Genetics News & Researches

Original research: The architecture of SARS-CoV-2 transcriptome by Dongwan Kim, Joo-Yeon Lee, Jeong-Sun Yang, Jun Won Kim, V. Narry Kim, and Hyeshik Chang

Researchers in Korea have harnessed two complementary sequencing techniques to better understand the genetic architecture of the SARS-CoV-2 genome. By combining nanopore-based direct RNA sequencing (DRS) sequencing, and DNA nanoball (DNB) sequencing, the scientists, led by Narry Kim, PhD, and Hyeshik Chang, PhD, at the Center for RNA Research within the Institute for Basic Science (IBS) in Seoul, generated new insights into subgenomic RNAs (sgRNAs) that are translated into viral proteins. Analyzing the sequence information of each RNA also revealed where the genes are located on the long viral genomic RNA.

Source: “Coronavirus Genomic and Subgenomic RNA Architecture Mapped” article

“Now we have secured a high-resolution gene map of the new coronavirus that guides us where to find each bit of genes on all of the total SARS-CoV-2 RNAs (transcriptome) and all modifications RNAs (epitranscriptome),” Kim stated. “It is time to explore the functions of the newly discovered genes and the mechanism underlying viral gene fusion. We also have to work on the RNA modifications to see if they play a role in virus replication and immune response. We firmly believe that our study will contribute to the development of diagnostics and therapeutics to combat the virus more effectively.”

Advance in understanding actin sheds light on cell function — Atomic-level insight into proteins furthers fundamental understanding of human life

Original paper: Mechanism of actin N-terminal acetylation by Grzegorz Rebowski, Malgorzata Boczkowska, Adrian Drazic, Rasmus Ree, Marianne Goris, Thomas Arnesen, Roberto Dominguez in Science Advances, 2020

A tiny chemical modification on one of the most abundant and important proteins in cells, actin, has long been somewhat mysterious, its function not fully understood, but scientists have now taken a big step towards clearing up the mystery. The scientists, who report their discovery on the post-translational modification of actin, believe their discovery sheds light on the foundational construction of life.

Rare Genetic Variants from Birth Have Negative Effect on Lifespan — The researchers found that the combined effects of rare, damaging mutations present at birth have a negative impact on healthspan and longevity.

Findings from the new study — published recently in eLife through an article titled “Germline burden of rare damaging variants negatively affects human healthspan and lifespan” — suggest one additional inherited damaging mutation could carve off six months of life, and combinations of these rare mutations determine how soon someone will develop diseases such as cancer, heart disease, and dementia.

“Genetic variants identified so far can explain only a small fraction of lifespan heritability in humans,” the authors wrote. “Here, we report that the burden of rarest protein-truncating variants (PTVs) in two large cohorts is negatively associated with human healthspan and lifespan, accounting for 0.4 and 1.3 years of their variability, respectively. In addition, longer-living individuals possess both fewer rarest PTVs and less damaging PTVs. We further find that somatic accumulation of PTVs accounts for only a small fraction of mortality and morbidity acceleration and hence is unlikely to be causal in aging.”

The scientists found that people who had a high burden of ultra-rare PTVs had a shorter healthspan and lifespan. Each additional ultra-rare PTV in a person’s genome accounted for a reduction in lifespan of six months and a reduction in healthspan of two months.

Cellectis says the U.S. patent issued to the company this month will facilitate the development of future T-cell immunotherapy treatments based on CRISPR-Cas. The company’s clinical-phase pipeline consists entirely of treatments that apply its proprietary TALEN® gene-editing technology.

Artificial Intelligence Is Helping Biotech Get Real by Catherine Shaffer in Gen Edge, April Vol.50 №4 — Whether modeling the real world or making sense of real-time data, AI can enhance drug development from candidate screening to trial management.AI may be used to extract insights from millions of experimental affinity measurements and thousands of protein structures to predict the binding of small molecules to proteins. This approach is being realized by Atomwise, the developer of AtomNet, a structure-based, deep convolutional neural network designed to predict the bioactivity of small molecules for drug discovery applications . AtomNet helped Stanford University researchers screen 6.8 million small molecules for their ability to target Miro1 , a protein implicated in Parkinson’s disease. In the space-filling structure for Miro1 shown here, the area in white represents the screening site. The most promising compound, the Miro1 Reducer, appears in the inset.

