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  • Chromatin accessibility: A new avenue for gene editing

    Chromatin accessibility: A new avenue for gene editing
    23rd April 2024

    TFDP1, a modulator of genome accessibility. Credit: Kanazawa University

    In a study recently published in Nature Genetics, researchers from Nano Life Science Institute (WPI-NanoLSI), Kanazawa University explore chromatin accessibility, i.e., endogenous access pathways to the genomic DNA, and its use as a tool for gene editing. Researchers from Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, led by Yusuke Miyanari, have used advanced genetic screening methods to unravel chromatin accessibility and its pathways.

    For the investigation, the team used a combination of two technologies CRISPR screening and ATAC-see. While the former is a method to suppress the function of a desired set of genes, the latter is a means to identify which ones are essential for chromatin accessibility. Thus, using this method all genes playing a crucial role in chromatin accessibility could be pinned down.

    With the help of these assays, novel pathways and individual players involved in chromatin accessibility were uncovered some playing a positive role and some negative. Of these, one particular protein, TFDP1, showed a negative effect on chromatin accessibility. When it was suppressed, a significant increase in chromatin accessibility was observed, accompanied by nucleosome reduction. A deeper dive into the mechanism of TFDP1 revealed that it functions by regulating the genes responsible for production of certain histone proteins. The team then focused their study toward exploring biotechnological applications of their findings. After suppressing TFDP1, two different approaches were tried. The first approach involved gene editing using the CRISPR/Cas9 tool. This revealed that deletion of TFDP1 made the gene editing process easier.

    By Nano Life Science Institute (NanoLSI)

    Article can be accessed on: phys.org

  • New stem cell model can help personalize stem cell treatment for immunodeficiency patients

    New stem cell model can help personalize stem cell treatment for immunodeficiency patients
    22nd April 2024

    Graphical abstract. Credit: Journal of Allergy and Clinical Immunology (2023). DOI: 10.1016/j.jaci.2023.11.914

    A collaborative research team has pioneered a new stem cell model to help personalize treatment for patients suffering from rare forms of immunodeficiency. The research findings were published in the Journal of Allergy and Clinical Immunology.

    Primary immunodeficiencies, also known as “inborn errors of immunity,” are debilitating diseases that compromise the immune system, leaving patients highly vulnerable to infections, autoimmunity, and even cancer. To date, about 500 primary immunodeficiencies are known, but the list is growing yearly as new diseases emerge. One example is a rare disorder called STAT1-Gain-of-Function (STAT1-GoF) disease. Patients with STAT1-GoF are born with an inheritable defect in their immune system, making them susceptible to life-threatening infections, autoimmune disorders, aneurysms, and cancers.

    Collaborating with partners at the Centre for Translational Stem Cell Biology (CTSCB) and the University of Cambridge, HKUMed has pioneered a new stem cell platform to help patients with primary immunodeficiencies. The research team led by Dr. Philip Li Hei, Professors Liu Pengtao, and Chak-sing Lau from the LKS Faculty of Medicine of the University of Hong Kong (HKUMed) took blood samples from patients and re-engineered the patients’ cells into Expanded Potential Stem Cells (EPSCs), which can be used as personalized disease models, enabling various therapies to be tested to identify the most effective and safest treatment options without causing unnecessary risk to the patients.

    By The University of Hong Kong

    Article can be accessed on: MedicalXpress

  • Study uses metabolomics to identify novel diagnostic markers for chronic obstructive pulmonary disease

    Study uses metabolomics to identify novel diagnostic markers for chronic obstructive pulmonary disease
    18th April 2024

     Credit: Dr. Dr. Tiantian Zhang and Dr. Hongmei Zhao from Peking Union Medical College (ars.els-cdn.com/content/image/1-s2.0-S2772558823000579-gr2.jpg)

    Chronic obstructive pulmonary disease (COPD) is a chronic lung disease with irreversible airflow limitation and a leading cause of death worldwide. COPD is characterized by chronic bronchitis and emphysema and is associated with malnutrition, muscle weakness, and an increased risk of infection. Although pulmonary tests are considered as the gold standard for COPD diagnosis, they cannot detect early stages of COPD, leading to underdiagnosis. This emphasizes the need for specific biomarkers for early diagnosis, classification, and clinical interventions.

