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Genome Mapping Reveals Autoimmune Disease Risk Genes in Innate Lymphoid Cells
A new study published in Nature Genetics suggests that looking beyond the nearest gene may be essential for understanding how immune disease risk variants act in rare immune cells.
The paper, “High-resolution promoter interaction analysis implicates genes involved in activation of type 3 innate lymphoid cells in immune disease risk,” was co-led by researchers at Cincinnati Children’s Hospital, the MRC Laboratory of Medical Sciences, Imperial College London, along with collaborators. The team mapped long-distance DNA interactions in type 3 innate lymphoid cells, or ILC3s, a rare population of tissue-resident immune cells enriched in the gut, airways, and mucosal lymphoid tissues.
ILC3s help regulate inflammation and maintain barrier integrity, but their rarity has made them difficult to study with conventional genome-organization methods. Many approaches for mapping chromosomal contacts require millions of cells, limiting their use in cell types that may be particularly relevant to disease.
“This work opens the door to studying long-distance DNA interactions in rare immune cells,” says Stephen Waggoner, PhD, scientist in the Center of Autoimmune Genomics and Etiology at Cincinnati Children’s. “Until now, most methods required millions of cells, which limited what we could learn from the cell types most relevant to disease.”
To address that limitation, the investigators used a low-input, high-resolution Promoter Capture Hi-C (PCHi-C) approach to map promoter-anchored chromosomal contacts in primary human ILC3s, alongside CD4+ T cells. They then combined those maps with genome-wide association study data using a Bayesian framework, multiCOGS, to connect Crohn’s disease risk variants with the genes they are most likely to regulate.
![Researchers mapped long-range DNA interactions in rare tonsil-derived ILC3 immune cells to identify regulatory mechanisms linked to autoimmune disease risk. [Cincinnati Children's]](https://www.genengnews.com/wp-content/uploads/2026/08/ILC3-in-autoimmune-risk-graphic_v2-300x141.jpg)
The analysis linked Crohn’s disease risk variants to more than 100 candidate genes in ILC3s, including both known inflammatory bowel disease genes and less expected candidates. Among the latter was CLN3, a gene best known for its role in Batten disease, a rare neurodegenerative disorder.
“While some disease risk variants act on the genes nearest to them, others do not, so if we only look at the nearest gene, we may get the underlying mechanisms wrong,” says Mikhail Spivakov, PhD, head of the Functional Gene Control Research Group at MRC Laboratory of Medical Sciences. “What is more, the patterns of genome folding differ across cell types, so it is important to study the 3D connections between variants and the genes they control in the cells that are relevant for the disease.”
Follow-up experiments in a mouse ILC3-like cell line supported a possible role for CLN3 in regulating inflammatory activity. According to the paper, CLN3 was downregulated after cytokine stimulation, while increasing CLN3 expression altered stimulation-induced transcriptional programs and cytokine secretion. The findings do not establish CLN3 as a causal gene in Crohn’s disease, but they point to a potential immune-related function for a gene more commonly discussed in the context of neurodevelopmental disease.
The researchers also extended the approach to five additional autoimmune conditions, generating a catalog of ILC3-linked risk genes. These genes were enriched for regulators of the ILC3 inflammatory response identified in a CRISPR interference screen.
The next steps appear to include clarifying how CLN3 influences immune-cell function, testing whether the pathways identified in ILC3s can help explain disease mechanisms, and applying the low-input mapping strategy to other rare cell types that have been difficult to study. “Studying genetic regulation in rare cell types allows us to move closer to mechanism, not just association, and that’s essential for making genetic findings meaningful across medicine,” says Waggoner.
The post Genome Mapping Reveals Autoimmune Disease Risk Genes in Innate Lymphoid Cells appeared first on GEN – Genetic Engineering and Biotechnology News.
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STAT+: As Trump administration pushes court-ordered mental health care, a new report raises questions
In the last three decades, as involuntary outpatient treatment for people with serious mental health conditions like schizophrenia have expanded to almost every state, the evidence for these programs’ efficacy has remained murky.
A new evaluation of New York’s involuntary outpatient treatment program adds another wrinkle to the complex existing scientific literature on this type of care. Assisted outpatient treatment (AOT) reduced hospitalizations, arrests, and more. So did voluntary treatment. The independent authors concluded that the state should funnel more money toward voluntary services, especially after hearing about the coercion and harms that people experienced under AOT orders.