. AtomNet helped Stanford University researchers screen 6.8 million small molecules for their ability to target , a protein implicated in Parkinson’s disease. In the space-filling structure for Miro1 shown here, the area in white represents the screening site. The most promising compound, the Miro1 Reducer, appears in the inset. Researchers Move Closer to Industrial Production of Heparin in Cell Culture

Scientists at the University of California-San Diego say they have moved one step closer to the ability to make heparin in cultured cells. Heparin is a potent anticoagulant and the most prescribed drug in hospitals, yet cell-culture-based production of heparin is currently not possible, according to the researchers who published their study, “ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis” in PNAS.

In particular, the researchers found a critical gene in heparin biosynthesis: ZNF263 (zinc-finger protein 263). The team believes this gene regulator is a key discovery on the way to industrial heparin production. The idea would be to control this regulator in industrial cell lines using genetic engineering, paving the way for safe industrial production of heparin in well-controlled cell culture.

Using JAX NSG™ Mice to Test Car T Therapy for Breast Cancer by Maya Dubey, PhD with the support of the Jackson Laboratory.

In a recent study by Zhou and colleagues, the authors examined the impact of a modified CAR T therapy on NSG™ mice from JAX, injected with a TNBC tumor cell line in one mammary fat pad. Using a human CAR that utilized the scFv motif from the monoclonal antibody, TAB004, the authors injected a single dose of the engineered T cells to tumor-bearing mice, after the tumor had been established. They observed that, in comparison to the control group, the tumor growth was dramatically reduced and the reduction was maintained until the study endpoint at day 57. Further analysis showed that the modified CAR T cells that infiltrated the tumors expressed high levels of both CD25 and PD1, which, as noted by the authors, indicates further activation by in vivo tumor antigen stimulation from the glycosylated tumor form of MUC1 (tMUC1).

Then, to determine whether the effects of the modified CAR T cells could extend beyond 57 days, the authors conducted a similar experiment as noted above, but extended the study endpoint to 81 days. They observed that, in comparison to the control group, the therapy reduced tumor growth until the study endpoint. However, they also observed that the treated tumors started to increase their growth after approximately 60 days post-treatment. The authors note that this may be due to several possibilities including requiring more than a single treatment injection, the loss of tMUC1 in the remaining tumors that progressed, or the increased PD1 expression in the tumor-infiltrating lymphocytes may block the anti-tumor response. They tested each possibility and found that the most likely solution to remain active would require additional injections of the therapy. In addition, the combination of CAR T cells and PD1 antibody enhanced the anti-tumor immune response.

Collectively, the data collected by the authors demonstrate the effectiveness of using a modified CAR T therapy to reduce TNBC tumor growth effectively, with minimal damage to normal cells. Moreover, they are exploring the use of this type of treatment against other tumor types as well as combining this therapy with others as potential treatments for solid tumors.

Super-charging drug development for COVID-19 — Cell-free production method scales up yield by 5,000 times.

Materials provided by Northwestern University. Originally written by Amanda Morris.

Researchers are ramping up the production of a promising drug that has proven effective in obliterating SARS-CoV in cellular cultures. The team hopes that the drug might also be effective in the fight against SARS’s close genetic cousin, the novel coronavirus (COVID-19).

Original materials: Peter Forster, Lucy Forster, Colin Renfrew, Michael Forster. Phylogenetic network analysis of SARS-CoV-2 genomes in “Proceedings of the National Academy of Sciences”, 2020

The first use of phylogenetic techniques shows the ‘ancestral’ virus genome closest to those in bats was not Wuhan’s predominant virus type. The study charts the ‘incipient supernova’ of COVID-19 through genetic mutations as it spread from China and Asia to Australia, Europe, and North America. Researchers say their methods could be used to help identify undocumented infection sources. By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.