    Recent studies suggested that changes in lipids, amino acids, glucose, nucleotides, and microbial metabolites in lungs and intestine can effectively diagnose early COPD. Metabolomics, a discipline that analyzes different metabolites from body fluids, has emerged as a prominent technique for COPD assessment. However, there are no studies that identify and summarize the metabolites that significantly change during COPD.

    A recent review by Dr. Wenqian Wu, Dr. Zhiwei Li, Dr. Tiantian Zhang, and Dr. Hongmei Zhao from the Peking Union Medical College, along with Dr. Yongqiang Wang from 302 Hospital of China Guizhou Aviation Industry Group, and Dr. Chuan Huang at the Chinese Academy of Medical Sciences, provided an in-depth account of the advances in metabolomics of COPD over the last five years, highlighting some potential diagnostic markers and therapeutic targets.

    By Cactus Communications

    Article can be accessed on: MedicalXpress

  • MEGA CRISPR: Engineering Better Immunotherapies with RNA Editing

    MEGA CRISPR: Engineering Better Immunotherapies with RNA Editing
    12th April 2024

    Credits: The scientist

    Many foundational research technologies have transformed cellular therapies, moving treatments from concept to clinic. In the past decade, chimeric antigen receptors (CAR) and genome editing are two standouts that led to breakthrough CAR T cell therapies for leukemia and lymphoma. Scientists engineer these treatments with virus-mediated gene insertion ex vivo, which instructs T cells to express synthetic receptors that detect tumor-specific antigens and guide cancer cell eradication after transplantation. Researchers investigate clustered regularly interspaced short palindromic repeats (CRISPR) editing to improve CAR T cell therapies and expand their applicability to more cancer types. However, CRISPR-associated nuclease 9 (Cas9)-based genome cutting tools face unique safety and efficacy limitations due to the permanent nature of DNA editing. To circumvent these limitations, bioengineer Lei (Stanley) Qi and physician immunologist Crystal Mackall at Stanford University developed an RNA editing tool called multiplexed effector guide arrays (MEGA). In a study published in Cell, the team used Cas9’s cousin, Cas13, and a pooled array of guide RNAs to simultaneously edit multiple gene transcripts in primary human T cells without targeting or cutting genomic DNA. This multi-targeting method addresses an unmet need in cell therapy optimization by allowing the researchers to dynamically regulate several pathways per T cell, rather than add or ablate individual genes completely, one at a time. The researchers screened for genes that synergistically affect T cell function and knocked down redundant transcripts that drive T cell exhaustion in culture and in mice.

    “Our years of experience on gene editing at the DNA level makes us realize that this technology, while very powerful, still has some intrinsic challenges, which possibly could only be addressed if we find methods to engineer RNA,” said Qi. Among these difficulties are off-target cuts and accumulation of genomic instability through multiple DNA edits. “RNA is completely different. If we target RNA, we do not touch the DNA all, and RNA editing is reversible,” Qi explained. Another advantage is Cas13’s ability to process several unique guide RNAs from a single array, which allowed the researchers to target multiple RNA transcripts at once in the same cell.

     

    By Deanna MacNeil, PhD

    Article can be accessed on: The Scientist

  • An exosome-based liquid biopsy shows promise for early detection of pancreatic cancer

    An exosome-based liquid biopsy shows promise for early detection of pancreatic cancer
    9th April 2024

    Pancreatic cancer cells (blue) growing as a sphere encased in membranes (red). Credit: National Cancer Institute

    An investigational exosome-based liquid biopsy accurately detected 97% of stage 1-2 pancreatic cancers when combined with the biomarker CA 19-9, according to research presented at the American Association for Cancer Research (AACR) Annual Meeting 2024, held April 5-10.

    “Pancreatic cancer is one of the most fatal malignancies, in large part because the majority of patients are diagnosed only after the cancer has already metastasized,” said Ajay Goel, Ph.D., senior author of the study and the chair of the Department of Molecular Diagnostics and Experimental Therapeutics at City of Hope.

    While the five-year relative survival rate for patients diagnosed at the earliest stages before the cancer has spread from the pancreas is 44.3%, it is only 3.2% for those diagnosed with metastatic disease. “It is of utmost importance to diagnose patients as early as possible so they have the opportunity to receive potentially curative surgery and treatment,” Goel said.

