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Through Pharma Collaborations, Predicine Aims to Enter the US CDx Market in as Little as Three Years


NEW YORK – Cancer test maker Predicine formed a partnership last month with Janssen on companion diagnostics development and commercialization, adding the Johnson & Johnson subsidiary to a growing list of Predicine's pharma collaborators as the firm prepares to commercialize its combined DNA and RNA next-generation sequencing-based assays.

The Hayward, California-based firm hopes that its first companion diagnostic assays will become available for patient testing in the US through US Food and Drug Administration premarket approval in the next three to five years. Though it has been focused lately on partnering with pharma companies for clinical trials and companion diagnostics, the company plans to soon emerge with FDA-approved tests as a patient testing firm. It intends to offer its liquid biopsy assays and tissue-based tests through both its network of laboratories in the US and China and as kitted tests that could be run by outside labs.

Predicine Founder and CEO Shidong Jia said the company is closing in on the commercialization of its next-generation sequencing-based PredicineCare assay. He said the firm has inked companion diagnostics development agreements with several firms for use of the assay as a blood-, urine-, and tissue-based test for the determination and treatment of bladder cancers and lung cancers, among other potential indications.

Jia noted that Predicine's recent partners include Johnson & Johnson, AstraZeneca, Roche, Bristol Myers Squibb, Pfizer, Merck, Boehringer Ingelheim, and BeiGene. He said those partnerships have been disclosed in publicly available documents.

The firm secured in August 2022 CE-IVD marking for the 152-gene assay to identify in blood or urine samples single nucleotide variants, insertions and deletions, DNA rearrangements, and copy number variations that provide actionable information on cancer therapies. In the same month, the FDA granted breakthrough device designation for PredicineCare, which could help Predicine hasten the assay's development and regulatory review.

The firm is simultaneously developing its companion diagnostics to aid cancer treatment in China, Europe, and Japan.

Predicine has so far limited the use in Europe of its CE-IVD marked PredicineCare assay and PredicineAtlas genomic profiling assay to supporting clinical trials. Jia said the company offers those same NGS-based assays in the US through its CLIA-certified facilities for use in clinical trials and has used them for small-scale patient testing.

He said that the simultaneous detection of ctDNA and ctRNA in a single sample allows the detection of both genomic variants and splicing variants, while also boosting the sensitivity and specificity of the tests compared to the detection of ctDNA alone.

"We are working on the next generation of the liquid biopsy," he said.

Though simultaneous testing for DNA and RNA in a liquid biopsy isn't universal, it's not unique to Predicine.

Caris Life Sciences also performs testing that combines results from cfDNA and cfRNA, and the firm secured about three years ago $830 million in funding to back its push into the liquid biopsy market with its blood-based comprehensive genomic profiling service for late-stage cancer patients. Precision oncology firm Lucence similarly has developed liquid biopsy assays that target cfDNA and cfRNA, and it presented data in September 2023 that indicated its LiquidHallmark liquid biopsy cancer biomarker test had high concordance with tissue biopsy results in patients with advanced non-small cell lung cancer.

The PredicineCare assay is used with blood, urine, or FFPE tissue to detect SNVs, insertions and deletions (indels), rearrangements, copy number variations, and microsatellite instability. In presentations, Predicine has also said the assay can be used to detect gene deletions as well as to determine mono- and bi-allelic loss of function. More than 90 biomarkers identified using the assay are clinically relevant for oncology or chemotherapy response, according to the firm.

The firm's PredicineBeacon minimal residual disease assay, which is the next up in the queue, is used is used with blood, urine, or tissue samples for custom variant determination. The firm also has been offering pharma firms the use of its 600-gene PredicineAtlas assay to detect SNVs, indels, rearrangements, copy number gains and reductions, tumor mutational burden, and microsatellite instability.

Jia said the company has been focusing its efforts on unmet needs in cancer testing, and the firm has built its reputation with pharmaceutical customers by being willing to take risks on difficult products such as urine-based liquid biopsies to aid bladder cancer treatment. He said the firm would rather fail at a challenge than not try at all.

"Whenever we design our assays, it's always because there's no better solution," he said.

Jia hopes to receive approval for the first indications for the PredicineCare assay within as little as three years, and the company is working to secure reimbursement commitments ahead of commercialization. Predicine has established four labs in the US and one in China that support the firm's work on clinical trials and companion diagnostics development. The firm has also established test kit manufacturing facilities in both countries.

Jia said study results published during the last several years show the company's ability to consistently detect the loss of PTEN, BRCA, RB, and p53 genes, which have been identified in previous studies as drivers of cancer and therapy resistance, as well as AR-V7 gene splicing that has been linked with resistance to androgen receptor inhibitors in prostate cancer patients. He said the results indicate the firm could help fulfil an unmet need for accurate, noninvasive liquid biopsy assays.

