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Our Research

 

Clinical utility of P-topol-Dx:

TopoI inhibitors are used to treat colorectal, gastric, pancreatic, ovarian, breast and small cell lung cancer. CRC is the third most common form of cancer and the second leading cause of cancer-related death in the US. Despite progress in effective screening, 20% of patients present with metastatic disease, and another 20% develop metastasis during clinical courses.  The standard first line therapy for mCRC is 5FU and leucovorin, combined with either oxaliplatin (FOLFOX) or irinotecan (FOLFIRI). These doublets, depending on the status of the RAS gene, are combined with targeted drugs.  The selection of chemotherapy as first or second line is not based on any predictive biomarker and the response rate of FOLFOX and FOLFIRI is similar. However, due to the failure of first line therapy, many patients do not get second line therapy. P-topoI-Dx has the potential to change the treatment paradigm in advanced CRC therapy management. Similarly, in pancreatic and gastric cancer therapy the predictive biomarker can be used very effectively to determine the best first line therapy options. For ADCs with topoI inhibitor payloads like Trodelvi and Enhertu, use of P-topoI-Dx can change the clinical endpoints like the response rate.  

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"Irinotecan is an important drug in CRC, a mainstay. It can be used in first, second and occasionally perhaps third line. Even with the new treatment in the future, they'll still be deployed with a FOLFIRI/FOLFOX background. It's not going away" -Academic Medical Oncologist.

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Cancer Incidence and patient population eligible for topoI inhibitors: TopoI inhibitors are one the most extensively used drugs in oncology. Recent approvals of two ADCs have further increased the clinical use of this class of drugs.

The Science

Topoisomerase I inhibitors overview: Human DNA-topoisomerase I (topoI) is an essential and ubiquitous enzyme that is involved in the release of torsional forces generated during DNA transcription and replication. The identification of TopoI as a specific target of the anticancer drug camptothecin (CPT) led to the rapid development of its structure function and a large number of CPT analogues. Hycamtin (topotecan), Camptosar (irinotecan), and Onivyde (irinotecan liposome) are FDA-approved CPTs that are used to treat metastatic colorectal cancer (CRC) and pancreatic cancer in first line therapy; gastric, ovarian, and small cell lung cancer in second line therapy. Notably, approval of two antibody drug conjugates (ADCs), Trodelvi and Enhertu, with topoI inhibitors as the cytotoxic warheads has placed this class of drug front and center in future anticancer drug discovery efforts.

Our Discovery

Three mechanisms have been proposed to define the CPT drug resistance mechanisms: the lack of accumulation of the drug due to ABC transporters/multi-drug resistance (MDR) genes,  mutations in topoI that alter the topoI-DNA-CPT interaction, and the rate of ubiquitin proteasomal pathway (UPP) dependent degradation of topoI. However, now it is established that CPTs are not MDR substrates and topoI mutations are very rare in the patient population, making UPP-mediated degradation of topoI a key regulator of CPT response. One of the most remarkable phenomena observed in the cellular response to CPTs is degradation of topoI. Importantly, the cells that degrade topoI rapidly are resistant to irinotecan. The seminal work carried out at Dr. Bharti’s lab defined the precise mechanism of topoI degradation by UPP and identified the molecular determinants of this pathway. Briefly, a decade of work has demonstrated that: i) topoI associates with DNA-PK, and DNA-PKcs phosphorylates topoI at Serine 10; ii) Phosphorylated topoI is ubiquitinated by BRCA1; iii) cells with higher basal levels of topoI-pS10 degrade topoI rapidly and are resistant to irinotecan; iv) the higher basal level of topoI-pS10 is maintained by phosphatases that deregulate kinase cascade and maintains steady state DNA-PKcs activation. The pathway has since been validated and published at several levels, including demonstration that CPT-resistant cells have a higher basal level of phosphorylated topoI-S10.

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Topoisomerase I co-localizes with BRCA1 and BRCA1 ubiquitinates topoI for proteasomal degradtion (Genomically edited HCT15 cells express topoI-GFP and BRCA1-RFP). Yellow color represents green (topoI)  and red (BRCA1) protein co-localization- visualized by super resolution microscope.

Our Product

Predictus Biosciences has developed a novel IHC test, P-topoI-Dx, that specifically immunostains phosphorylated topoI-S10. The test can stratify the responder and non-responder patient populations for topoI inhibitors using an FFPE slide.  We have completed retrospective clinical validation of 176 CRC patients and 96 gastric cancer patients. Statistical analysis of the multi-cohort retrospective validation study showed very high predictive values and a <0.0001 correlation coefficient with the topoI-pS10 percent positive nuclei. The IHC assays are the gold standard and the P-topoI-Dx assay will fit very well in the work flow of clinical pathology labs.

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Schema depicting the deregulated kinase cascade effecting the rate of topoI degradation and visualization of topoI-pS10 in patient FFPE tissue

Illustrative Healthcare Value Model

In addition to breakthrough science, this test also has strong economic value:

The total expenditure for topoI inhibitors is estimated at $1.3 billion annually, although most patients don't benefit from the drug (estimated only 30% of patients responded to treatment). Implementing this diagnostic would result in an estimated 66% cost savings, which is over $1.8 million per 100 patients treated.

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"The need for topoisomerases lies embedded in the double helical structure of DNA" (James Wang 2002)

Product Related Publications

1. Camptothecin resistance is determined by regulation of topoisomerase I degradation mediated by ubiquitin proteasomal pathway. Oncotarget. 2017 Jul 4; 8(27): 43733-43751. Ando, K, Shah, AK, Sachdev V, Kleinstiver BP, Welch MM, Taylor-Parker J, Hu Y, Salgia R, White FM, Parvin JD, Ozonoff A, Rameh LE, Joung JK and Bharti A.

 

2. Developing a phosphospecific Immunohistochemistry Assay as a Predictive Biomarker for Topoisomerase I Inhibitors. J. Histochemistry and Cytochemistry. 2018 66(8): 549-561 Ando K, Tohme Y, Srinivasiah A, Taylor-Parker J , Harrington Y, Shah AK, Oki E, Brahmandam M and Bharti A.

 

3.  CTDSP1 inhibitor rabeprazole regulates DNA-PKcs dependent topoisomerase I degradation and irinotecan drug resistance in colorectal cancer. PLoS One 2020 Aug 7;15(8):e0228002.doi: 10.1371/journal.pone.0228002. eCollection 2020.

Matsuoka H , Ando K, Swayze EJ , Unan EC , Mathew J, Hu Q , Tsuda Y , Yuichiro N,  Saeki  H, Oki E, Bharti A,  Mori M

 

4. Multi-Cohort Retrospective Validation of a Predictive Biomarker for Topoisomerase I Inhibitors. Ando K, Ozonoff A, Lee S, Voisine M, Parker J, Nakanishi R, Nishimura S, Yang J, Grace Z, Tran B, Diefenbach T, Maehara Y, Yasui H, Irino T, Salgia R, Terashima M, Gibbs P, Ramanathan R, Oki E, Mori M, Kulke M, Hartshorn K, and Bharti A. Clinical Colorectal Cancer (In Press)

 

5. Rapid rate of Ubiquitination and proteasomal degradation of topoI protein ensures anticancer drug resistance. Unan E, Bharti A et al (Cancers-invited review)