Single-Cell Survival Modeling Tool Offers New Precision in Cancer Prognosis

Oregon Health & Science University (OHSU) researchers have developed a first of its kind tool, scSurvival, that directly links information from individual tumor cells to patient survival outcomes, allowing clinicians to understand which specific cells are driving disease progression rather than treating them all the same.

“Traditional survival models in cancer rely on bulk data, which average signals across millions of cells and obscure important heterogeneity,” explained senior author Zheng Xia, PhD, associate professor of biomedical engineering in the OHSU School of Medicine and a member of the OHSU Knight Cancer Institute. “Tumors are highly complex ecosystems where different cell subpopulations can have very different and sometimes opposing effects on patient outcomes.”

He told Inside Precision Medicine that “scSurvival is designed to directly model survival using single-cell data, preserving this heterogeneity. Instead of treating a tumor as a single entity, it treats it as a collection of individual cells and learns which specific subpopulations are most associated with survival outcomes. This enables both more accurate prediction and deeper biological insight.”

The tool was designed using a statistical method known as an attention-based multiple-instance Cox regression framework, which constructs survival prediction models from single-cell cancer cohort data while simultaneously identifying cell subpopulations that are strongly associated with patient risk.

“The attention mechanism preserves cellular heterogeneity within each patient, allowing [cell] subpopulations with higher attention scores to be more closely linked to survival probability,” the researchers explain in Cancer Discovery. “The resulting outputs of scSurvival are the attention-adjusted hazard score for each cell along with patient-level risk scores.”

Xia and team tested the performance of scSurvival in two cohorts that included 32 patients with melanoma and 124 patients with liver cancer. Together, the cohorts provided single cell RNA sequencing data for more than 1.1 million individual cells.

They found that key immune cell types were enriched for higher- or lower-hazard cells. For example, monocytes/macrophages were enriched for high-risk subpopulations in both the melanoma and liver cancer cohort, but B cells were enriched for low-risk subpopulations in the melanoma cohort and high-risk subpopulations in the liver cancer cohort.

In both groups, the tool accurately predicted patient outcomes, with cells taken from melanoma patients who did not respond to immunotherapy having significantly higher hazard scores than those taken from responders.

Xia noted that the information scSurvival provides has several translational applications. “Differential gene expression between high- and low-risk cells can be used to develop prognostic biomarkers,” he said. “Pathways enriched in high-risk populations may reveal actionable therapeutic targets, while the abundance of specific cell types can support patient stratification for treatment selection. Importantly, these insights are derived at single-cell resolution, providing greater biological precision than bulk approaches.”

At present, scSurvival is primarily a research tool but Xia believes that longer term, it has potential clinical relevance. “For example, signatures derived from survival-associated cell populations could be translated into more practical assays (e.g., bulk RNA or targeted panels) for patient stratification,” he suggested. “However, direct clinical deployment would require further validation, simplification, and standardization.”

According to Xia, one of the biggest challenges to widespread adoption of the tool is the limited availability of large, well-annotated single-cell datasets with matched survival data, as single-cell sequencing is not yet routine in clinical workflows. But as more clinical trials adopt single-cell sequencing, he expects scSurvival to see broader use in resolving disease at cellular resolution.

The investigators now plan to extend the framework to incorporate spatial transcriptomics, which will allow them to account for how cells are organized within the tumor microenvironment. “We also aim to improve the model’s robustness across datasets and sequencing platforms, and to enhance its biological interpretability. Ultimately, we hope to translate the survival-associated signatures identified by scSurvival into clinically practical tests,” Xia said.

The study findings were also presented at the American Association for Cancer Research Annual meeting 2026 and the open-source scSurvival program and its tutorials are freely available at GitHub, Zenodo and Code Ocean.

The post Single-Cell Survival Modeling Tool Offers New Precision in Cancer Prognosis appeared first on Inside Precision Medicine.

