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Machine learning reveals a functional network of genes and proteins in human cancer

Large-scale protein and gene profiling have massively expanded the landscape of cancer-associated proteins and gene mutations, but it has been difficult to discern whether they play an active role in the disease or are innocent bystanders.

In a study published in Nature Cancer, researchers at Baylor College of Medicine revealed a powerful and unbiased machine learning-based approach called FunMap for assessing the role of cancer-associated mutations and understudied proteins, with broad implications for advancing and informing therapeutic strategies.

“Gaining functional information on the genes and proteins associated with cancer is an important step toward better understanding the disease and identifying potential therapeutic targets,” said corresponding author Dr. Bing Zhang, professor of molecular and and part of the Lester and Sue Smith Breast Center at Baylor.

DNA sequencing test can predict prognosis for advanced prostate cancer patients

Published in Nature Communications, a new study led by the University of Minnesota Medical School and Duke University found that a DNA sequencing test for advanced prostate cancer patients can distinguish between patients with poor and favorable prognoses.

The new blood-based —called AR-ctDETECT—is designed to detect and analyze small fragments of tumor-derived DNA in the blood of certain with advanced, .

In this new study, the AR-ctDETECT test was used to analyze DNA from more than 770 from a phase 3 clinical trial of advanced prostate cancer patients. The test identified circulating tumor DNA (ctDNA) in 59% of patients with metastatic prostate cancer. Patients with detectable circulating tumor DNA had significantly worse overall survival compared to those without. These results demonstrate the potential of the AR-ctDETECT test to provide key genetic information to tailor treatments based on similar characteristics among patients.

Centromeres could be ‘hotspots’ for evolutionary innovation

New research reveals that centromeres, which are responsible for proper cell division, can rapidly reorganize over short time scales. Biologists at the University of Rochester are calling a discovery they made in a mysterious region of the chromosome known as the centromere a potential game-changer in the field of chromosome biology.

“We’re really excited about this work,” says Amanda Larracuente, the Nathaniel and Helen Wisch Professor of Biology, whose lab oversaw the research that led to the findings, which appear in PLOS Biology.

The discovery involves an intricate and seemingly carefully choreographed genetic tug-of-war between elements in the centromere, which is responsible for proper cell division. Instead of storing genes, centromeres anchor proteins that move chromosomes around the cell as it splits. If a centromere fails to function, cells may divide with too few or too many chromosomes.

Cas9-PE system achieves precise editing and site-specific random mutation in rice

Achieving the aggregation of different mutation types at multiple genomic loci and generating transgene-free plants in the T0 generation is an important goal in crop breeding. Although prime editing (PE), as the latest precise gene editing technology, can achieve any type of base substitution and small insertions or deletions, there are significant differences in efficiency between different editing sites, making it a major challenge to aggregate multiple mutation types within the same plant.

Recently, a collaborative research team led by Li Jiayang from the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Science, developed a multiplex gene editing tool named the Cas9-PE system, capable of simultaneously achieving precise editing and site-specific random mutagenesis in rice.

By co-editing the ALSS627I gene to confer resistance to the herbicide bispyribac-sodium (BS) as a selection marker, and using Agrobacterium-mediated transient transformation, the researchers also achieved transgene-free gene editing in the T0 generation.

Genetic study breaks the silence on how fish and lizards regenerate hearing

A new USC Stem Cell study published in the Proceedings of the National Academy of Sciences has identified key gene regulators that enable some deafened animals—including fish and lizards—to naturally regenerate their hearing. The findings could guide future efforts to stimulate the regeneration of sensory hearing cells in patients with hearing loss and balance disorders.

Led by first author Tuo Shi and co-corresponding authors Ksenia Gnedeva and Gage Crump at the Keck School of Medicine of USC, the study focuses on two cell types in the inner ear: the sensory cells that detect sound, and the that create an environment where sensory cells can thrive.

In highly regenerative species such as fish and lizards, supporting cells can also transform into replacement sensory cells after injury—a capacity absent in humans, mice and all other mammals.

Weaving Textiles from Recombinant Spider Silk

Precious few garments have been made of spider silk. In 2012, a cape and shawl made from natural spider silk were displayed at the Victoria and Albert Museum, where visitors learned that the garments were the result of a unique project that spanned eight years and involved the harvesting of silk from 1.2 million spiders. In 2019, a rather less painstaking project utilized fibroin, the protein found in natural spider silk, to fabricate an outerwear jacket, North Face’s Moon Parka. Starting with fibroin meant that silk could be sourced from genetically modified bacteria, which are easier to work with than spiders. Nonetheless, the Moon Parka, which takes its name from the word moonshot, was never meant to be mass produced. It was available by lottery for just a limited time.

Museum pieces and moonshots are hardly synonymous with “mass production.” Is there another way to generate spider silk–based textiles, one that has more commercial potential? Yes, according to Kraig Biocraft Laboratories, which uses transgenic silkworms to produce lines of recombinant spider silk. The company plans to produce up to 10 metric tons of spider silk in 2025. Production of actual spider silk lines on this scale would allow textile manufacturers to test the silk on their own equipment.

It’s not just textiles that may benefit. Recombinant spider silk’s tensile strength, weight, and durability make it attractive for myriad applications, including tissue scaffolds and sutures in the biomedical field, as well as textiles and ballistic materials.

Genetic code discovery could redefine understanding of cancer origins

A group of scientists at VCU Massey Comprehensive Cancer Center has revealed a new genetic code that acts like a cancer ringleader, recruiting and deploying a gang of tumor cells to incite a biological turf war by invading healthy organs and overpowering the normal cells.

This discovery— published today, Dec. 9, in Nature Biotechnology —could unveil an entirely different understanding of the origins of cancer within the body, as well as offer insight into new treatment strategies that could target the growth of tumors in their earliest stages.

The study authors have also developed an intravenous therapy that empowers healthy cells to mount an and build up a defensive resistance against these invading tumor cells. This treatment has already been proven effective in ovarian tumors, but the implications of this research could be universal to all .

FDA Approves New Cancer Treatments

In August, the Food and Drug Administration (FDA) granted accelerated approval of Tecelra (afamitresgene autoleucel)— the first T-cell receptor therapy for solid tumors—for people with inoperable or metastatic synovial sarcoma. Tecelra is a gene therapy created from a patient’s own T cells. A sample of cells is removed and genetically modified to express a natural T-cell receptor that targets MAGE-A4, an antigen expressed on cancer cells. In the Phase II SPEARHEAD-1 trial, the overall response rate was 43%, and 39% of responders were still doing well a year later.

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