute of Child Health & Human Development in 2018to do this work. This could connect gestational iron deficiency to these very complex disorders. Understanding that connection could lead to changes to healthcare recommendations and potential targets for future therapies.

Michael Rudy, PhD, and Garrick Salois, who were both graduate students in the lab and co-first authors of the study, worked backward to make this connection. By looking at the brains of adults and young mice born with known GID, they found disruption of interneurons, cells that control the balance of excitation and inhibition and ensure that the mature brain can respond appropriately to incoming signals. These interneurons are known to develop in a specific region of the embryonic brain called the medial ganglionic eminencewhere specific factors define the fate of early neuronal progenitor cells that then divide, migrate, and mature into neurons that populate the developing cerebral cortex. The researchers found that this specific progenitor cell pool was disrupted in embryonic brains exposed to GID. These findings provide evidence that GID affects the behavior of embryonic progenitor cells causing the creation of a suboptimal network of specialized neurons later in life.

As we looked back, we could identify when the progenitor cells started acting differently in the iron-deficient animals compared to iron normal controls, Mayer-Proschel said. This confirms that the correlation between the cellular change and GID happens in early utero. Translating the timeline to humans would put it in the first three months of gestation before many women know they are pregnant.

Margot Mayer-Proschel

Having identified cellular targets in a mouse model of GID, Neuroscience graduate student Salois in the Mayer-Proschel lab is now establishing a human model of iron deficiency using brain organoidsa mass of cells, in this case that represent a brain. These mini brains that look more like tiny balls that need a microscope to be studied, can be instructed to form specific regions of the ganglionic eminences of the embryonic human brain. With these researchers can mimic the development of the neuronal progenitor cells that are targeted by GID in the mouse.

We believe this model will not only allow us to determine the relevance of our finding in the mouse model for the human system but will also enable us to find new cellular targets for GID that are not even present in mouse models, said Mayer-Proschel. Understanding such cellular targets of this prevalent nutritional deficiency will be imperative to take the steps necessary to make changes to how we think of maternal health. Iron is an important part of that, and the limited impact of iron supplementation after birth makes it necessary to identify alternative approaches,

Additional authors include Janine Cubello, PhD, and Robert Newell at the University of Rochester. This research was supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development at the National Institute of Health, the Toxicology training grant of the Environmental Health Department at the University of Rochester, the New York Stem Cell Training Grant, and the Kilian J. and Caroline F. Schmitt Foundation through the Del Monte Institute for Neuroscience Pilot Program.

See the article here:
Iron & the brain: Where and when neurodevelopmental disabilities ... - URMC

Umbilical Cord Keepsakes Are Going Viral: OB-GYNs Weigh In On … – Scary Mommy

Among the many treasured keepsakes out there to celebrate your little one coming into the world, youre probably aware of the classics: memory books, photo albums, framed hand- and footprints. But if youve been on TikTok lately, you may have noticed a decidedly different kind of keepsake flooding your feed some parents are preserving their umbilical cords as a way to cherish the connection between themselves and their babies, creating a memory they can hold onto for years to come.

If this is the first youre hearing of umbilical cord keepsakes, you likely have some questions. Namely, how does one ask for their umbilical cord? Is it even safe and sanitary to handle it? And how do you transform it into something special, like a heart or a star, especially if youre not particularly crafty or handy?

Granted, if youre being honest, the idea might even make your stomach turn a little especially if youre not a mom whos crunchy enough to have ever considered preserving placental parts for any reason. Thats understandable. But in learning a little more about why certain parents opt for this very intimate art form, you might be surprised to find that you sort of see the appeal. Or, at the very least, you understand why they see the appeal.

The first thing that might pop into your head is, Huh, I didnt even really know people were allowed to keep their umbilical cord. But yep, thats a thing people can (and often) do. Scary Mommy asked two OB-GYNs about the protocol here, and they explained you can certainly ask your obstetrician or someone on your delivery care team to hold onto the umbilical cord. If youre adopting or working with a surrogate, you can also ask the birth mom or gestational carrier for it as well. Most hospitals have policies and processes for patients to request to keep their placentas, which would include the umbilical cord. Its not a very common request, but it does happen, explains Staci Tanouye, MD FACOG.

Still, its not exactly the type of thing you can handle willy-nilly, as caring for an umbilical cord requires some pretty measured safety precautions you will not want to skimp on. Wearing gloves is essential, and Kim Langdon, MD, an OB-GYN with Medzino, explains that parents can request a section of the umbilical cord, placed in a plastic bag, rinsed clear of blood and debris, and refrigerated or have it placed in a desiccator, a specialized sealable container or package that prevents moisture from developing within.

Hospital staff can help ensure that all safety measures are adhered to, with Tanouye adding, As long as its not being ingested and it can be fully dehydrated so it doesnt grow mold, I dont see a safety problem with keeping a portion of the umbilical cord. The biggest precaution is ensuring it is fully dehydrated and dried to minimize the risk of it developing mold.

Bringing it home is only half the adventure, and youre likely also wondering how the heck to transform it into a work of art. Thats where artists like Casey Merrell of uCord Keepsakes can help. Merrell has created umbilical cord keepsakes for parents for more than seven years, working closely with families every step of the way.

Merrell recommends asking someone you trust (dads, doula, birth partners, or another family member) to keep track of the umbilical cord, as things can get chaotic in the hustle and bustle of labor and delivery. She adds that legally, your healthcare provider or birth facility cannot prevent you from taking home the placenta (which includes the umbilical cord), and it is your right to keep it. Depending on the policies of your provider/facility, you may be required to sign a release form or liability form in order to keep your umbilical cord, she adds.