STAT+: Pharmalittle: We’re reading about the FDA speeding up trials, a Supreme Court hearing on ‘skinny labels,’ and more

Top of the morning to you. The middle of the week is upon us and, since you made it this far, why not forge ahead? After all, there is always light at the end of the proverbial tunnel. You never know what you may accomplish. So please join us as we celebrate this notion with a cup or three of delicious stimulation. Our choice today is chocolate raspberry. Meanwhile, we have assembled the latest menu of tidbits to help you along. So please dig in. Have a smashing day, and please feel free to forward any secrets you come across. Our “in basket” is always open. …

The U.S. Food and Drug Administration announced efforts to make clinical trials more efficient, starting by reviewing data in real time from trials conducted by AstraZeneca and Amgen, STAT writes. The agency also asked the public to weigh in on a potential pilot program to work with companies that use AI to enhance safety monitoring and medication dose selections, identify safety signals, and improve patient recruitment in clinical trials. The trials will rely on a real-time data platform built by Paradigm Health, and the goal is to cut down on the time regulators and companies spend sending data back and forth. FDA Commissioner Marty Makary said at a press conference that agency reviewers will be able to view safety signals and clinical endpoints via Paradigm’s platform.  

Pfizer settled ‌patent disputes with three generic drugmakers over its blockbuster heart drug Vyndamax, effectively extending its patent protection until 2031 and delaying cheaper ​copies from entering the market, Reuters says. The deals resolve ​patent infringement lawsuits against Dexcel Pharma, Hikma Pharmaceuticals, ⁠and Cipla in Delaware federal court over Pfizer’s ​oral drug Vyndamax. A trial over the patent had started ​this week. Pfizer sold nearly $6.4 billion of Vyndamax and related drugs, which treat a serious heart condition called transthyretin amyloid cardiomyopathy, in 2025. The settlements extend ​U.S. patent protection for Vyndamax until June 1, ​2031, subject to other pending litigation. The company had previously expected ‌a ⁠sharp drop in U.S. revenue for the drug in 2029 but now expects sales to hold relatively steady from 2028 through mid-2031.

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New report shows some health equity wins. Experts fear they will be short-lived

A report released Wednesday highlights successes in reducing health disparities in U.S. states. Since the last iteration of the analysis by the Commonwealth Fund, two states expanded eligibility for Medicaid, many states extended postpartum coverage for mothers, and enrollment in Affordable Care Act marketplace plans increased at an unprecedented clip. 

But given the report covered the years 2022 to 2024, many equity researchers fear the gains may be short-lived. Outside experts who reviewed the report predict that policies from the second Trump administration, including changes to insurance coverage and vaccine policies and cuts to programs promoting diversity, equity, and inclusion, will exacerbate inequities.

Read the rest…

STAT+: Health system CEOs get off easy at Congressional hearing on affordability 

The four health system CEOs summoned before a Congressional committee Tuesday likely breathed sighs of relief early in the hearing, when it became clear they had friends in the audience. 

Instead, committee members largely blamed the other party’s health care policies for driving U.S. health care prices to levels inaccessible to many Americans.

The hearing was part of the House Ways and Means Committee’s effort to understand the root causes of rising health care costs in the U.S. It comes three months after the committee heard from the CEOs of the country’s largest health insurers, who largely deflected blame onto hospitals and drugmakers. 

In attendance were the CEOs of some of the country’s largest health systems: HCA Healthcare, a for-profit system of 190 hospitals, and CommonSpirit Health, a nonprofit system of 158 hospitals. The CEOs of New York-Presbyterian and North Carolina’s ECU Health were also there.

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FDA Accepts Label Expansion of Immuno-Oncology Drug to Lupus

For decades, systemic lupus erythematosus (SLE) has resisted tidy solutions, a shapeshifting autoimmune disease that crosses into different organ systems, flares without warning, and leaves cumulative damage in its wake. More than three million people worldwide live inside that uncertainty, navigating cycles of remission and relapse that can erode health over time. Treatments have advanced, but slowly and often not far enough to fundamentally change the trajectory of disease.

Genentech’s obinutuzumab (marketed as Gazyva) is gaining regulatory momentum after submitting a supplemental Biologics License Application (sBLA) to expand its use into SLE, as it repurposes an established immuno-oncology biologic therapy. The U.S. Food and Drug Administration (FDA) is expected to make a decision by the end of 2026 on the label expansion for obinutuzumab, which was first approved on November 1, 2013, for treating previously untreated chronic lymphocytic leukemia (CLL) in combination with chlorambucil.

