Cofactor Genomics studies T cell state profiling to predict immunotherapy response
April 2022—Cofactor Genomics announced publication of a study showing that its multianalyte biomarkers based on T cell subtype profiling (TCSP) predicted patient response to anti-PD-1 therapy in three cancers (lung, melanoma, head and neck) and outperformed the indicated PD-L1 test and tumor mutational burden (Schillebeeckx I, et al. Sci Rep. 2022;12[1]:1342).
By understanding T cell state or subtype (activated versus exhausted state), the company said, the research moves beyond immune cell quantification in the tumor to more detailed immune state profiling.
The authors reported that characterizing the five T cell subtypes in formalin-fixed, paraffin-embedded patient samples “enables new opportunities for researching the tumor-immune microenvironment, studying response to immunotherapies, and developing biomarkers to predict patient response to treatment.”
To create a better biomarker, Cofactor said in a news release, it built five novel RNA models that were used to characterize the full spectrum of T cell adaptive immunity. The T cell subtype profiling presented in its work, the company explains, enables researchers to use RNAseq to deeply investigate the adaptive immune response in any tissue, including readily available but preserved clinical samples.
In the study, patient cohorts with head and neck squamous cell carcinoma, non-small cell lung cancer, and melanoma were characterized for the five T cell states (naive, activated, exhausted, effector memory, central memory). Using machine learning methods, the combined estimates created a multianalyte biomarker. This biomarker was predictive of objective response and survival. The T cell subtype profiling method had predictive performance superior to other expression signatures, as well as PD-L1 IHC and tumor mutational burden. For example, in lung cancer, the TCSP predicted durable clinical benefit with an AUC of 0.78, while PD-L1 IHC and tumor mutational burden measures had AUCs of 0.73 and 0.71, respectively.
In a continuation of this research, Cofactor is recruiting patients across multiple indications and in more than 20 health care systems to validate these biomarkers and the T cell state models.
Program aims to accelerate SARS-CoV-2 variant ID
Thermo Fisher Scientific says it is collaborating with the National Institutes of Health Rapid Acceleration of Diagnostics (RADx) initiative, Helix, and Rosalind to develop a new genotyping method for SARS-CoV-2 that could speed up the identification of variants.
The program, which will make it possible to scale up surveillance efforts in the United States, uses a PCR-based genotyping approach that can be implemented in any testing laboratory that uses real-time PCR. The data generated from the program will be available to the public through the Rosalind Tracker website.
The effort was funded by the National Institute of Biomedical Imaging and Bioengineering as part of the RADx initiative to increase SARS-CoV-2 testing capacity and accessibility.
FDA clears Vitek MS Prime
The Food and Drug Administration has cleared the Vitek MS Prime, BioMérieux’s new MALDI-TOF mass spectrometry identification system. The benchtop system is a new generation of the Vitek MS.
BioMérieux says the new system integrates with Vitek 2 for antimicrobial susceptibility testing and with Myla middleware for data integration and insights.
Roche to collaborate with Bristol Myers Squibb
Roche is collaborating with Bristol Myers Squibb to support the advancement of two assays for use in clinical trials with the development and deployment of two new digital pathology algorithms.
In the first project under this collaboration, Roche Digital Pathology is creating an AI-based image analysis algorithm to aid pathologists in interpreting the on-market Ventana PD-L1 (SP142) assay. Bristol Myers Squibb will use this algorithm to generate biomarker data from clinical trial samples.
In the second project, Roche will leverage its Open Environment collaboration with PathAI to integrate a PathAI-developed algorithm for CD8 biomarker analysis into the Navify Digital Pathology workflow software. Bristol Myers Squibb will use the algorithm to analyze clinical trial samples that have been stained with Roche’s CD8 assay and generate quantitative spatial biomarker data.
“By using our Navify Digital platform to interpret tissue-based assays and AI algorithms, pathologists are better able to identify targeted therapy options, ultimately improving patient care,” Jill German, head of Roche Diagnostics pathology customer area, said in a March 25 statement.