Working with a placenta specialist like Merrell is your best bet for a seamless, stress-free, and safe process: A trained professional is going to be trained/certified in bloodborne pathogens, storage, and sanitation guidelines. Merrell only works with one cord at a time to prevent cross-contamination or any other mix-ups. A professional will also wear all needed PPE and all safety procedures are followed, including supplies sanitized and disposed of between each client, she says. Giving it to a friend or family member might mean theyre dehydrating your cord in a personal kitchen near foodborne items, pets and kids, or other non-trained people, leading to a host of potential mishaps.

Merrell notes that each cord is unique, requiring different preservation methods, and the amount of equipment required often means its cheaper and easier to work with a trained professional. At UCord Keepsakes, it costs $149 total, so by the time you gather a dehydrator, payment paper, finishing/sealing materials, gloves/other PPEs, cutting supplies, sanitation supplies, display box, etc., youll likely be over that price point, she says.

A trained placenta specialist can also create a truly unique work of art, with Merrell noting that some cords are long enough to spell out words like love or the babys name or initials. Metallic gold and rose gold options are most popular for finishing, but some moms like to leave them with a clear coating so you can visibly see the vessels that attach mom/baby.

If youre easily grossed out by bodily fluids and the like, your initial reaction might still be, well, grossed out. But before you brand umbilical cord keepsakes as a ridiculous idea, consider this: It helps some people cope with the grief of losing a child.

Merrell, a mom of four living children and a sleeping little boy, is passionate about providing the service, especially to those who have experienced a stillbirth or infant loss and would like a tangible memory of their angel baby. Most cords do work, but both doctors note some instances in which a parent will not be able to keep the umbilical cord after delivery.

If the cord or placenta is abnormal in any way or was the cause of fetal distress, if there was suspicion of an infection, then you probably wouldn't be allowed to have a section until it had been analyzed by the lab or pathologist, says Langdon, with Tanouye adding that some complications during pregnancy or childbirth (like an infection) might prevent parents from taking it home. In Merrells experience, this is rare, and most parents are able to bring it home without issue.

One final tip, per Langdon: Make sure you collect the cord blood before you cut a section of the cord for future storage as embryonic stem cells, if that is something you plan to do. Otherwise, youll likely get the green light to preserve such this link between you and your little one if thats something that speaks to you. If not, just remember before you bash it... it is very meaningful to some parents.

View original post here:
Umbilical Cord Keepsakes Are Going Viral: OB-GYNs Weigh In On ... - Scary Mommy

Solnica-Krezel honored for contributions to developmental biology … – Washington University School of Medicine in St. Louis

Visit the News Hub

Scientist to receive Conklin Medal for work in vertebrate embryonic development

Solnica-Krezel

Lilianna Solnica-Krezel, PhD, the Alan A. and Edith L. Wolff Distinguished Professor and head of the Department of Developmental Biology at Washington University School of Medicine in St. Louis, is to receive the 2023 Edwin G. Conklin Medal from the Society for Developmental Biology. She is being recognized for her significant contributions to the understanding of early embryonic development in vertebrates, with a particular focus on zebrafish as a model organism.

The society awards the Edwin G. Conklin Medal in Developmental Biology annually to recognize developmental biologists who have made extraordinary research contributions to the field and are excellent mentors helping to train the next generation of scientists. Solnica-Krezel will receive the honor in July at the societys annual meeting in Chicago, where she will deliver a lecture.

Studying zebrafish, Solnica-Krezel and her team are focused on understanding the earliest stages of development, when different tissues first arise and are arranged into the body plan. Her team also works with human stem cells to test whether the same processes are relevant in people. The research has implications for understanding miscarriage, birth defects and cancer.

Read the original:
Solnica-Krezel honored for contributions to developmental biology ... - Washington University School of Medicine in St. Louis

An old model with new insights: endogenous retroviruses drive the … – Nature.com

Maenner MJ, Shaw KA, Bakian AV, Bilder DA, Durkin MS, Esler A, et al. Prevalence and characteristics of autism spectrum disorder among children aged 8 years - autism and developmental disabilities monitoring network, 11 sites, United States, 2018. Morbidity Mortal Wkly Rep. 2021;70:116.

Google Scholar

Bourgeron T. From the genetic architecture to synaptic plasticity in autism spectrum disorder. Nat Rev Neurosci. 2015;16:55163.

Article CAS PubMed Google Scholar

Geschwind DH. Genetics of autism spectrum disorders. Trends Cogn Sci. 2011;15:40916.

Article PubMed PubMed Central Google Scholar

Rylaarsdam L, Guemez-Gamboa A. Genetic causes and modifiers of autism spectrum disorder. Front Cell Neurosci. 2019;13:385.

Article CAS PubMed PubMed Central Google Scholar

Takumi T, Tamada K. CNV biology in neurodevelopmental disorders. Curr Opin Neurobiol. 2018;48:18392.

Article CAS PubMed Google Scholar

Moy SS, Nadler JJ, Young NB, Perez A, Holloway LP, Barbaro RP, et al. Mouse behavioral tasks relevant to autism: phenotypes of 10 inbred strains. Behav Brain Res. 2007;176:420.

Article PubMed Google Scholar

Silverman JL, Yang M, Lord C, Crawley JN. Behavioural phenotyping assays for mouse models of autism. Nat Rev Neurosci. 2010;11:490502.