The ALLEGORY trial

SLE is not a single-pathway disease. It is a systemic autoimmune condition in which the immune system misfires, attacking healthy tissues across the body. Skin, joints, blood vessels, and vital organs, particularly the kidneys, can all be affected by the disease. In roughly half of patients, lupus nephritis develops within five years of diagnosis and significantly increases the risk.

B cells, a type of white blood cell that makes antibodies, are at the heart of this problem. In lupus, these cells generate autoantibodies that target the body’s own structures, triggering chronic inflammation. Over time, repeated flares can lead to irreversible organ damage.

Even diagnosing lupus can be a challenge. Its symptoms mimic those of other diseases, and its presentation varies widely from patient to patient. Delays of two to six years are common, time during which the disease can quietly progress. Against this backdrop, the need for therapies that do more than manage symptoms and actually alter disease biology has become increasingly pressing.

That urgency is what makes the Phase III ALLEGORY trial so consequential. Designed as a randomized, double-blind, placebo-controlled study, ALLEGORY evaluated obinutuzumab in adults with active SLE who were already receiving standard therapy. The goal was not just to see if the drug worked, but to measure whether it could meaningfully shift disease outcomes.

The primary endpoint was the SLE Responder Index 4 (SRI-4), a composite metric that captures improvement across multiple dimensions of disease activity. At 52 weeks, 76.7% of patients receiving obinutuzumab attained an SRI-4 response, in contrast to 53.5% in the placebo group. That difference is both statistically significant and clinically meaningful, representing a substantial improvement in disease control.

In addition, patients treated with obinutuzumab experienced fewer disease flares, reduced reliance on glucocorticoids, and higher rates of remission. In fact, remission rates more than doubled compared to placebo. A greater proportion of patients also reached consistent, low disease activity states, an increasingly important benchmark for a disease defined by unpredictability.

Precision over suppression

What sets obinutuzumab apart is not just its efficacy but how it works. Traditional lupus therapies often rely on broad immunosuppression to dampen the immune system as a whole to control inflammation. While this approach can be effective, it comes with trade-offs, including increased susceptibility to infections and long-term toxicity.

Obinutuzumab takes a more targeted route. It is a glycoengineered, type II anti-CD20 monoclonal antibody designed to bind to a protein expressed on the surface of certain B cells. Once attached, it triggers both direct cell death and enhanced immune-mediated cytotoxicity, leading to potent depletion of the B cells that drive lupus pathology. This dual mechanism allows for a more precise intervention by focusing on the source of disease activity rather than suppressing the immune system indiscriminately. The distinction is more than technical. It represents a broader shift in immunology toward therapies that are not only effective but also strategic.

Regarding safety risk, the data from ALLEGORY offers reassurance. Adverse events were somewhat more frequent in the treatment group, but the overall safety profile remained consistent with what is already known about the drug. Importantly, no new safety signals were identified. In context, the benefit-risk balance appears favorable, particularly given the magnitude of clinical improvement observed. For clinicians, that balance is critical. Lupus is a chronic disease that often requires long-term management, making tolerability as important as efficacy.

If approved for SLE, obinutuzumab would become the first anti-CD20 therapy specifically indicated for the condition, a milestone that could reshape the treatment landscape. It would also expand a therapeutic arsenal that has remained limited for far too long. Despite decades of research, only a small number of therapies have been approved for lupus, so many patients have limited options.

For patient advocates, the significance is immediate and tangible. Albert T. Roy, president and CEO of the Lupus Research Alliance, emphasized both the burden of disease and the promise of new treatments. “The filing submission for Gazyva is a significant step and could provide another treatment option for people with systemic lupus erythematosus (SLE),” Roy told Inside Precision Medicine. “With only two approved therapies for SLE, the potential availability of another option is significant.”

Obinutuzumab enters a field that is changing quickly, with new technologies expanding the possibilities of immune-targeted therapies. Among the most promising are CAR T-cell therapies. They’re also on the far end of the complexity scale, especially as autologous therapies, which involve the extraction of a patient’s T cells, genetically engineering them to target specific immune cells, and reinfusing them into the body. Early studies in lupus have shown intriguing results.

But there are practical limitations. CAR T-cell therapies are resource-intensive, requiring specialized manufacturing, inpatient care, and significant infrastructure. They remain in early-stage trials for lupus and are not yet widely accessible.

