NBC 2025 Preview: Inside CheckImmune’s playbook for cell-specific drug insights

At next week’s National Biotechnology Conference, Berlin-based clinical research firm CheckImmune GmbH will showcase how layering single-cell multi-omics provides insights into drug action and immune responses that bulk readouts (averaged measurements from a large population of cells) often miss. In rapid-fire talks on May 6, the Berlin startup will show how single-cell multiomics and spatial skin profiling expose cellular dynamics that standard assays miss.​

Single-cell multiomics: A fuller picture in 15 minutes

Traditional scRNA-seq pinpoints which genes fire inside individual cells, but it leaves a gap between RNA potential and protein reality. CheckImmune co-founder vice president Levent Akyuez, Ph.D., says the answer is to layer protein and epigenetic readouts on the same cells, based on their multi-omic workflow experience. “Some markers, or even lineage markers, are not so well expressed on the mRNA level,” Akyuez said. “For real cell characterization, it’s mandatory to also have proteomics.”

Experience suggests the multiomic view provides crucial detail, especially for specific cell subpopulations. “If you narrow down the population… [and rely only on RNA] information you will lose,” Akyuez explained. Analyzing protein alongside RNA for these distinct populations, he stressed, prevents this loss of information.

The approach’s Achilles’ heel is validation under GCLP guidelines, demanding reproducibility across a complex, multi-step workflow. “Since this workflow is much more complicated, we increase the number of the inter-operator comparisons from two to three operators to see what is the difference of the assay if different operators are performing these,” Akyuez explained. “You have many layers of your qualification.”

Failures often stem from initial sample handling, making pre-analytics key. Akyuez explained their simplified protocol addresses this directly: “Our cryomedia approach – just mixing blood… and [freezing] – was a big help,” he said, noting it avoids the “20–30% dropout” common with traditional multi-step PBMC processing and cryopreservation.

Looking ahead, Akyuez stressed that making the multi-omic workflow faster is paramount for broader clinical adoption, although adding future layers like metabolomics remains of scientific interest. He contrasted the current state with faster methods: “In flow cytometry, you have a very short turnaround time… these data may be used for decision-making within a clinical trial.” This speed, he noted, is lacking for multi-omics: “And this is something which you don’t have currently in the single-cell field… all this approach – making libraries, having the sequencing and then downstream analysis – takes a lot of time to get the data and draw conclusions out of it.”

Skin profiling: Where location meets function

Scientist Sandra Jagdmann, Ph.D., explains CheckImmune’s focus on skin, a key site for studying immune responses, especially for dermatological diseases and injection site reactions. Her workflow couples high-parameter flow cytometry with GeoMx spatial transcriptomics to understand both cellular composition and location.

The skin analyses are particularly important in clinical studies involving patients with skin disorders such as psoriasis or atopic dermatitis, Jagdmann said. “It is especially crucial to understand exactly how the drug acts within the skin lesions and how it alters the immune cell profile.” 

Understanding where cells are located provides critical context that flow cytometry alone cannot. “But we have no information of the exact location within the tissue, and we also have no information about cell-cell interaction or gene activity,” Jagdmann noted. “GeoMx analysis is really important to get this information.”

Successfully analyzing skin requires carefully optimized cell dissociation protocols. “We have tested various conditions to optimize our protocol,” she explained. “On the one hand, the incubation time… must be carefully balanced… We also have tested different compositions of the digestion media: collagenase, benzonase, and DNase… the optimal protocol was three hours digestion with benzonase and collagenase, and we have qualified this protocol.”

Sample integrity post-collection is paramount, as improper handling quickly affects viability and specific cell markers. “There’s a really critical step… whether you’re working with tissue or blood: Both must be frozen immediately after being transferred into the cryomedia,” Jagdmann stressed. “Because most cryomedia contain DMSO [dimethyl sulfoxide], if these samples are left at room temperature, cell death can occur very rapidly.” She warned that sensitive markers are particularly affected: “Critical markers are the chemokine marker(s), also CD45RA and CCR7,” detailing those used to identify specific memory T cell populations.

To mitigate this risk, Jagdmann stressed their site management approach: “But yeah, to address this, we have created, for example, a training video for the sites, and also very detailed collection guidelines. We have also seen that it’s really important to provide really prompt feedback to the sites if the sample quality is not so optimal.”

Deep science, regulated rigor

CheckImmune’s founders spun out of Charité with a simple premise: translate academic single-cell techniques into GCLP-grade services. Rare-cell enrichment, multiplexed barcoding and in-house bioinformatics aim to give sponsors mechanistic answers inside tight trial timelines.

“Our aim is to be different compared to the big CROs. If we offer immune assays, they should be more sophisticated or include some additional support in analyzing the data,” Akyuez said. Among the company’s 30 employees, half have Ph.D.s. “The service is quite academic-driven,” Akyuez added.

As modalities grow more complex with bispecifics, gene-edited cells, and lipid-nanoparticle RNA the cost of not knowing what each cell is doing climbs. CheckImmune’s case in Boston is that the tools to gain this deep cellular understanding are finally robust enough for routine trials, and that sponsors who ignore them risk missing core mechanistic insights.

(Session details: Commonwealth Ballroom, May 6. Akyuez 2:45 p.m.; Jagdmann 3:15 p.m. ET.)

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Filed Under: Biospecimens, Immunology, Omics/sequencing

 

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