“The viral network we have detailed is a snapshot of the early stages of an epidemic, before the evolutionary paths of COVID-19 become obscured by vast numbers of mutations. It’s like catching an incipient supernova in the act” they stated.

Original research paper, Reactivation of Myc transcription in the mouse heart unlocks its proliferative capacity, was presented by Megan J. Bywater, Deborah L. Burkhart, Jasmin Straube, Arianna Sabò, Vera Pendino, James E. Hudson, Gregory A. Quaife-Ryan, Enzo R. Porrello, James Rae, Robert G. Parton, Theresia R. Kress, Bruno Amati, Trevor D. Littlewood, Gerard I. Evan, Catherine H. Wilson in Nature Communications, 2020.

Researchers trying to turn off a gene that allows cancers to spread have made a surprising U-turn. By making the gene overactive and functional in the hearts of mice, they have triggered heart cell regeneration. Since adult hearts cannot usually repair themselves once damaged, harnessing the power of this gene represents major progress towards the first curative treatment for heart disease.

“This is really exciting because scientists have been trying to make heart cells proliferate for a long time. None of the current heart disease treatments are able to reverse degeneration of the heart tissue — they only slow progression of the disease. Now we’ve found a way to do it in a mouse model,” said Dr Catherine Wilson, a researcher in the University of Cambridge’s Department of Pharmacology, who led the study.

Call it Protein Logic Gate 2.0. The 1.0 version, which rewired native signaling pathways, was admirably direct, bypassing awkward rewiring at the DNA and RNA levels, but it wasn’t very scalable or extensible. It relied on a limited pool of building blocks, in this case, native proteins presenting interfaces open to fabricated protein-protein interactions. Artificial proteins can offer more flexibility. They can come in sets of modular units that interact with each other in clearly defined ways to read inputs, complete logical operations, and generate outputs.

The equivalent of Protein Logic Gate 2.0 has been launched by scientists based at the University of Washington (UW) School of Medicine. They’ve already run demonstrations of how it can be used to manipulate gene expression. These demonstrations, which involved cell-free extracts, yeast cells, and T cells, were presented in the journal Science, in an article titled, “De novo design of protein logic gates.”

This graphic table compares how electronic and protein AND logic gates respond when no input is present, when only A or B is present, and when both A and B are present. Source: UW Medicine Institute for Protein Design

Original paper: Minimum epistasis interpolation for sequence-function relationships by Juannan Zhou, David M. McCandlish in Nature Communications, 2020

Quantitative biologists have designed a new machine learning technique for predicting evolutionary pathways. It could prove a valuable tool for biologists studying rapidly evolving viruses or cancer. Described in Nature Communications, the algorithm called “minimum epistasis interpolation” results in a visualization of how a protein could evolve to either become highly effective or not effective at all. They compared the functionality of thousands of versions of the protein, finding patterns in how mutations cause the protein to evolve from one functional form to another.

Scientists from the Center for Precision Disease Modeling at the University of Maryland School of Medicine (UMSOM) say they have uncovered a mechanism that appears to explain how certain genetic mutations give rise to a rare genetic kidney disorder called nephrotic syndrome. Using a drosophila model, they found mutations in genes that code for certain proteins leads to a disruption of the recycling of the cell membrane. This disruption leads to an abnormal kidney cell structure and function, according to the study “Exocyst Genes Are Essential for Recycling Membrane Proteins and Maintaining Slit Diaphragm in Drosophila Nephrocytes” published in the Journal of the American Society of Nephrology.

