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Researchers uncover principles of gene expression regulation in cancer and cellular functions

A research team at KAIST has identified the core gene expression networks regulated by key proteins that fundamentally drive phenomena such as cancer development, metastasis, tissue differentiation from stem cells, and neural activation processes. This discovery lays the foundation for developing innovative therapeutic technologies.

A joint research team led by Professors Seyun Kim, Gwangrog Lee, and Won-Ki Cho from the Department of Biological Sciences has uncovered essential mechanisms controlling gene expression in animal cells.

The findings were published on January 7 in the journal Nucleic Acids Research in a paper titled “Single-molecule analysis reveals that IPMK enhances the DNA-binding activity of the transcription factor SRF.”

Scientists engineer CRISPR enzymes that evade the immune system

The core components of CRISPR-based genome-editing therapies are bacterial proteins called nucleases that can stimulate unwanted immune responses in people, increasing the chances of side effects and making these therapies potentially less effective.

Researchers at the Broad Institute of MIT and Harvard and Cyrus Biotechnology have now engineered two CRISPR nucleases, Cas9 and Cas12, to mask them from the immune system. The team identified protein sequences on each nuclease that trigger the immune system and used computational modeling to design new versions that evade immune recognition. The engineered enzymes had similar gene-editing efficiency and reduced immune responses compared to standard nucleases in mice.

Appearing today in Nature Communications, the findings could help pave the way for safer, more efficient gene therapies. The study was led by Feng Zhang, a core institute member at the Broad and an Investigator at the McGovern Institute for Brain Research at MIT.

New Research Uncovers Long-Lived DNA Damage Linked to Cancer

In a groundbreaking shift in our understanding of mutations, researchers have discovered types of DNA

DNA, or deoxyribonucleic acid, is a molecule composed of two long strands of nucleotides that coil around each other to form a double helix. It is the hereditary material in humans and almost all other organisms that carries genetic instructions for development, functioning, growth, and reproduction. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

A man was cured of HIV and leukemia after stem cell transplant

Research into stem cells has paid off as 68-year-old Paul Edmonds remains effectively cured of both HIV and leukemia following treatment that included a breakthrough stem cell transplant in 2019. Now, five years after the treatment, Edmonds continues to live his life free of HIV and leukemia.

This makes Edmonds one of only five people in the world who have achieved full remission of HIV. Further, his 31 years of living with the virus also means he had it the longest out of the five in remission. It’s a striking accomplishment that he has remained in remission for so long and showcases just how effective these kinds of treatments can be.

Stem cell transplants aren’t a new idea, either. What particularly makes this treatment so effective and intriguing, though, is that the transplant donor had a rare genetic mutation called homozygous CCR5 delta 32. This mutation makes people immune to most types of HIV.

Mutations Drive Aging and Shape Epigenetic Clock

New research shows somatic mutations drive epigenetic changes tied to aging. This discovery reshapes our understanding of aging and challenges current anti-aging strategies.


Summary: A new study has uncovered a direct link between somatic mutations and epigenetic modifications, challenging established views on aging. Researchers found that random genetic mutations drive predictable changes in DNA methylation, offering new insights into the relationship between mutation accumulation and epigenetic clocks.

This suggests that epigenetic changes may track, rather than cause, aging, making it harder to reverse aging than previously thought. These findings redefine our understanding of aging at the molecular level and hold significant implications for future anti-aging therapies.

Complete recombination map of the human genome created

Scientists at deCODE genetics/Amgen have constructed a complete map of how human DNA is mixed as it is passed down during reproduction. The map marks a major step in the understanding of genetic diversity and its impact on health and fertility. It continues 25 years of research at deCODE genetics into how new diversity is generated in the human genome, and its relationship to health and disease.

The new map, appearing today in the online edition of Nature, is the first to incorporate shorter-scale shuffling, (non crossover) of grandparental DNA, which is difficult to detect due to the high DNA sequence similarity. The map also identifies areas of DNA that are devoid of major reshuffling, likely to protect critical genetic functions or prevent chromosomal problems. This insight offers a clearer picture of why some pregnancies fail and how the genome balances diversity with stability.

While this shuffling, known as , is essential for genetic diversity, errors in the process can lead to serious reproductive issues. These failures can result in genetic errors that prevent pregnancies from continuing, helping to explain why infertility affects around one in ten couples worldwide. Understanding this process offers new hope for improving fertility treatments and diagnosing pregnancy complications.

Mitochondria may be a promising therapeutic target for inflammatory diseases

Scientists in the laboratory of Navdeep Chandel, Ph.D., the David W. Cugell, MD, Professor of Medicine in the Division of Pulmonary and Critical Care, have discovered how mitochondria influence the body’s immune response through modulating specific cell signaling pathways, according to a study published in Science Advances.

