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A new tool is revealing the invisible networks inside cancer

Spanish researchers have created a powerful new open-source tool that helps uncover the hidden genetic networks driving cancer. Called RNACOREX, the software can analyze thousands of molecular interactions at once, revealing how genes communicate inside tumors and how those signals relate to patient survival. Tested across 13 different cancer types using international data, the tool matches the predictive power of advanced AI systems—while offering something rare in modern analytics: clear, interpretable explanations that help scientists understand why tumors behave the way they do.

Optogenetic Cancer Therapy Using the Light-Driven Outward Proton Pump Rhodopsin Archaerhodopsin-3 (AR3)Click to copy article linkArticle link copied!

Medicines used for cancer treatment often cause serious side effects by damaging normal cells due to nonspecific diffusion. To address this issue, we previously developed an optical method to induce apoptotic cell death via intracellular pH alkalinization using the outward proton pump rhodopsin, Archaerhodopsin-3 (AR3) in various noncancer model cells in vitro and in vivo. In this study, we applied this method to cancer cells and tumors to evaluate its potential as an anticancer therapeutic strategy. First, we confirmed that AR3-expressing murine cancer cell lines (MC38, B16F10) showed apoptotic cell death upon green light irradiation, as indicated by increased levels of cell death and apoptosis-related markers. Next, we established stable AR3-expressing MC38 and B16F10 cells by using viral vectors. When these AR3-expressing cells were subcutaneously transplanted into C57BL/6 mice, the resulting tumors initially grew at a rate comparable to that of control tumors lacking AR3 expression or light stimulation. However, upon green light irradiation, AR3-expressing tumors exhibited either a marked reduction in size or significantly suppressed growth, accompanied by the induction of apoptosis signals and decreased proliferation signals. These results demonstrate that AR3-mediated cell death has potent antitumor effects both in vitro and in vivo. This optical method thus holds promise as a novel cancer therapy with potentially reduced side effects.

Scientists chart over 140,000 DNA loops to map human chromosomes in the nucleus

One of the most detailed 3D maps of how the human chromosomes are organized and folded within a cell’s nucleus is published in Nature.

Chromosomes are thread-like structures that carry a cell’s genetic information inside the nucleus. Rather than existing as loose strands or only as the familiar X-shapes seen in textbooks, chromosomes fold into specific three-dimensional forms. How they fold, the structures they form, and their placement play crucial roles in maintaining proper cellular functions, gene expression, and DNA replication.

The team involved in the 4D Nucleome Project, whose goal was to understand the 3D organization of human chromosomes in the nucleus and how it changes over time, identified over 140,000 DNA looping interactions in human embryonic stem cells and fibroblasts. They also presented computational methods that can predict genome folding solely from its DNA sequence, making it easier to determine how genetic variations—including those linked to disease—affect genome structure and function.

Cardiovascular Disease Biomarker Deep Dive (Test #7 In 2025)

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Chromosome shattering in cancer

Cancer cells often contain an abnormal number of chromosomes as a result of incorrect chromosome segregation during cell division.

These fragments of genetic material can be encapsulated by a membrane, forming small nucleus-like structures called micronuclei. These structures often rupture, exposing chromatin (DNA and associated proteins) to the harsh environment of the cytoplasm, which can lead to large-scale DNA damage in a process called chromothripsis, or chromosome shattering and scrambling.

In a new Science study, researchers report that the cytoplasmic protein NEDD4-binding protein 2 may be responsible for chromothripsis.

Learn more in a new.


A protein that cuts double-stranded DNA contributes to chromosome scrambling in human cancer cells.

Stanley Clarke and Marcin Imieliński Authors Info & Affiliations

Pressing pause: A small genetic stop may have helped complex life evolve

Humans have it. So does Drosophila. But not yeast. That “it” is a small pause at the start of gene activity—a brief molecular halt that may have helped life evolve from simple cells to complex animals.

A new study by Charles Danko, associate professor in life science and technology at Cornell’s Baker Institute for Animal Health and in the Department of Biomedical Sciences in the College of Veterinary Medicine, and colleagues explores how this key step in gene regulation—promoter-proximal pausing—evolved across species.

Promoter-proximal pausing occurs just after a cell’s molecular “copy machine”– RNA polymerase II—is activated. The polymerase temporarily stops, usually after about 20 to 60 nucleotides or “letters” of the gene, waiting for further signals.

How ancient viral DNA shapes early embryonic development

A new study from the MRC Laboratory of Medical Sciences (LMS) in London, UK reveals how ancient viral DNA once written off as “junk” plays a crucial role in the earliest moments of life. The research, published in Science Advances, begins to untangle the role of an ancient viral DNA element called MERVL in mouse embryonic development and provides new insights into a human muscle wasting disease.

Transposable elements are stretches of DNA that can move around the genome. Many of these DNA sequences originate from long ago, when viruses inserted their genetic material into our ancestors’ genomes during infection. Today, these viral transposable elements make up around 8–10% of the mammalian genome.

Once disregarded as “junk” DNA, we now know that many transposable elements play an important role in influencing how genes are turned on and off, especially during early development. They have a variety of beneficial and harmful roles in the body, for example, some help regulate normal immune responses, while others can disrupt genes and contribute to diseases like cancer.

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