Original article: Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome Coronavirus 2 with high potency by Calvin J Gordon, Egor P Tchesnokov, Emma Woolner, Jason K Perry, Joy Y. Feng, Danielle P Porter, Matthias Gotte in the Journal of Biological Chemistry, April 13, 2020

Scientists have shown that drug remdesivir is highly effective in stopping the replication mechanism of the coronavirus that causes COVID-19. The finding follows closely on research demonstrating how the drug worked against the Middle East Respiratory Syndrome (MERS) virus, a related coronavirus.

by Qiuxia Xu, Min Wang, Sujing Huang, Lin Xu, Hongqiong Guan, Hong Zhu from the Department of Obstetrics, The Second Affiliated Hospital of Hainan Medical College, Haikou City, Hainan Province, China

This paper studies the correlation between TSC1/TSC2 mutations and phenotypes of tuberous sclerosis (TSC) gene in prenatal diagnosis based on sensor measurement technology high-throughput sequencing platform. The paper mainly performs sensor measurement technology-based high-throughput sequencing of the gene coding region of TSC1/TSC2 and adjacent intron regions of 10 familial probands with the clinical diagnosis of tuberous sclerosis. High-throughput sequencing was used to validate the discovered gene mutations and prenatal diagnosis for disease-causing mutations. The results of the study found that 10 cases of probands found TSC1/TSC2 mutations, including 1 case of TSC1 mutation, 9 cases of TSC2 mutation, 9 cases of missense mutations in 6 cases, 2 cases of nonsense mutations, frameshift 1 case of mutation. Further, 9 prenatal diagnoses were made for the mother, and one mutant positive foetus was found. The research has found that the high-throughput sequencing platform based on sensor measurement technology can effectively verify and detect gene mutations, which has certain advantages and effectiveness. Therefore, it can be widely used in clinical diagnosis and treatment of gene mutations, which is effective for preventing gene mutations in postpartum infants.

The paper discovered and reported a new TSC gene mutation, namely TSC2 gene C. It not only provides direction for genetic counseling of sick families but also assists in the formulation and prognosis analysis of perinatal management strategies, directly affecting the outcome and outcome of the foetus.

Technique offers path for biomanufacturing medicines during space flights — Research simulating instrument aboard international space station nurtures E. coli bacteria.

Original research Growth of microorganisms in an interfacially driven space bioreactor analog by Joe A. Adam, Shreyash Gulati, Amir H. Hirsa, Richard P. Bonocora in npj Microgravity, 2020

Research published in Nature Microgravity used an Earth-bound simulator of the space station instrument to grow E. coli, demonstrating that it can be nurtured with methods that promise to be more suitable for space travel than existing alternatives. An instrument currently aboard the International Space Station could grow E. coli bacteria in space, opening a new path to bio-manufacturing drugs during long term space flights.

“If we can get microorganisms to grow well in space, astronauts can use them to make pharmaceuticals on demand. This could be vital for survival on long missions where resupplying is not an option.” said Richard Bonocora, senior author and a faculty member in the Department of Biological Sciences at Rensselaer Polytechnic Institute. “Here we were asking: ‘Is there a better way to grow microorganisms that what is currently being used is space?’ And what we find is that — with shear force — yes, there likely is.”

Original paper: Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat by Hongwei Wang, Silong Sun, Wenyang Ge, Lanfei Zhao, Bingqian Hou, Kai Wang, Zhongfan Lyu, Liyang Chen, Shoushen Xu, Jun Guo, Min Li, Peisen Su, Xuefeng Li, Guiping Wang, Cunyao Bo, Xiaojian Fang, Wenwen Zhuang, Xinxin Cheng, Jianwen Wu, Luhao Dong, Wuying Chen, Wen Li, Guilian Xiao, Jinxiao Zhao, Yongchao Hao, Ying Xu, Yu Gao, Wenjing Liu, Yanhe Liu, Huayan Yin, Jiazhu Li, Xiang Li, Yan Zhao, Xiaoqian Wang, Fei Ni, Xin Ma, Anfei Li, Steven S. Xu, Guihua Bai, Eviatar Nevo, Caixia Gao, Herbert Ohm, Lingrang Kong in Science, 2020

Agricultural Research Service (ARS) scientists and their colleagues have discovered a gene that can be used to develop varieties of wheat that will be more resistant to Fusarium Head Blight (FHB), a disease that is a major threat both overseas and to the nation’s $10 billion annual wheat crop.