    Caiming Xu, MD, Ph.D., a postdoctoral fellow in Goel’s research group, added that early detection of pancreatic cancer remains challenging due to the nonspecific symptoms of the disease and because the pancreas is located deep within the abdomen, where it cannot be easily palpated during physical examination. Furthermore, existing biomarkers, such as CA19-9, are not reliable on their own to detect early-stage pancreatic cancer. Goel, Xu, and colleagues explored the potential of an exosome-based liquid biopsy to detect pancreatic cancer at early stages.

    By American Association for Cancer Research

    Article can be accessed on: MedicalXpress

  • When an antibiotic fails: Scientists are using AI to target ‘sleeper’ bacteria

    When an antibiotic fails: Scientists are using AI to target 'sleeper' bacteria
    9th April 2024

    Credit: Massachusetts Institute of Technology

    Since the 1970s, modern antibiotic discovery has been experiencing a lull. Now the World Health Organization has declared the antimicrobial resistance crisis as one of the top 10 global public health threats. When an infection is treated repeatedly, clinicians run the risk of bacteria becoming resistant to the antibiotics. But why would an infection return after proper antibiotic treatment? One well-documented possibility is that the bacteria are becoming metabolically inert, escaping detection of traditional antibiotics that only respond to metabolic activity. When the danger has passed, the bacteria return to life and the infection reappears. Tales of bacterial “sleeper-like” resilience are hardly news to the scientific community ancient bacterial strains dating back to 100 million years ago have been discovered in recent years alive in an energy-saving state on the seafloor of the Pacific Ocean.

    In this case, researchers in the Collins Lab employed AI to speed up the process of finding antibiotic properties in known drug compounds. With millions of molecules, the process can take years, but researchers were able to identify a compound called semapimod over a weekend, thanks to AI’s ability to perform high-throughput screening.

    Semapimod is an anti-inflammatory drug typically used for Crohn’s disease, and researchers discovered that it was also effective against stationary-phase Escherichia coli and Acinetobacter baumannii.

    By Alex Ouyang, Massachusetts Institute of Technology

    Article can be accessed on: phys.org

  • Gene editing technology reveals molecular mechanisms governing diatom population density signals

    Gene editing technology reveals molecular mechanisms governing diatom population density signals
    2nd April 2024

    Model of SLC24A-mediated population density perception and regulation mechanism. Credit: IOCAS

    The intricate dynamics of diatom blooms, influenced by a myriad of external factors and internal signals, continue to fascinate scientists. After recognizing the potential role of density perception and intracellular signaling in dictating these phenomena, researchers have begun to elucidate the molecular basis of diatom population density regulation. Recently, a research team led by Prof. Wang Guangce from the Institute of Oceanology of the Chinese Academy of Sciences (IOCAS) reported the significant role of the marine diatom SLC24A in population density signal perception and regulation.

    The study was published in The ISME Journal. The researchers meticulously identified and targeted potential genes involved in density signaling, culminating in the discovery of the central hub gene PtSLC24A. Two PtSLC24A knockout mutants of Phaeodactylum tricornutum were obtained using CRISPR/Cas9 gene editing technology. Intracellular Ca2+ concentration measurements indicated that cell density could induce Ca2+ responses, and knockout of PtSLC24A increased intracellular Ca2+ concentration. Three-dimensional structural modeling and simulation calculations of the PtSLC24A protein supported its Ca2+ transport function.

    The results showed that high density could induce cell apoptosis, and knockout of PtSLC24A exacerbated this phenomenon. PtSLC24A also affected the expression of density-dependent genes at different cell densities. Beyond the laboratory, the ecological relevance of SLC24A was underscored by its ubiquitous distribution across the Tara Oceans sites, with expression patterns positively correlating with chlorophyll content in different marine phytoplankton taxa.

    By Zhang Nannan, Chinese Academy of Sciences

    Article can be accessed on: phys.org

  • A Master Regulator of Gene Expression

    A Master Regulator of Gene Expression
    25th March 2024

    Researchers used a CRISPR-based platform to identify master regulators of T cell function.
    ELLA MARU STUDIO

    Immunotherapies such as chimeric antigen receptor (CAR) T cell therapy are promising approaches in the fight against cancer. How well the therapies work depends on T cell function, which is determined by the network of genes that these immune cells express. Recently, researchers at Duke University developed a CRISPR-based screening platform to identify key epigenetic regulators of human T cell function, and discovered the central role of the transcription factor Basic leucine zipper transcription factor ATF-like 3 (BATF3) in reprogramming the expression of several genes and improving the efficacy of CAR T cells in eliminating cancer cells. Their findings, published in Nature Genetics, may aid in the development of more effective T cell-based immunotherapies.