He coauthored study results published in 2021 in JCO Precision Oncology that indicate Predicine's cfDNA assay could detect in blood samples the loss of the PTEN tumor suppressant gene in 37 percent of 231 patients with metastatic castration-resistant prostate cancer. The prevalence of PTEN loss detected was comparable with the results of previous tissue-based studies. The authors wrote that the assay could be used to complement PTEN tissue testing to identify patients who would benefit from treatment with PTEN-PI3K-AKT pathway inhibitors such as Roche's ipatasertib and AstraZeneca's capivasertib, marketed as Truqap.

He also coauthored study results published that year in Frontiers in Oncology that indicate the PredicineCare NGS-based assay could detect copy number loss in blood samples with low concentrations of circulating tumor DNA and be used to aid evaluation of PTEN, RB1, and TP53 gene loss in samples from patients with metastatic prostate cancer. According to the authors, the PredicineCare assay also detected PTEN loss in a cohort of 15 patients with 87 percent concordance in comparison with immunohistochemistry of tumor tissue biopsies from the same patients.

Roger Li, a genitourinary oncologist at the Houston Lee Moffitt Cancer Center in Florida, said the PredicineCare assay could be a practice-changing tool to help guide the treatment of bladder cancer patients by more clearly identifying how advanced a patient's cancer has become. He was part of a team from Moffitt, Predicine, Northwestern University in Chicago, Weill Cornell Medicine in New York, and the IRCCS San Raffaele Hospital and Scientific Institute in Milan, Italy, that published last year in European Urology study results that indicate the PredicineCare assay, through its combined detection of molecular alterations and copy number changes, was used to identify patients who had muscle-invasive and non-organ-confined upper tract urothelial carcinoma with 79 percent sensitivity and 94 percent specificity.

Li said that clinical staging of upper tract urothelial carcinoma is often difficult and inaccurate because it relies on the results of biopsies from tough-to-access anatomical locations and unreliable cross-sectional imaging, yet a patient's treatment options vary by clinical stage. Many would benefit from neoadjuvant chemotherapy prior to surgical removal of the kidneys and ureter, and an accurate liquid biopsy could help determine which patients would benefit from surgery.

"You could imagine, if a patient were to have a persistently high ctDNA level despite chemotherapy, that may be a patient that's at high risk of advancing disease despite the surgery," he said. "So, the surgical extirpation of the kidney and the ureter may not necessarily render the patient disease-free and, hence, may not be beneficial for the patient."

However, Li said those potential benefits will need to be proven in larger-scale, multi-institution studies.

Li also was the lead author of a poster presented last month at the American Society of Clinical Oncology's Genitourinary Cancers Symposium on the use of a urine-based PredicineCare liquid biopsy to identify bladder cancer patients who were likely to benefit from treatment with the TAR-210 intravesical drug delivery system for the continuous release of erdafitinib.

Predicine is one of several companies making progress in expanding the testing options available to cancer patients, including the bladder cancer treatment market that has been a focus area for much of Predicine's work.

NeoGenomics, Natera, and Foundation Medicine all reported in 2023 promising steps toward use of their technologies to guide the treatment of bladder cancer patients. Guardant Health, too, has also been building out its liquid biopsy menu and has reported promising results for multiple cancers, including bladder cancer.

Similarly, Predicine isn't alone in its work on urine-based bladder cancer testing, a field which includes Informed Genomics and Vesica Health, both of which said late last year they were preparing to launch urine-based bladder cancer detection tests for patients with hematuria, or blood in the urine. AnchorDx also said about the same time that it was conducting a registrational and prospective clinical trial for its urine-based bladder cancer early detection test, UriFind. Meantime, Nucleix secured FDA 510(k) clearance in May 2023 for its qPCR-based Bladder EpiCheck cancer recurrence test.

Jia said that urine-based liquid biopsies require overcoming difficulties inherent to urine samples as those assays can be confounded by the variations in urine content and the degradation of DNA in that environment. However, Li said that the DNA shed in urine provide a rich reservoir of information on disease progression and potential treatment response.

Jia said Predicine developed a urine ctDNA workflow that integrates wet-lab chemistry and dry-lab bioinformatics algorithms to identify urine-based ctDNA variants.

He also noted that Predicine's blood- and urine-based PredicineBeacon liquid biopsy assay, which is next up in the pipeline behind PredicineCare, has been used in recent studies for MRD testing. In a New England Journal of Medicine article published in August 2023, for example, the authors described the use of Predicine's PredicineBeacon MRD assay as part of their study on the use of the KRAS G12C inhibitor divarasib for the treatment of patients with advanced or metastatic solid tumors with KRAS G12C mutation.

Adrian Sacher, lead author of that study and a thoracic oncologist and affiliate scientist at the Princess Margaret Cancer Centre in Toronto, said by email that the PredicineBeacon assay was used to detect KRAS G12C mutations even at very low variant allele frequencies, and he noted that the test allowed the research team to monitor with high sensitivity KRAS G12C variant allele frequencies simultaneously with total ctDNA levels.

While much of Predicine's recent work has been tied to drug development, Jia said he sees Predicine as a patient testing company, and it has begun work toward expanding into early cancer detection.