Scientists have discovered a new role for the brain chemical dopamine that is independent of classic neurotransmission. The new role appears to be critical to changes in gene expression related to chronic exposure to, or abuse of, cocaine. To be more precise, scientists at the Icahn School of Medicine at Mount Sinai have discovered a new role for the brain chemical dopamine that is independent of classic neurotransmission. The new role appears to be critical to changes in gene expression related to chronic exposure to, or abuse of, cocaine, according to a study published Friday, April 10, in the journal Science.

Vascular Supply of the Human Spiral Ganglion: Novel Three-Dimensional Analysis Using Synchrotron Phase-Contrast Imaging and Histology by Xueshuang Mei, Rudolf Glueckert, Annelies Schrott-Fischer, Hao Li, Hanif M. Ladak, Sumit K. Agrawal, Helge Rask-Andersen in Scientific Reports, 2020

What does it actually look like deep inside our ears? This has been very difficult to study as the inner ear is protected by the hardest bone in the body. But with the help of synchrotron X-rays, it is now possible to depict details inside the ear three-dimensionally. Researchers have now used the method to map the blood vessels of the inner ear.

Human spiral ganglion (HSG) cell bodies located in the bony cochlea depend on a rich vascular supply to maintain excitability. These neurons are targeted by cochlear implantation (CI) to treat deafness, and their viability is critical to ensure successful clinical outcomes. The blood supply of the HSG is difficult to study due to its helical structure and encasement in hard bone. The objective of this study was to present the first three-dimensional (3D) reconstruction and analysis of the HSG blood supply using synchrotron radiation phase-contrast imaging (SR-PCI) in combination with histological analyses of archival human cochlear sections. Twenty-six human temporal bones underwent SR-PCI. Data were processed using volume-rendering software, and a representative three-dimensional (3D) model was created to allow visualization of the vascular anatomy. Histologic analysis was used to verify the segmentations. Results revealed that the HSG is supplied by radial vascular twigs which are separate from the rest of the inner ear and encased in bone. Unlike most organs, the arteries and veins in the human cochlea do not follow the same conduits. There is a dual venous outflow and a modiolar arterial supply. This organization may explain why the HSG may endure even in cases of advanced cochlear pathology.

by Batuhan Mert Kalkana, Ezgi Yagmur Kalaa, Melek Yucea, Medine Karadag Alpaslana, Fatih Kocabasa from a Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey

Recent developments in gene-editing technology have enabled scientists to modify DNA sequence by using engineered endonucleases. These gene-editing tools are promising candidates for clinical applications, especially for the treatment of inherited disorders like sickle cell disease (SCD). SCD is caused by a point mutation in the human βglobin gene (HBB). Clinical strategies have demonstrated substantial success, however, there is not any permanent cure for SCD available. CRISPR/Cas9 platform uses a single endonuclease and a single guide RNA (gRNA) to induce sequence-specific DNA double-strand break (DSB). When this accompanies a repair template, it allows repairing the mutated gene. In this study, it was aimed to target the HBB gene via the CRISPR/Cas9 genome editing tool to introduce nucleotide alterations for efficient genome editing and correction of point mutations causing SCD in a human cell line, by Homology Directed Repair (HDR). They have achieved to induce target specific nucleotide changes on HBB gene in the locus of mutation causing SCD. The effect of the on-target activity of bone fide standard gRNA and newly developed longer gRNA were examined. It is observed that longer gRNA has a higher affinity to target DNA while having the same performance for targeting and Cas9 induced DSBs. HDR mechanism was triggered by the co-delivery of donor DNA repair templates in circular plasmid form. In conclusion, they have suggested a methodological pipeline for efficient targeting with a higher affinity to target DNA and generating desired modifications on HBB gene.