Ata Tuna Ciftlik, PhD, Lunaphore founder, CEO, and board member

A decade ago, the term “spatial biology” had not been coined when Ata Tuna Ciftlik, PhD, developed the core technology behind Lunaphore Technologies while a PhD student at Ecole Politechnique Fédérale de Lausanne (EPFL), the Swiss Federal Institute of Technology.

“We were basically saying that our vision is to bring ‘omics-like approaches in tissue and tumor analytics,” Ciftlik recalled.

He won a Dimitris N. Chorafas Foundation award in 2012 for the technology, focusing on establishing quantitative diagnostic immunohistochemistry for breast cancer diagnosis. The technology applied high-pressure microfluidic circuits that enabled higher fluidic exchange rates, so that both the throughput and the accuracy in biomarker detection could be improved. Ciftlik showed quantification by immunofluorescence of the expression of biomarkers on human tissues in under five minutes, and that the technique could eliminate more than 90% of ambiguous results produced by conventional assays for analysis of the biomarker HER2.

Two years later, in 2014, EPFL spun off Lunaphore, which has worked since then to bring spatial biology into all stages of research, including biomarker discovery, immunotherapy development, and late-stage translational research focused on targeted treatments for cancer and other diseases.

Lunaphore says its solutions are intended to enable adoption of technologies with ease to make spatial biology mainstream among research laboratories. The company intends to do so with user-friendly and hands-off systems, eliminating the need for complex, conjugation-based reagents, and through continuous guidance and support.

“We can package all these in a sampling data automation with same day results, which is really almost exactly the same vision that Illumina brought to next-generation sequencing—that there is a box that you load your reagents in, and then you can get your results out,” said Ciftlik, Lunaphore’s founder, CEO, and board member. “This way, we can bring a spatial capability to every lab in the world. This is our bold vision.”

Spatial biology made its way into the mainstream of genomic science when, under the term spatially resolved transcriptomics, it was unanimously recognized in January by Nature Methods as the journal’s “Method of the Year 2020.” The editors wrote: “This maintenance of spatial context is crucial for understanding key aspects of cell biology, developmental biology, neurobiology, tumor biology and more, as specialized cell types and their specific organization are crucially tied to biological activity and remain poorly explored on the scale of whole tissues and organisms.”

Spatially resolved transcriptomics technology is being applied by large consortia such as the Human Cell Atlas and Brain Initiative Cell Census Network (BICCN), with the ultimate goal of generating complete maps of large and complex tissues like the human brain, Nature Methods noted.

Spatial initiation

Spatial biology is among the smaller segments of the broader life sciences market. One recent estimate issued last August by Research And Markets has the market growing over the next seven years at a 10% compound annual growth rate to $484 million, which would put its value this year at just under $250 million.

Lunaphore markets a pair of spatial biology products. One is LabSat®, a compact and open automated tissue staining instrument designed to help labs automate standard protein detection assays such as immunohistochemistry (IHC) and immunofluorescence (IF), both in singleplex or multiplex stainings. Also possible are RNA detection assays (RNAscope®) for applications that include In Situ Hybridization (ISH), but as a beta application.

Launched in 2019 and authorized for research use only, LabSat consists of one chamber where one tissue slide can be placed for staining. LabSat is designed to carry out IHC/IF staining cycles within minutes, using a patented microfluidic technology called Fast Fluidic Exchange (FFeX™) and a pressurized system that reduces incubation times by accelerating reagent flow inside the closed staining chamber. The system is designed to deliver reagents uniformly onto the tissue section, producing homogenous signal intensity across the area of confinement.

A single frozen section can be stained in under 20 minutes for each cycle; one FFPE sample, in under 30 minutes. Six markers can be stained in under four hours, according to Lunaphore.

“LabSat targets small basic academic research labs. It is really a sort of initiation to spatial biology. You would use LabSat if you’re trying to bring core spatial capabilities to your lab,” Ciftlik said. “The advantage of the technology is that it’s completely application agnostic, so anything that you can run on a spatial basis over a tissue, we are able to automate that.”