Article CAS PubMed PubMed Central Google Scholar

Bolivar VJ, Walters SR, Phoenix JL. Assessing autism-like behavior in mice: variations in social interactions among inbred strains. Behav Brain Res. 2007;176:216.

Article PubMed Google Scholar

Lin CW, Septyaningtrias DE, Chao HW, Konda M, Atarashi K, Takeshita K, et al. A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model. Mol Psychiatry. 2022;27:334354.

RBRC01206 - BTBRTF/ArtRbrc - RIKEN Bioresource Research Center[online] https://knowledge.brc.riken.jp/resource/animal/card?__lang__=en&brc_no=RBRC01206.

002282 - BTBR T<+> Itpr3/J - The Jackson Laboratory [online] https://www.jax.org/strain/002282.

Kishimoto K, Nomura J, Ellegood J, Fukumoto K, Lerch JP, Moreno-De-Luca D, et al. Behavioral and neuroanatomical analyses in a genetic mouse model of 2q13 duplication. Genes Cells. 2017;22:43651.

Article CAS PubMed Google Scholar

de Guzman AE, Wong MD, Gleave JA, Nieman BJ. Variations in post-perfusion immersion fixation and storage alter MRI measurements of mouse brain morphometry. NeuroImage. 2016;142:68795.

Article PubMed Google Scholar

Bock NA, Nieman BJ, Bishop JB, Mark, Henkelman R. In vivo multiple-mouse MRI at 7 Tesla. Magn Reson Med. 2005;54:13116.

Article PubMed Google Scholar

Jones DK, Simmons A, Williams SC, Horsfield MA. Non-invasive assessment of axonal fiber connectivity in the human brain via diffusion tensor MRI. Magn Reson Med. 1999;42:3741.

Article CAS PubMed Google Scholar

Collins DL, Neelin P, Peters TM, Evans AC. Automatic 3D intersubject registration of MR volumetric data in standardized Talairach space. J Comput Assist Tomogr. 1994;18:192205.

Article CAS PubMed Google Scholar

Avants BB, Epstein CL, Grossman M, Gee JC. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal. 2008;12:2641.

Article CAS PubMed Google Scholar

Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC. A reproducible evaluation of ANTs similarity metric performance in brain image registration. NeuroImage. 2011;54:203344.

Article PubMed Google Scholar

Lerch JP, Carroll JB, Dorr A, Spring S, Evans AC, Hayden MR, et al. Cortical thickness measured from MRI in the YAC128 mouse model of Huntingtons disease. NeuroImage. 2008;41:24351.

Article PubMed Google Scholar

Lerch JP, Carroll JB, Spring S, Bertram LN, Schwab C, Hayden MR, et al. Automated deformation analysis in the YAC128 Huntington disease mouse model. NeuroImage. 2008;39:3239.

Article PubMed Google Scholar

Nieman BJ, Flenniken AM, Adamson SL, Henkelman RM, Sled JG. Anatomical phenotyping in the brain and skull of a mutant mouse by magnetic resonance imaging and computed tomography. Physiol Genom. 2006;24:15462.

Article CAS Google Scholar

Dorr AE, Lerch JP, Spring S, Kabani N, Henkelman RM. High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice. NeuroImage. 2008;42:609.

Article CAS PubMed Google Scholar

Steadman PE, Ellegood J, Szulc KU, Turnbull DH, Joyner AL, Henkelman RM, et al. Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas. Autism Res: Off J Int Soc Autism Res. 2014;7:12437.

Article Google Scholar

Ullmann JF, Watson C, Janke AL, Kurniawan ND, Reutens DC. A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex. NeuroImage. 2013;78:196203.

Article PubMed Google Scholar

Genovese CR, Lazar NA, Nichols T. Thresholding of statistical maps in functional neuroimaging using the false discovery rate. NeuroImage. 2002;15:8708.

Article PubMed Google Scholar

Baust C, Gagnier L, Baillie GJ, Harris MJ, Juriloff DM, Mager DL. Structure and expression of mobile ETnII retroelements and their coding-competent MusD relatives in the mouse. J Virol. 2003;77:1144858.

Article CAS PubMed PubMed Central Google Scholar

Vitullo P, Sciamanna I, Baiocchi M, Sinibaldi-Vallebona P, Spadafora C. LINE-1 retrotransposon copies are amplified during murine early embryo development. Mol Reprod Dev. 2012;79:11827.

Article CAS PubMed Google Scholar

Scattoni ML, Gandhy SU, Ricceri L, Crawley JN. Unusual repertoire of vocalizations in the BTBR T+tf/J mouse model of autism. PloS One. 2008;3:e3067.

Article PubMed PubMed Central Google Scholar

Takao K, Tanda K, Nakamura K, Kasahara J, Nakao K, Katsuki M, et al. Comprehensive behavioral analysis of calcium/calmodulin-dependent protein kinase IV knockout mice. PloS One. 2010;5:e9460.

Article PubMed PubMed Central Google Scholar

Yao I, Takao K, Miyakawa T, Ito S, Setou M. Synaptic E3 ligase SCRAPPER in contextual fear conditioning: extensive behavioral phenotyping of Scrapper heterozygote and overexpressing mutant mice. PloS One. 2011;6:e17317.

Article CAS PubMed PubMed Central Google Scholar

Paul LK, Brown WS, Adolphs R, Tyszka JM, Richards LJ, Mukherjee P, et al. Agenesis of the corpus callosum: genetic, developmental and functional aspects of connectivity. Nat Rev Neurosci. 2007;8:28799.

