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Forecasting Protein Aggregation with an Improved Algorithm

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A new, improved algorithm for studying protein aggregation could help biologics manufacturers design better-performing products with less experimental effort. The software, developed by scientists based in Barcelona, offers the ability to analyze the aggregation of proteins drawn from the AlphaFold protein structure database, as well as helping companies identify more soluble alternatives.

“Protein aggregation is a bottleneck in the production and manufacturing of biologics,” explains Salvador Ventura, PhD, a professor in the department of biochemistry and molecular biology at the Autonomous University of Barcelona (UAB).

The problem, he explains, is that many proteins used as therapies evolved to be soluble at the concentrations found in the human body. But therapeutics, such as antibodies, are produced in as high a concentration as possible.

“We want the product to deliver the maximum dose with the minimum amount of injection,” he says. “But proteins aren’t designed to be soluble at these concentrations, and their aggregation causes different effects.”

These can include the patient’s immune system reacting negatively or the aggregated product ceasing to work.

To overcome this problem, Ventura says, companies and labs try to forecast protein aggregation, usually experimentally with high-throughput combinational assays. But these approaches are not convenient for startups or small spinoff companies.

A computational approach, such as his algorithm, now in its fourth generation, can help these companies predict and design around protein aggregation.

It offers the ability to draw protein structures from AlphaFold to analyze likely protein aggregation using simulations of molecular dynamics. Users, he says, can also choose to mutate selected parts of the protein, identify other proteins in the same family, and even look at the possible impact of pH on solubility.

“Our lab is both computational and experimental, so most of the designs we’ve made, we’ve already proved by experiment,” Ventura says.

Limitations include the scarcity of high-quality experimental data available to train the algorithm, he explains.

Going forward, the team intends to model which solution and formulation conditions best maintain the stability of therapeutic proteins in manufacturing and clinical settings. “We’re working on these next steps already,” he says. “Although, as yet, we don’t have an algorithm for this.”

Ventura spoke about the latest version of his algorithm at the Bioprocessing Summit Europe in March.

The post Forecasting Protein Aggregation with an Improved Algorithm appeared first on GEN – Genetic Engineering and Biotechnology News.

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STAT+: Trump order to advance psychedelic treatments generates excitement — and worries

President Trump’s executive order aimed at loosening restrictions on psychedelics as mental health treatments was largely applauded by advocates. But some also quietly worry the White House’s role in trying to bolster the field risks politicizing it and undermining the credibility of research.

The order, which Trump said originated with a text from podcaster Joe Rogan about psychedelics research, directs the Food and Drug Administration to expedite the review of some compounds and calls for the establishment of a new regulatory pathway for experimental psychedelics to be tried by terminally ill patients. It also allocates funding to states developing research programs.

While the order does not actually reschedule any drugs or change legislation, many advocates and researchers welcomed the move, saying it signals the administration’s interest in advancing psychedelics as treatments and could help ease bottlenecks in expanding access.

Continue to STAT+ to read the full story…

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President Trump’s executive order aimed at loosening restrictions on psychedelics as mental health treatments was largely applauded by advocates. But some also quietly worry the White House’s role in trying to bolster the field risks politicizing it and undermining the credibility of research.

The order, which Trump said originated with a text from podcaster Joe Rogan about psychedelics research, directs the Food and Drug Administration to expedite the review of some compounds and calls for the establishment of a new regulatory pathway for experimental psychedelics to be tried by terminally ill patients. It also allocates funding to states developing research programs.

While the order does not actually reschedule any drugs or change legislation, many advocates and researchers welcomed the move, saying it signals the administration’s interest in advancing psychedelics as treatments and could help ease bottlenecks in expanding access.

Continue to STAT+ to read the full story…

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AACR 2026: Cancers of Unknown Primary Identified by DNA Methylation AI Model

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SAN DIEGO – Researchers from Kindai University in Japan have developed a machine learning model that accurately predicts the origin of diverse cancer types in patients with cancers of unknown primary (CUP) by analyzing CpG-based DNA methylation. Results showed that the model correctly identified the cancer type in about 95% of cases in the test cohort, and achieved 87% accuracy when applied to an independent validation cohort from 31 cases representing 17 different cancer types. The work was presented at the American Association for Cancer Research (AACR) Annual Meeting.  

“Our findings suggest that DNA-based approaches can help identify where a cancer may have started, even when the original tumor is not visible,” said Marco A. De Velasco, PhD, a faculty member in the department of genome biology at Kindai University in Japan.  

CUP are metastatic malignancies in which the primary cancer site could not be identified. These cancers are often associated with poorer outcomes, as patients are typically treated with broad, nonspecific chemotherapy regimens rather than therapies targeted to a specific cancer type. 

Approximately only 15-20% of patients with CUP show features that allow site-specific therapies. Patients receiving site-directed therapy can survive up to 24 months, compared with six to nine months for those receiving standard treatment. 

Patterns in tumor biology, such as gene activity or chemical modifications to DNA, can differ between cancer types and persist even after the cancer has spread and guide development of these therapies. While some methods have shown promise, they have yet to demonstrate clear survival benefits in clinical trials. 

The model was developed using methylation data from nearly 7,500 patients with 21 different cancer types obtained from The Cancer Genome Atlas Program and other public datasets. Using machine learning, the researchers identified CpG methylation and built methylation profiles that were associated with different tumor types. 

Del Velasco emphasized that the study achieved high accuracy in predicting the origin of diverse cancer types using a small subset of DNA markers, about 1,000 CpG regions selected from hundreds of thousands across the genome. “This is important because it shows that we can simplify complex molecular data while still maintaining strong predictive performance,” he said. 

As a limitation, the model was developed using cancers with known origins, rather than true CUP. Testing in CUP patients is important to understand how well the model performs in clinical settings. Additionally, not all tumors are easily accessible for genetic testing, particularly tumors in advanced stage. Looking ahead, the authors aim to adapt and evaluate the model using blood-based biopsy to analyze circulating tumor DNA instead of relying on DNA from tissue samples. 

The post AACR 2026: Cancers of Unknown Primary Identified by DNA Methylation AI Model appeared first on GEN – Genetic Engineering and Biotechnology News.

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Viatris recalls extended-release Xanax over dissolution test failure

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Viatris, which Pfizer created in 2020, voluntarily withdrew extended-release products made at a plant in Ireland after an analysis revealed an issue that could affect bioavailability.

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