On January 12, 2026, 10x Genomics, one of the leading providers of single-cell and spatial biology technologies, announced a collaboration with Brigham and Women’s Hospital (Boston) that is expected to attract significant attention in rheumatology and immunology. The aim of the large-scale, longitudinal study is to generate high-resolution, single-cell-based immune signatures from peripheral blood from 1,000 patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and giant cell arteritis (GCA), which are intended to objectively map disease activity, relapses, remission and treatment response.

Why the topic is so explosive

Autoimmune diseases are among the greatest therapeutic challenges of modern medicine. In the USA alone, about 24 million people suffer from it, and more than 80 million worldwide. Diagnostics and therapy control are still largely based on:

• Non-specific inflammation parameters (ESR, CRP)
• autoantibodies (which often appear long before clinical signs or persist even though the disease is inactive)
• Subjective symptom scores (DAS28, SLEDAI etc.)
• Doctor’s experience

The result is aptly described by experts as a “clinical random walk”: You often try different drugs for months or years until you accidentally land the right hit – or not. While biologics and JAK inhibitors have massively expanded treatment options, the response rate remains as low as 30-50% after 6 months for many indications. Predictors of response are almost completely absent.

This is exactly where the cooperation comes in: Instead of looking at a few soluble markers, the entire circulating immune system is to be mapped in its cellular heterogeneity and dynamics.

Technical basis: Chromium Flex and longitudinal design

The study uses 10x Genomics’ Chromium Flex Single-Cell Gene Expression Kit – one of the most robust and scalable platforms for highly parallel single-cell RNA sequencing available today. Chromium Flex allows the fixation of samples immediately after blood collection, which is essential for multicenter studies with routine laboratories.

The plan is:

• Recruitment of 1,000 patients (RA, SLE, GCA) + healthy controls
• Longitudinal blood samples during routine rounds over several years
• Parallelization with clinical scores, laboratory data, medication and imaging
• Creation of a reference atlas of circulating immune cells in different disease states

The aim is to identify patterns that can distinguish between:

• controlled vs. active disease
• imminent relapse vs. stable remission
• Therapy Responders vs. Non-Responders
• different phases and subtypes of the disease

Clinical relevance: From research to clinical report

Particularly interesting is the explicitly formulated plan to develop a framework for a future clinical report from the data. This would mean that few, clear, interpretable scores or classifiers should be derived from the complex single-cell data – similar to the Oncotype DX score in oncology or PAM50 subtyping in breast cancer.

If this succeeds, one could routinely send in blood samples in the future and receive a report within a few days telling the rheumatologist:

• “Current molecular activity corresponds to a high disease activity status → escalation of therapy makes sense”
• “Immune profile shows incipient relapse 4–6 weeks in advance → Preventive dose adjustment possible”
• “Patient belongs to subgroup X → high probability of response to IL-6 blockers”

This would be a real paradigm shift: away from symptom- and CRP-driven “trial-and-error” to data-driven, predictive rheumatology.

Realistic assessment of the chances of success

Positive:

• The cohort is very large for single-cell studies with 1,000 patients
• Longitudinal design with clinical phenotyping is the gold standard
• Brigham and Women’s Hospital is one of the world’s best clinical immunology facilities
• 10x Genomics already has experience with large-scale translational projects (e.g. Human Cell Atlas contributions)

Critical points:

• Single-cell data are extremely noisy and heterogeneous – extracting robust, clinically actionable signatures from blood (as opposed to tissue) is technically challenging
• Translation into a validated, reproducible clinical trial typically takes 8-12 years (FDA CLIA certification, prospective validation, cost-benefit analysis)
• Competition: Several groups worldwide are working on similar approaches (e.g. with CyTOF, Olink, RNA-Seq panels). Whoever brings a validated test to market first wins

Strategic importance for 10x Genomics

The cooperation is part of a clear strategic realignment of 10x: The company wants to develop from a pure RUO tool provider to a player in the clinical-translational sector. Further indications:

• Announcing a CLIA Certified Lab
• Partnership with Dana-Farber Cancer Institute
• Several parallel initiatives in oncology and immunology

This is consistent: The RUO market continues to grow, but the large margins and long-term contracts are in the clinical sector.

Conclusion

The announced study is one of the most ambitious attempts to date to bring single-cell technology directly into daily rheumatology practice. If robust, predictive immune signatures can be extracted from the blood samples of 1,000 patients and translated into a clinically usable report, this could fundamentally change the treatment of RA, SLE and vasculitides – away from trial-and-error to data-driven precision medicine.

However, the road is still long, technically demanding and fraught with risk. But that’s exactly why the cooperation between 10x Genomics and Brigham and Women’s Hospital is so exciting: If anyone can do it, it’s this combination of technology powerhouse and clinically top institution.

The article was originally published by LabNews Media LLC

Editor: X-Press Journalistenbüro GbR

Gender Notice. The personal designations used in this text always refer equally to female, male and diverse persons. Double/triple naming and gendered designations are used for better readability. ected.