Article CAS PubMed Google Scholar

Khan S, Gramfort A, Shetty NR, Kitzbichler MG, Ganesan S, Moran JM, et al. Local and long-range functional connectivity is reduced in concert in autism spectrum disorders. Proc Natl Acad Sci USA 2013;110:310712.

Article CAS PubMed PubMed Central Google Scholar

Paul LK, Corsello C, Kennedy DP, Adolphs R. Agenesis of the corpus callosum and autism: a comprehensive comparison. Brain: J Neurol. 2014;137:181329.

Article Google Scholar

Yang M, Clarke AM, Crawley JN. Postnatal lesion evidence against a primary role for the corpus callosum in mouse sociability. Eur J Neurosci. 2009;29:166377.

Article PubMed PubMed Central Google Scholar

Stott D, Kispert A, Herrmann BG. Rescue of the tail defect of Brachyury mice. Genes Dev. 1993;7:197203.

Article CAS PubMed Google Scholar

Ellegood J, Babineau BA, Henkelman RM, Lerch JP, Crawley JN. Neuroanatomical analysis of the BTBR mouse model of autism using magnetic resonance imaging and diffusion tensor imaging. NeuroImage. 2013;70:288300.

Article PubMed Google Scholar

Ellegood J, Anagnostou E, Babineau BA, Crawley JN, Lin L, Genestine M, et al. Clustering autism: using neuroanatomical differences in 26 mouse models to gain insight into the heterogeneity. Mol Psychiatry. 2015;20:11825.

Article CAS PubMed Google Scholar

Morcom L, Edwards TJ, Rider E, Jones-Davis D, Lim JW, Chen KS, et al. DRAXIN regulates interhemispheric fissure remodelling to influence the extent of corpus callosum formation. eLife. 2021;10:e61618.

Miura I, Kikkawa Y, Yasuda SP, Shinogi A, Usuda D, Kumar V, et al. Characterization of single nucleotide polymorphisms for a forward genetics approach using genetic crosses in C57BL/6 and BALB/c substrains of mice. Exp Anim. 2022;71:24051.

Zhang C, Clough SJ, Adamah-Biassi EB, Sveinsson MH, Hutchinson AJ, Miura I, et al. Impact of endogenous melatonin on rhythmic behaviors, reproduction, and survival revealed in melatonin-proficient C57BL/6J congenic mice. J Pineal Res. 2021;71:e12748.

Article CAS PubMed Google Scholar

Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K. Evidence of a large-scale functional organization of mammalian chromosomes. PLoS Genet. 2005;1:e33.

Article PubMed PubMed Central Google Scholar

Petkov PM, Ding Y, Cassell MA, Zhang W, Wagner G, Sargent EE, et al. An efficient SNP system for mouse genome scanning and elucidating strain relationships. Genome Res. 2004;14:180611.

Article CAS PubMed PubMed Central Google Scholar

Sultana T, Zamborlini A, Cristofari G, Lesage P. Integration site selection by retroviruses and transposable elements in eukaryotes. Nat Rev Genet. 2017;18:292308.

Article CAS PubMed Google Scholar

Cutler G, Kassner PD. Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease. Cytogenet Genome Res. 2008;123:297306.

Article CAS PubMed Google Scholar

McCarthy EM, McDonald JF. Long terminal repeat retrotransposons of Mus musculus. Genome Biol. 2004;5:R14.

Article PubMed PubMed Central Google Scholar

Beck CR, Garcia-Perez JL, Badge RM, Moran JV. LINE-1 elements in structural variation and disease. Annu Rev Genom Hum Genet. 2011;12:187215.

Article CAS Google Scholar

Campbell IM, Gambin T, Dittwald P, Beck CR, Shuvarikov A, Hixson P, et al. Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination. BMC Biol. 2014;12:74.

Article PubMed PubMed Central Google Scholar

Stocking C, Kozak CA. Murine endogenous retroviruses. Cell Mol Life Sci. 2008;65:338398.

Article CAS PubMed PubMed Central Google Scholar

Cipriani C, Ricceri L, Matteucci C, De Felice A, Tartaglione AM, Argaw-Denboba A, et al. High expression of endogenous retroviruses from intrauterine life to adulthood in two mouse models of autism spectrum disorders. Sci Rep. 2018;8:629.

Article PubMed PubMed Central Google Scholar

Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007;8:27285.

Article CAS PubMed Google Scholar

Kalish BT, Kim E, Finander B, Duffy EE, Kim H, Gilman CK, et al. Maternal immune activation in mice disrupts proteostasis in the fetal brain. Nat Neurosci. 2021;24:20413.

Article CAS PubMed Google Scholar

Schoof M, Wang L, Cogan JZ, Lawrence RE, Boone M, Wuerth JD, et al. Viral evasion of the integrated stress response through antagonism of eIF2-P binding to eIF2B. Nat Commun. 2021;12:7103.

Article CAS PubMed PubMed Central Google Scholar

Li S. Regulation of ribosomal proteins on viral infection. Cells. 2019;8:508.

See the rest here:
An old model with new insights: endogenous retroviruses drive the ... - Nature.com

This stem cell startup is designing a therapy to restore and boost … – The Boston Globe

That bold vision has now attracted personal investments from several local life science leaders, including George Church, the Harvard University geneticist who has founded and advised dozens of biotech companies. Church told Wang a former postdoctoral researcher in his lab that his thymus cell therapy was one of the most exciting ideas hed come across, since it has the potential to impact almost every person on the planet.

