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SHP1 loss augments DLBCL cellular response to ibrutinib: a candidate predictive biomarker

Abstract

SHP1, a tyrosine phosphatase, negatively regulates B-cell receptor (BCR) signaling. Ibrutinib selectively inhibits BTK and has been approved for the treatment of several types of B-cell lymphomas, but not yet in diffuse large B-cell lymphoma (DLBCL). A phase 3 clinical trial of ibrutinib–containing regimen has been completed to evaluate its activity in subtypes or subsets of DLBCL patients. Although the subtype of activated B-cell like (ABC) DLBCL is characterized by chronic active BCR signaling, only a fraction of ABC-DLBCL patients seem to benefit from ibrutinib-containing regimen. New alternative predictive biomarkers are needed to identify patients who better respond. We investigated if SHP1 plays a role in defining the level of the BCR activity and impacts the response to ibrutinib. A meta-analysis revealed that lack of SHP1 protein expression as well as SHP1 promoter hypermethylation is strongly associated with NHL including DLBCL. On a tissue microarray of 95 DLBCL samples, no substantial difference in SHP1 expression was found between the GCB and non-GCB subtypes of DLBCL. However, we identified a strong reverse correlation between SHP1 expression and promoter methylation suggesting that promoter hypermethylation is responsible for SHP1 loss. SHP1 knockout in BCR-dependent GCB and ABC cell lines increased BCR signaling activities and sensitize lymphoma cells to the action of ibrutinib. Rescue of SHP1 in the knockout clones, on the other hand, restored BCR signaling and ibrutinib resistance. Further, pharmacological inhibition of SHP1 in both cell lines and patient-derived primary cells demonstrate that SHP1 inhibition synergized with ibrutinib in suppressing tumor cell growth. Thus, SHP1 loss may serve as an alternative biomarker to cell-of-origin to identify patients who potentially benefit from ibrutinib treatment. Our results further suggest that reducing SHP1 pharmacologically may represent a new strategy to augment tumor response to BCR-directed therapies.

Schematic diagram summarizing the major findings. Left panel. When SHP1 is present and functional, it negatively regulates the activity of the BCR pathway. Right pane. When SHP1 is diminished or lost, cells depend more on the increased BCR signaling and making them vulnerable to BTK inhibitor, ibrutinib. Diagram was generated using BioRender.

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Fig. 1: Meta-analysis of SHP1 IHC and promoter methylation.
Fig. 2: SHP1 protein expression is low in DLBCL and is similar between GCB and non-GCB subtypes.
Fig. 3: SHP1 protein expression is reversely correlated with promoter hyper-methylation in DLBCL cell lines.
Fig. 4: SHP1 knockout increases the activity of early B-cell receptor signaling.
Fig. 5: SHP1 knockout increase the sensitivity of DLBCL cells to ibrutinib.
Fig. 6: SHP1 rescue in knockout cells restores normal sensitivity to ibrutinib.
Fig. 7: Pharmacological SHP1 inhibition sensitizes cell lines to ibrutinib.
Fig. 8: Pharmacological SHP1 inhibition sensitizes primary DLBCL cells to ibrutinib.

Data availability

Data are available upon request addressed to the corresponding author.

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Acknowledgements

We thank LLS for partial funding of this project. We also thank the Cell Culture, Cell Sorting and Histopathology core facilities at the Fox Chase Cancer Center for their assistance in performing tissue culture, flow cytometry and IHC assays.

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WW and YLW formed the hypothesis and developed the ideas. WW and JM developed the assays, designed and performed the experiments, solved technical problems, and analyzed the data. QC, VSM, SP, RN and YLW constructed tissue microarray and interpreted the IHC results. PL contributed to useful discussions of the project. All authors participated in the manuscript writing. YLW directed, supervised, and coordinated the project, designed the experiments, analyzed the data and wrote the manuscript.

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Correspondence to Y. Lynn Wang.

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Wu, W., Lu, P., Patel, P. et al. SHP1 loss augments DLBCL cellular response to ibrutinib: a candidate predictive biomarker. Oncogene (2022). https://doi.org/10.1038/s41388-022-02565-7

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