The findings highlight the potential of targeting specifically in immune cells to treat a range of inflammation-related diseases.

“Therapies aimed at improving mitochondrial activity could benefit inflammatory diseases such as , sepsis, and chronic infections by enhancing the immune system’s ability to regulate inflammation,” said Chandel, also a professor of Biochemistry and Molecular Genetics and a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.

Why our biological clock ticks: Research reconciles major theories of aging

Researchers at University of California San Diego School of Medicine have published results that shed new light on an old question: what causes aging at the molecular level? Their findings, published in Nature Aging, describe a never-before-seen link between the two most accepted explanations: random genetic mutations and predictable epigenetic modifications. The latter, also known as the epigenetic clock theory, has been widely used by scientists as a consistent, quantitative measure of biological aging.

However, the new research suggests that the process may not be so simple.

“Major research institutions and companies are betting on turning back the epigenetic clock as a strategy to reverse the effects of aging, but our research suggests that this may only be treating a symptom of aging, not the underlying cause,” said co-corresponding author Trey Ideker, Ph.D., a professor at UC San Diego School of Medicine and UC San Diego Jacobs School of Engineering.

Personalized whole-brain neural mass models reveal combined Aβ and tau hyperexcitable influences in Alzheimer’s disease

Alzheimer’s disease (AD) is defined by synaptic and neuronal degeneration and loss accompanied by amyloid beta (Aβ) plaques and tau neurofibrillary tangles (NFTs)1,2,3. In vivo animal experiments indicate that both Aβ and tau pathologies synergistically interact to impair neuronal circuits4. For example, the hypersynchronous epileptiform activity observed in over 60% of AD cases5 may be generated by surrounding Aβ and/or tau deposition yielding neuronal network hyperactivity5,6. Cortical and hippocampal network hyperexcitability precedes memory impairment in AD models7,8. In an apparent feedback loop, endogenous neuronal activity, in turn, regulates Aβ aggregation, in both animal models and computational simulations9,10. Multiple other factors involved in AD pathogenesis-remarkably, neuroinflammatory dysregulations-also seemingly influence neuronal firing and act on hypo/hyperexcitation patterns11,12,13. Thus, mounting evidence suggest that neuronal excitability changes are a key mechanistic event appearing early in AD and a tentative therapeutic target to reverse disease symptoms3,4,7,14. However, the exact patterns of Aβ, tau and other disease factors’ neuronal activity alterations in AD’s neurodegenerative progression are unclear as in vivo and non-invasive measuring of neuronal excitability in human subjects remains impractical.

Brain imaging and electrophysiological monitoring constitute a reliable readout for brain network degeneration likely associating with AD’s neuro-functional alterations3,15,16,17,18. Patients present distinct resting-state blood-oxygen-level-dependent (BOLD) signal content in the low frequency fluctuations range (0.01–0.08 Hz)16,19. These differences increase with disease progression, from cognitively unimpaired (CU) controls to mild cognitive impairment (MCI) to AD, correlating with performance on cognitive tests16. Another characteristic functional change is the slowing of the electro-(magneto-) encephalogram (E/MEG), with the signal shifting towards low frequency bands15,18. Electrophysiological spectral changes associate with brain atrophy and with losing connections to hub regions including the hippocampus, occipital and posterior areas of the default mode network20. All these damages are known to occur in parallel with cognitive impairment20. Disease processes also manifest differently given subject-specific genetic and environmental conditions1,21. Models of multiple pathological markers and physiology represent a promising avenue for revealing the connection between individual AD fingerprints and cognitive deficits3,18,22.

In effect, large-scale neuronal dynamical models of brain re-organization have been used to test disease-specific hypotheses by focusing on the corresponding causal mechanisms23,24,25. By considering brain topology (the structural connectome18) and regional profiles of a pathological agent24, it is possible to recreate how a disorder develops, providing supportive or conflicting evidence on the validity of a hypothesis23. Generative models follow average activity in relatively large groups of excitatory and inhibitory neurons (neural masses), with large-scale interactions generating E/MEG signals and/or functional MRI observations26. Through neural mass modeling, personalized virtual brains were built to describe Aβ pathology effects on AD-related EEG slowing25 and several hypotheses for neuronal hyperactivation have been tested27. Simulated resting-state functional MRI across the AD spectrum was used to estimate biophysical parameters associated with cognitive deterioration28. In addition, different intervention strategies to counter neuronal hyperactivity in AD have been tested10,22. Notably, comprehensive computational approaches combining pathophysiological patterns and functional network alterations allow the quantification of non-observable biological parameters29 like neuronal excitability values in a subject-specific basis1,3,18,21,23,24, facilitating the design of personalized treatments targeting the root cause(s) of functional alterations in AD.

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