Wangs startup recently raised $7 million in seed financing, bringing the total to $13 million, he said. Thymmunes investors include the biotech venture capital firm Pillar VC and NYBC Ventures, the investment arm of the New York Blood Center. Biotech entrepreneurs and investors Mark Bamforth, James Fordyce, John Maraganore, Judy Pagliuca, Philip Reilly, and Mark de Souza pitched in, too.

Maraganore, the former founding chief executive of Alnylam Pharmaceuticals, a genetic medicines company in Cambridge worth more than $23 billion, said he was fascinated by both the near-term and long-term goals of Wangs vision for what thymus cell therapies might do for rare and common conditions alike.

If successful, it could be pretty transformative, Maraganore said. At the end of the day, we all age and die due to our immune system falling apart, and if theres a way to reconstitute it, that would be pretty cool.

Physicians once thought that the thymus, a small gland situated behind the breastbone, between the lungs, and above the heart, was a dispensable organ. But it plays a vital role in developing immunity.

Its job is to basically be the schoolhouse for T cells, those critical cells in your immune system that help you fight everything from pathogens to cancer, Wang said. From a young age, the thymus also teaches T cells about the inventory of molecules normally found in people so that they dont attack their own body and cause an autoimmune disease.

The thymus is perhaps the most important organ youve never heard of. Many folks dont even know it exists, said Thomas de Vlaam, an investor at Pillar VC. If it works well, its unnoticeable, but once it starts failing for whatever reason, the effects are detrimental.

Thymmunes ambitions span the gamut of thymus biology, from replacing missing thymuses to bolstering shrinking ones, and its technology is largely based on work from a group of scientists at the University of California, San Francisco. In 2010, Audrey Parent, a postdoctoral researcher working with UCSF professors Matthias Hebrok and Mark Anderson, was trying to figure out how to make thymus cells in the lab for the first time.

Parent, now an assistant professor at UCSF, said the project involved a lot of trial and error to find a molecular recipe that could turn a stem cell into a thymus cell. There was no recipe to do that at the time, Parent said. We looked at how the embryo does it, we tried to replicate what nature has been doing really successfully, and then transferred that into a recipe that you can do in a dish.

Their results, published in 2013, used human embryonic stem cells to make thymus cells that were transplanted into mice that lacked a thymus. Crucially, the implants allowed the mice to make their own T cells. Thymmune has licensed patents from UCSF, and like many new startups in the stem cell field, it is forgoing difficult-to-source and ethically fraught embryonic stem cells in favor of induced pluripotent stem cells, or iPSCs, which can be made from adult skin cells.

Sometime in the next few years, Wang plans to start a clinical trial in children who are born without a thymus. Its a ticking time bomb where these kids usually dont survive past one or two years, Wang said.

The Food and Drug Administration approved the first therapy for the condition, called congenital athymia, in 2021. Slices of thymus obtained from organ donations, cultured in a lab and surgically implanted into an infants thigh, improved the chances of surviving the otherwise fatal condition to 76 percent after two years. The results there have been fantastic, Wang said. He hopes to replicate them and make an off-the-shelf product that doesnt require organ donations.

If that approach is successful, Wang wants to use his companys thymus cells as a therapy that helps people getting bone marrow or organ transplants recover more quickly and trains their immune systems to not reject the transplant. He also has plans to develop engineered thymus cells that can quell autoimmune diseases by retraining haywire immune cells to stand down and stop attacking the body.

Wangs ultimate vision, and the one thats especially invigorated investors like Church and Maraganore, is to inject thymus cells into aging people to bolster their immune response. To be clear, theres a lot more we need to do before getting to that point, Wang said. But that is the level of aspiration were aiming for. ... We want to provide everyone the opportunity for healthier aging.

Ryan Cross can be reached at ryan.cross@globe.com. Follow him on Twitter @RLCscienceboss.

More:
This stem cell startup is designing a therapy to restore and boost ... - The Boston Globe

How to generate new neurons in the brain – Science Daily

Some areas of the adult brain contain quiescent, or dormant, neural stem cells that can potentially be reactivated to form new neurons. However, the transition from quiescence to proliferation is still poorly understood. A team led by scientists from the Universities of Geneva (UNIGE) and Lausanne (UNIL) has discovered the importance of cell metabolism in this process and identified how to wake up these neural stem cells and reactivate them. Biologists succeeded in increasing the number of new neurons in the brain of adult and even elderly mice. These results, promising for the treatment of neurodegenerative diseases, are to be discovered in the journal Science Advances.

Stem cells have the unique ability to continuously produce copies of themselves and give rise to differentiated cells with more specialized functions. Neural stem cells (NSCs) are responsible for building the brain during embryonic development, generating all the cells of the central nervous system, including neurons.

Neurogenesis capacity decreases with age

Surprisingly, NSCs persist in certain brain regions even after the brain is fully formed and can make new neurons throughout life. This biological phenomenon, called adult neurogenesis, is important for specific functions such as learning and memory processes. However, in the adult brain, these stem cells become more silent or ''dormant'' and reduce their capacity for renewal and differentiation. As a result, neurogenesis decreases significantly with age.The laboratories of Jean-Claude Martinou, Emeritus Professor in the Department of Molecular and Cellular Biology at the UNIGE Faculty of Science, and Marlen Knobloch, Associate Professor in the Department of Biomedical Sciences at the UNIL Faculty of Biology and Medicine, have uncovered a metabolic mechanism by which adult NSCs can emerge from their dormant state and become active.