“When people are engaged in services, they have better outcomes,” said Bevin Croft, director of Human Services Research Institute’s Behavioral Health team and one of the study’s authors. “Whether or not that engagement is voluntary doesn’t seem to make a huge difference.”
In the last three decades, as involuntary outpatient treatment for people with serious mental health conditions like schizophrenia have expanded to almost every state, the evidence for these programs’ efficacy has remained murky.
A new evaluation of New York’s involuntary outpatient treatment program adds another wrinkle to the complex existing scientific literature on this type of care. Assisted outpatient treatment (AOT) reduced hospitalizations, arrests, and more. So did voluntary treatment. The independent authors concluded that the state should funnel more money toward voluntary services, especially after hearing about the coercion and harms that people experienced under AOT orders.
“When people are engaged in services, they have better outcomes,” said Bevin Croft, director of Human Services Research Institute’s Behavioral Health team and one of the study’s authors. “Whether or not that engagement is voluntary doesn’t seem to make a huge difference.”
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STAT+: California Supreme Court sides with Gilead in ‘duty’ to innovate case
The California Supreme Court sided with Gilead Sciences in a closely watched case brought by thousands of patients who argued the company was negligent for slow-walking development of an HIV medicine that was safer than another drug it was already selling.
In a 6-1 decision, the court overturned a state appeals court ruling two years ago that Gilead could be held liable, raising alarm in the pharmaceutical industry that drug development decisions could be influenced by the fear of legal liability.
The case began after more than 24,000 people claimed in federal and state court lawsuits that they unnecessarily suffered kidney injury and bone loss from the older drug. They maintained that Gilead cynically managed its product pipeline at the expense of people who should have been treated with a safer medicine.
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Combined Phage Therapy and FMT Reduces Recurrent UTIs and Antibiotic Use in First Human Case Series
Recurrent urinary tract infections (rUTIs) are among the most common bacterial infections worldwide. The difficult-to-treat condition, which affects primarily women, is defined as two urinary tract infections (UTIs) within six months or three UTIs within the past year. They are a leading cause of outpatient antibiotic use, accounting for more than 15% of all prescriptions.
While antibiotics remain the standard treatment, frequent recurrences and rising antibiotic resistance highlight the need for alternative therapeutic approaches. Now, researchers have, for the first time, administered a combined phage therapy (PT) with fecal microbiota transplantation (FMT), to decolonize urinary and intestinal reservoirs of rUTI patients.
The novel treatment approach, combining PT and elective FMT, was administered to three female patients, between May and July 2023, with rUTI that did not respond to antibiotics and commonly used non-antibiotic strategies. All had microbiologically confirmed E. coli in multiple infections.
All three women received PT orally and intravesically (locally applied to the bladder via catheter) for eight days outside of acute episodes. Two of these three patients were elected to receive subsequent FMT. Since the bacteria causing the recurring infections often reside in the gut as well as the urinary tract, the FMT treatment targeted the intestinal reservoirs of E. coli that survive antibiotic treatment of acute infections and can become increasingly resistant.
“While phage therapy acts to remove the pathogen, FMT aims to restore a healthy microbiome, combining both immediate and long-term effects,” Lena Biehl, MD, PhD, group leader at Fraunhofer ITMP, deputy lead of Cologne Microbiota Bank, University Hospital Cologne.
This work is published in Nature Microbiology in the paper, “Combined Phage therapy and fecal microbiota transplantation to treat recurrent urinary tract infection: a case series.”
The treatments were well tolerated and did not result in noticeable side effects. The two patients who received the combination therapy have experienced a long-term reduction of UTIs over the course of two years, while the one patient with PT only has experienced further episodes but with reduced symptoms. For all patients, although E. coli was detected in follow-up samples, quality of life improved significantly, while the need for antibiotic treatment was substantially reduced.
“Three patients are not a sufficiently large sample to establish this new therapy, and control groups were lacking. However, this experience has helped to lay the foundation for a clinical trial in order to test the clinical utility of this treatment approach and make it more widely available and sustainable for patients,” comments Shawna McCallin, MD, at the Balgrist University Hospital in Zurich.
The clinical trial is scheduled to begin in June 2027 at the participating institutions as part of the REPhRAME project, which is funded by the European Commission through the Horizon Europe funding programme.
The post Combined Phage Therapy and FMT Reduces Recurrent UTIs and Antibiotic Use in First Human Case Series appeared first on GEN – Genetic Engineering and Biotechnology News.
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