    “It’s a very elegant study. It’s really interesting to see how this field of CRISPR screen is developed here using primary human T cells, which are not the easiest to work with,” said Fredrik Wermeling, an immunologist at the Karolinska Institute who was not involved in the research.

    For years, biomedical engineer and study author Charles Gersbach from Duke University and his team have developed technologies to screen and manipulate the expression of genes in cells. In previous studies, they used these epigenome editing tools to reprogram fibroblasts to become neuronal cells and to control cell differentiation in human neuronal and pluripotent stem cell populations. Interested in exploring a more therapeutic application of these tools, the researchers turned their attention to T cell-based immunotherapies, specifically CAR T cells. According to Gersbach, the use of such epigenetic enhancement approaches on T cells may help expand T cell-based therapies beyond the cancer types, such as blood cancers, in which they have been effective.

    By Mariella Bodemeier Loayza Careaga, PhD

    Article can be accessed on: The Scientist

  • Researchers identify novel genetic variants associated with Alzheimer’s disease

    Researchers identify novel genetic variants associated with Alzheimer's disease
    25th March 2024

    Credit: Unsplash/CC0 Public Domain

    Identifying genetic variants and the role they play in predisposing people to Alzheimer’s disease can help researchers better understand how to treat the neurodegenerative condition for which there is currently no cure. A new study led by Boston University School of Public Health (BUSPH) and UTHealth Houston School of Public Health has identified several genetic variants that may influence Alzheimer’s disease risk, putting researchers one step closer to uncovering biological pathways to target for future treatment and prevention.

    Published in the journal Alzheimer’s & Dementia, the study utilized whole genome sequencing and identified 17 significant variants associated with Alzheimer’s disease in five genomic regions. This data enables researchers to pinpoint rare and important genes and variants, building upon genome-wide association studies, which focus only on common variants and regions. The findings underscore the value of whole genome sequencing data in gaining long-sought insight into the ultimate causes and risk factors for Alzheimer’s disease, which is the fifth leading cause of death among people 65 and older in the United States. As the most common form of dementia, Alzheimer’s disease currently affects more than 6 million Americans and that number is expected to skyrocket to nearly 13 million by 2050.

    “Prior genome-wide association studies using common variants have identified regions of the genome, and sometimes genes, that are associated with Alzheimer’s disease,” says study co-senior author Dr. Anita DeStefano, professor of biostatistics at BUSPH.

    By Boston University 

    Article can be accessed on: MedicalXpress

     

     

  • New insights into genetic mechanisms could improve treatment of liver fibrosis

    New insights into genetic mechanisms could improve treatment of liver fibrosis
    18th March 2024

    Graphical abstract. Credit: iScience (2024). DOI: 10.1016/j.isci.2024.109301

    The liver is not only the largest internal organ but also vital for human life as a metabolic center. It also possesses remarkable self-healing powers: even when large portions are removed, such as during surgery, they quickly regenerate in healthy individuals. However, in cases of repeated or chronic injury to the liver tissue, as caused by excessive alcohol consumption or viral hepatitis, this regenerative capacity fails. Scarring occurs, known as fibrosis, where liver cells are replaced by fibrous tissue. The liver hardens and becomes increasingly unable to perform its function in the worst case, this leads to liver failure.

    To better understand the scarring process, a research team led by Thomas Reiberger, Professor of Gastroenterology and Hepatology at MedUni Vienna and Adjunct Principal Investigator at CeMM, examined gene activity in two different mouse models exhibiting varying degrees of liver disease severity, also capturing certain phases of spontaneous regression of the disease.

    At the same time, important indicators of disease severity, such as portal venous pressure, blood markers of liver injury, or the extent of liver fibrosis based on liver tissue samples, were recorded. The study, “Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension,”was published in the journal iScience.

    By CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

    Article can be accessed on: MedicalXpress