''We found that mitochondria, the energy-producing organelles within cells, are involved in regulating the level of activation of adult NSCs,'' explains Francesco Petrelli, research fellow at UNIL and co-first author of the study with Valentina Scandella. The mitochondrial pyruvate transporter (MPC), a protein complex discovered eleven years ago in Professor Martinou's group, plays a particular role in this regulation. Its activity influences the metabolic options a cell can use. By knowing the metabolic pathways that distinguish active cells from dormant cells, scientists can wake up dormant cells by modifying their mitochondrial metabolism.

New perspectives

Biologists have blocked MPC activity by using chemical inhibitors or by generating mutant mice for the Mpc1gene. Using these pharmacological and genetic approaches, the scientists were able to activate dormant NSCs and thus generate new neurons in the brains of adult and even aged mice. ''With this work, we show that redirection of metabolic pathways can directly influence the activity state of adult NSCs and consequently the number of new neurons generated,'' summarizes Professor Knobloch, co-lead author of the study. ''These results shed new light on the role of cell metabolism in the regulation of neurogenesis. In the long term, these results could lead to potential treatments for conditions such as depression or neurodegenerative diseases'', concludes Jean-Claude Martinou, co-lead author of the study.

See original here:
How to generate new neurons in the brain - Science Daily

Enhanced mitochondrial biogenesis promotes neuroprotection in … – Nature.com

Reagents and resources

All the reagents including qPCR primers, antibodies, and software used are listed in Supplementary Table1

Human embryonic stem cell (H7-hESCs; WiCell, Madison, WI, https://www.wicell.org) reporter line with CRISPR-engineered multicistronic BRN3B-P2A-tdTomato-P2A-Thy1.2 construct into the endogenous RGC specific BRN3B locus was used for isogenic control20. CRISPR mutated H7-hESC reporter with OPTNE50K-homozygous mutation (H7-E50K) was done as explained previously25. Patient-derived induced pluripotent stem cells (iPSCs) with E50K mutation24 (iPSC-E50K), E50K mutation corrected to WT by CRISPR in the patient-derived iPSC (iPSC-E50Kcorr)25 with BRN3B::tdTomato reporter were obtained from the Jason Meyer lab. All the above cell lines were grown in mTeSR1 media (mT) at 37C in 5% CO2 incubator on matrigel (MG) coated plates. These cells were maintained by clump passaging using Gentle Cell Dissociation Reagent (GD) after 7080% confluency. Media was aspirated and GD was added to cells followed by incubation at 37C in 5% CO2 incubator for 5min. Next, mT was used to break up the colonies into small clumps by repeated pipetting and then seeded onto new MG plates.

For differentiation, stem cells were dissociated to single cells using accutase for 10min and then quenched with twice the volume of mT with 5M blebbistatin (blebb). The cells were centrifuged at 150xg for 6minutes and resuspended in mT with 5M blebb, then 100,000 cells were seeded per well of a 24-well MG coated plate. The next day, media was replaced with mT without blebb. After 24h, media was replaced with differentiation media (iNS) and further small molecule-based differentiation was carried out with iNS media as elucidated previously23. Differentiation of hRGCswas monitored by tdTomato expression and cells were purified during days 4555 using THY1.2 microbeads and magnetic activated cell sorting system (MACS, Miltenyi Biotec) as explained before20,23. Next, hRGCs were resuspended in iNS media, counted using a hemocytometer and seeded on MG-coated plates, coverslips, or MatTek dishes for experiments.

Purified hRGCs were seeded at 30,000 cells per well of a 96-well MG-coated plate and maintained for 3 days. For measuring mitochondrial mass, hRGCs were labeled with mitochondria-specific MTDR dye. To measure mitochondrial degradation, hRGCs were labeled with 10nM MTDR dye for 1h, washed, and then treated with 10M CCCP for a time course. To measure mitochondrial biogenesis, hRGCs were labeled with MTDR first, treated with 10M CCCP or equal amount of DMSO for 3h, then washed and incubated with fresh media with MTDR for the time course. After treatments, hRGCs were dissociated to single-cell suspension using accutase and analyzed using Attune NxT flow cytometer (Thermo Fisher).

Purified hRGCs were seeded at 500,000 cells per well of 24-well MG-coated plates and maintained for 3 days. Cells were then treated with indicated molecules and time points. DMSO was used as the control as the small molecules were dissolved in DMSO. The cells were lysed and collected in 100l of M-PER extraction buffer with 5mM EDTA and protease inhibitors. Protein quantification was done using a BSA standard following the DC Protein Assay Kit II (Bio-Rad) and measured on microplate reader. Loading samples were prepared with heat denaturation at 95C for 5minutes with laemmli sample buffer (1X). 1020g protein per sample were run on Bio-Rad Mini-PROTEAN TGX precast gels, in running buffer (Tris-Glycine-SDS buffer; Bio-Rad) at 100V until the dye front reached to the bottom. The transfer sandwich was made using PVDF membrane (activated in methanol) in Tris-Glycine transfer buffer (Bio-Rad) with 20% methanol and transferred for 2h at 30V, 4C. For the visualization of proteins, the membranes were blocked in 5% skim milk in TBST (TBS buffer with 20% Tween20) for 2h at room temperature and incubated overnight at 4C in 1:1000 dilution of primary antibodies for PGC1 (Abcam), Phospho-PGC1Ser571 (R&D Systems), PGC1 (Abcam), AMPK (Cell Signaling Technologies, CST), Phospho-AMPKThr172 (CST), LC3B (Sigma), GAPDH (CST), or ACTIN (CST). Membranes were then washed three times for 5minutes each in TBST, followed by 2h of incubation in 5% milk in TBST containing anti-rabbit HRP linked secondary antibody (CST) at 1:10,000 dilution. The membranes were again washed three times with TBST and then placed in Clarity Max Western ECL (Bio-Rad) substrate for 5min. The membranes were imaged in a Bio-Rad ChemiDoc Gel Imager, and the raw integrated density for each band was measured and normalized with respect to the corresponding GAPDH or actin loading control using Image J. Treatment conditions were further normalized to the corresponding DMSO control for each experiment. Complete blots of the representative western blot images, with protein molecular weight marker (Thermo Scientific), are provided in Supplementary Fig.6. Protein bands corresponding to the appropriate size were quantified following product datasheets and published literature.