Lunaphore has expanded its offerings to larger labs through COMET™, an all-in-one automated staining and imaging platform that integrates a microfluidic-based staining system with an imaging system consisting of a microscope and image acquisition software.

Through its multiplex sequential immunofluorescence (Multiplex SeqIF™) technology, COMET is designed to visualize up to 40 markers in a single tissue sample within a day, capable of processing four slides at a time, with an average turnaround time of 40 minutes per every two markers.

Using FFeX, a consumable imaging chip is clamped over a standard histological glass slide, forming a closed chamber of reaction over the sample. This creates an ultra-controlled staining environment where reagents are delivered onto the tissue fast and uniformly. Overall staining times are greatly decreased, according to Lunaphore, as a result of active flow of reagents and the shallow depth of the chamber of reaction, there is a decrease in reagent diffusion time and improved fluidic exchange control.

Until now, Lunaphore has made pilot COMET units available through a priority access program.

One beta user, Sweden’s SciLifeLab, has said it expects to fully integrate COMET™ into its workflow and offer it as a service next year. In a recent webinar, Charlotte Stadler, PhD, head of the National Spatial Proteomics Facility and platform coordination officer for the Spatial and Single Cell Biology Platform (SSCB) at SciLifeLab, showed results obtained with COMET on several tissue types. At SSCB, Stadler’s Spatial Proteomics team offers a service to analyze up to 30 proteins in the same tissue section using DNA-barcoded antibodies.

At another beta user, researchers have used COMET to characterize the inflammatory response associated with a complication from maternal COVID-19 infection.

Matthew Pugh, FRCPath (University of Birmingham) presented how his team used the instrument to conduct a multiplex immunohistochemistry analysis of 30 markers to characterize the processes that drive COVID-19 placentitis—an inflammation of the placenta caused by SARS-CoV-2—at the Society for Immunotherapy of Cancer (SITC) 36th Annual Meeting last month. Pugh and colleagues found that COVID-19 placentitis was characterized by direct infection of the villous trophoblast, histiocytic intervillousitis and associated CXCL10 & interferon mediated inflammation.

Studying tumor budding

Another user of COMET is the Institute of Pathology at the University of Bern. Last July, Lunaphore launched a partnership of undisclosed value with the Institute, through which its Translational Research Unit will use COMET to study isolated cancer cell clusters called tumor buds in colorectal cancer. By expanding understanding of tumor budding events, the partners said, they also aim to improve cancer prognosis as well as personalized medicine.

“The question that remains is, how we can understand which buds are going to be really aggressive? How can we classify those buds according to which criteria? It’s not only about the buds but also the environment they are in. In which environments can which buds escape? Which buds can be contained? That can give a lot of insights on preventing metastasis or preventing growth of those buds,” Ciftlik explained.

“We are trying to understand and gain insights into, what are the differentiation points of those buds? And at the same time, the inflammatory cells that are surrounding those buds: Which ones are helpful and which ones cannot prevent them to escape?”

Since launch, Lunaphore has raised CHF 38.3 million ($41 million)  placing the company fourth among private companies ranked in GEN’s A-List of “Top 10 Spatial Biology Companies.” Most of that capital comes from a CHF 23 million (about $25 million) Series A round completed in February 2020.

Lunaphore has also grown its workforce to more than 100 people. “We are expecting to grow around 110 to 120 by the end of 2022,” Ciftlik said. Much of that growth, he added, will be achieved by adding to the company’s commercial staff, including its field customer service team, as well as its senior management.

Lunaphore named Diane Castex de la Guéronnière as vice president of Human Resources in September. She was previously director of international HR at Nexthink, where she created the company’s HR department and supporting its global expansion from 80 to over 650 employees. Everton Robinson joined as VP of sales late last year.

The company has also beefed up its boards in recent months, naming Carlo Bifulco, MD, of Providence Cancer Institute to its scientific advisory board, formed in January, and appointing former Leica Biosystems President Matthias Weber to its board of directors.