The way Roy sees it, monoclonal antibodies like obinutuzumab offer a different path that balances innovation with scalability. “Both approaches target B cells—drivers of lupus pathogenesis—but they work differently,” explained Roy. “Monoclonal antibodies like Gazyva are easier to scale and administer to patients in an outpatient setting, making them more accessible and cost-effective. CAR T immunotherapies, by contrast, require a more complex manufacturing process, as well as inpatient care to prepare the patient for the CAR T infusion. Additionally, CAR T immunotherapies are in early-phase clinical trials, where safety and efficacy are still being evaluated in lupus.”

Reconsidering SLE standard of care

The accessibility of obinutuzumab could prove definitive. Even if approved, obinutuzumab will not automatically transform lupus care. Several challenges remain. Awareness is one. Both patients and healthcare providers need to understand where this therapy fits and who is most likely to benefit. Access is another. As with many biologic therapies, cost and insurance coverage will play a significant role in determining availability.

Then there is the question of personalization. Lupus is a heterogeneous disease, and responses to treatment can vary widely. Identifying biomarkers or clinical characteristics that predict response to B-cell depletion will be essential for helping clinicians improve outcomes.

“The biggest challenges are awareness, education, and access,” said Roy. “If approved by the FDA, patients and providers need to know that this therapy could be an option and understand who may benefit most from it. Given the heterogeneity of lupus, Gazyva might not work for everyone, but having another option would be a big win for patients and their providers.

The emergence of obinutuzumab reflects a broader transformation in lupus research and care. The field is moving away from a reactive model, treating flares as they occur, toward a proactive one aimed at preventing them altogether. There is growing emphasis on reducing or eliminating long-term steroid use, which has long been a cornerstone of lupus treatment but carries significant side effects. At the same time, researchers are exploring combination strategies and new therapeutic targets, building on the foundation of B-cell biology.

The ultimate goal is ambitious but increasingly plausible: sustained remission, potentially even without ongoing therapy. “We’re excited about the potential of Gazyva to build on what’s been shown in lupus nephritis and extend those benefits to a broader lupus population,” Roy said. “Looking ahead, we hope the field continues to shift from broad immunosuppression to targeted therapies, with a continued focus on reducing reliance on steroids and, ultimately, achieving drug-free remission.

Obinutuzumab does not solve lupus. It does not eliminate the complexity of the disease or the challenges that come with it. But it does signal something important: progress that is measurable, meaningful, and potentially transformative. For patients who have long navigated a landscape of limited options and uncertain outcomes, that progress matters. It offers not just another treatment but a different kind of treatment grounded in precision, backed by strong clinical data, and designed with real-world use in mind.

If the regulatory path leads to approval, obinutuzumab could mark the beginning of a new chapter in lupus care defined less by compromise and more by control. And for a disease that has long resisted both, that shift may be the most powerful development yet.

 

The post FDA Accepts Label Expansion of Immuno-Oncology Drug to Lupus appeared first on Inside Precision Medicine.

STAT+: AIDS group sues Trump administration over undisclosed agreement with Gilead

An AIDS activist group filed a lawsuit against the Trump administration for failing to disclose a research and development agreement that was at the heart of a settlement between the U.S. government and Gilead Sciences over patents for HIV prevention.

The settlement resolved a contentious lawsuit that was filed six years ago by the previous Trump administration after the Centers for Disease Control and Prevention maintained that Gilead infringed its patent rights. The agency had helped fund academic research that later formed the basis for two Gilead HIV pills, Truvada and Descovy.

The administration had alleged that Gilead ignored the contributions by CDC scientists, exaggerated its own role in developing HIV prevention drugs, and refused to sign a licensing agreement despite “multiple attempts” at reaching a deal after unfairly reaping hundreds of millions of dollars from research funded by taxpayers.

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DeviceTalks Minnesota 2026 show preview: Speakers, exhibitors and more

It’s almost time for our May 4 DeviceTalks Minnesota show at the University of Minnesota’s McNamara Alumni Center in Minneapolis. We’ve got a great lineup of keynotes — Abbott’s Lisa Earnhardt, Solventum’s Heather Knight, Mike Blue at HistoSonics and Medical 21’s Manny Villafaña — plus more interviews and panels of experts from medical device OEMs…

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