Purified hRGCs were seeded on MG-coated coverslips (1.5 thickness) at a density of 30,00040,000 cells per coverslip and grown for 3 days. Next, hRGCs were treated with indicated molecules and time points. After treatment the media was aspirated, the cells were washed with 1 PBS, and then fixed with 4% Paraformaldehyde for 15min at 37C. Fixed cells were permeabilized with 0.5% Triton-X100 in PBS for 5min and then washed with washing buffer (1% donkey serum, 0.05% Triton-X100 in PBS) three times for 5min each. Cells were blocked with blocking buffer (5% donkey serum, 0.2% Triton-X100 in PBS) for 1h. After blocking, antibodies against TOM20 (Mouse, Santa Cruz), Tubulin 3 (mouse, Biolegend), RBPMS (rabbit, GeneTex) and Optineurin (Rabbit, Cayman Chemicals) were added (1:200 in blocking buffer) and the coverslips were incubated overnight at 4C. Next, coverslips were washed with washing buffer three times for 5min each and incubated for 2h at room temperature in the dark with fluorophore conjugated anti mouse or rabbit secondary antibodies (1:500). The coverslips were washed with washing buffer three times for 5min each, with 1.43M DAPI added to the second wash. The coverslips were then mounted onto slides with DAKO mounting medium. Visualization of above proteins and nucleus was done by confocal immunofluorescence microscopy using Zeiss LSM700 with 63x/1.4 oil objective. Analysis was carried out using ImageJ with maximum projections of DAPI channel (number of nuclei) and sum projections of TOM20 and OPTN channels for the corresponding confocal z-stacks. For OPTN aggregate size, we analyzed particles from 0.02 a.u. to infinity to account for the small and big aggregates.

Purified hRGCs were seeded at 300,000 cells per well of 24-well MG-coated plates and maintained for 3 days. Cells were then treated with indicated molecules and durations. Media was aspirated and cells were incubated in 200l accutase for 10min and then quenched with 400l iNS media. Cells were centrifuged at 150xg for 6min, media aspirated, and the cell pellets were stored at 20C. RNA was extracted from cell pellets following the kit protocol (Qiagen 74104). The RNA concentration was measured using Nanodrop 2000c (Thermo) and 6l of RNA was used to prepare cDNA following the kit protocol (Abm #G492). Primers were designed as detailed in TableS1 and qPCR were performed using BlasTaq qPCR MasterMix with 100ng total cDNA in a 20l reaction mixture using QuantStudio6 Flex RT PCR system (Applied Biosystems). GAPDH or actin was used as a housekeeping gene in every plate to calculate the Ct values. The Ct was calculated with respect to (w.r.t) the average Ct of the control sample. All conditions were measured by averaging three technical repeats for each biological repeat with total three biological replicates.

Purified hRGCs were seeded at 50,00075,000 cells per well of 96-well MG-coated plates and maintained for 3 days. Cells were then treated with indicated molecules for the designated durations. Media was aspirated and cells were incubated in 30l accutase for 10min and then quenched with 100l iNS media. Cells were centrifuged at 150xg for 6min, media aspirated, and the cell pellets were stored at 20C. DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen) and eluted with 30l elution buffer. DNA concentration was measured using Nanodrop 2000c (Thermo). 10ng of DNA was used to measure both mitochondrial ND1 gene and internal control, human nuclear RNase P gene copy numbers, as done previously23.

hRGCs were seeded on MG-coated glass bottom (1.5 thickness)MatTek dishes at 40,000 cells per dish and maintained for 3 days. For the experiments in Fig.2ac, cells were incubated with 250l of JC1 media (1:100 in iNS) for 30min in the incubator, then an additional 1.75ml of dilute JC1 (1:1000 in iNS) was added to the dish. The dish was then transferred to the live cell chamber (5% CO2, 37C, Tokai Hit) and confocal z-stacks were acquired prior to (before) and 10minutes after CCCP (10M) treatment using Zeiss LSM700 with 63x/1.4 oil objective. For experiments in Fig.2df, cells were treated with 10M CCCP or equivalent DMSO for 30min. Next, cells were washed with iNS media, and then incubated with 250l of JC1 media (1:100 in iNS) for 30min in the incubator. The JC1 media was then removed, cells were washed again, and 2ml of new iNS was added to the dish. The dish was then transferred to the live cell chamber and imaged. Analysis was carried out using ImageJ with sum projections of red and green channels. The red fluorescence from the tdTomato expressed by the hRGCs was much less intense than the JC1 red staining of mitochondria, thus the red fluorescence measured from the cytoplasm was considered background and subtracted out of the measurements. For the green fluorescence, background was measured from outside the cell. Red-to-Green ratios were calculated by dividing the red intensity by green intensity. These values were then normalized to the control condition, hRGCWT-before (Fig.2c) or average DMSO ratio for each cell line (Fig.2f).

The 96-well seahorse plate was coated with MG and hRGCs were seeded at 250,000 cells per well and maintained for 2 days. 24h before measurements, media was exchanged with 100l iNS with 1g/ml BX795 or equivalent vehicle control DMSO. A day prior to the assay, the sensor cartridge was fully submerged with 200l of sterile water to hydrate it overnight in a non-CO2, 37C incubator. The next day, sterile water was replaced with pre-warmed XF calibrant buffer(Agilent) and the sensors were again submerged and incubated in the non-CO2, 37C incubator for 4560min. Seahorse media was made by adding stock solutions to XF DMEM to have final concentrations of 21.25mM glucose, 0.36mM sodium pyruvate, and 1.25 mM L-glutamine (Agilent), with pH adjusted to 7.387.42. Depending upon the assay, 20M Oligomycin (Oligo), 20M FCCP, 2.5g/ml Rotenone plus 5M Antimycin A (Rot/AA), and/or 175mM 2-deoxy-d-glucose (2-DG) solutions were then prepared in Seahorse media. In the Seahorse plate with hRGCs, iNS media was carefully exchanged to Seahorse media by removing, 60l iNS from all wells and adding 140l of Seahorse media. Next, 140l of the mixed media was removed by pipette and then an additional 140l seahorse media was added to each well to have a final volume of 180l. 180l of Seahorse media was then added to any empty wells. The plate was placed in Incucyte S3 (Sartorius) and one image of each well was taken for cell area normalization using brightfield and red fluorescence (tdTomato) channels. The hRGC seahorse plate was then placed into a non-CO2, 37C incubator for at least 45min. The reagents were added into their respective ports in the cartridge with the final concentrations in the wells as follows. For ATP rate assay, 2.0M Oligo and 0.25g/ml Rotenone plus 0.5M Antimycin A; for the glycolytic rate assay, 0.25g/ml Rotenone plus 0.5M Antimycin A and 17.5mM 2-DG; and for the Mito stress test, 2.0M Oligo, 2.0M FCCP (optimal concentration from FCCP titration), and 0.25g/ml Rotenone plus 0.5M Antimycin A. After loading all ports, the cartridge was placed into a non-CO2, 37C incubator while the experiment was setup in WAVE software (Agilent). The cartridge was then placed into the XFe96 analyzer (Agilent) and run for calibration. After the machine calibrations were successful, the hRGC seahorse plate was placed into the machine and the assay was run (ATP rate assay, glycolytic rate assay, or Mito stress test). Cell area from Incucyte images were measured using Image J and extrapolated for the total cell area in each well for normalization. The assay results were then exported into the appropriate excel macro using Seahorse Wave Desktop software (Agilent) for analysis.

hRGCs were seeded at 25,000 cells per well of a 96-well clear bottom black-walled plate and maintained for 3 days. The cells were then treated with indicated molecules for the designated time points. The caspase activity was measured using the ApoTox-Glo Triplex assay kit (Promega). 100l of Caspase-Glo 3/7 reagent was added to all wells and incubated for 30minutes at room temperature before measuring luminescence (Caspase). Measurements were normalized to DMSO control.

hRGCs were seeded at 250,000 cells per well on MG-coated 6-well plates and maintained for 3 days. The cells were then treated with 1 g/ml BX795 or equivalent DMSO for 24h. Media was aspirated, 500 l of fixative solution (3% Glutaraldehyde, 0.1M Cacodylate) was added, and the cells were incubated for 15min. Next, hRGCs were scraped and pelleted by centrifugation at 10,000xg for 20minutes. The pellets were fixed overnight at 4C, then rinsed the next day in 0.1M cacodylate buffer, followed by post fixation with 1% osmium tetroxide, 0.1M cacodylate buffer for 1h. After rinsing again with 0.1M cacodylate buffer, the cell pellets were dehydrated through a series of graded ethyl alcohols from 70 to 100%, and 2 changes of 100% acetone. The cell pellets were then infiltrated with a 50:50 mixture of acetone and embedding resin (Embed 812, Electron Microscopy Sciences, Hatfield, PA) for 72h. Specimen vial lids were then removed, and acetone allowed to evaporate off for 3h. Then the pellets were embedded in a fresh change of 100% embedding resin. Following polymerization overnight at 60C the blocks were then ready for sectioning. All procedures were done in centrifuge tubes including the final embedding. Sections with cut at 85nm, placed on copper grids, stained with saturated uranyl acetate, viewed, and imaged on a Tecnai Spirit (ThermoFisher, Hillsboro, OR) equipped with an AMT CCD camera (Advanced Microscopy Techniques, Danvers, MA). 49000X images were analyzed using Image J to measure mitochondrial parameters as explained in Fig.5.

Samples were treated with CCCP or BX795 at different time points as independent biological samples. Statistical tests between two independent datasets were done by Students t-test, each data point within a dataset is from an independent culture wellor cell (Figs.1cf, h, 1m; j, l, 2c, f, 3ad, fi, 4bd, fi, 5b, 6b, e, hl, Supplementary Figs.3b, 4bc). We used t-test rather than ANOVA because we did not want to assume that each group has the same variance. For non-normal data distribution, we performed MannWhitney U test to compare between two independent data sets (Fig.5ce, Supplementary Fig.5b). Graphs were made using GraphPad Prism 9.0 softwareand figures were made using Adobe Illustrator.

Further information on research design is available in theNature Portfolio Reporting Summary linked to this article.

Read the original:
Enhanced mitochondrial biogenesis promotes neuroprotection in ... - Nature.com