POS0715 TREATMENT OF SLE PATIENTS WITH ZETOMIPZOMIB (KZR-616), A SELECTIVE INHIBITOR OF THE IMMUNOPROTEASOME, RESULTS IN CIRCULATING GENE EXPRESSION, PROTEIN LEVEL, AND IMMUNE CELL PHENOTYPIC CHANGES WITH POTENTIAL CORRELATIONS TO CLINICAL RESPONSE

Background

Systemic lupus erythematosus (SLE), a severe multiorgan autoimmune disease, involves dysfunction of multiple immune system components. In preclinical studies, KZR-616, a first-in-class small molecule selective inhibitor of the immunoproteasome, demonstrated pleiotropic immunomodulatory functions encompassing both innate and adaptive immune pathways1,2. In the recently completed MISSION Phase 1b trial in SLE patients (pts), KZR-616 exhibited encouraging safety, tolerability, and clinical improvements3. Preliminary biomarker analysis of the first two cohorts was previously reported4. Here, we present complete biomarker results from all cohorts in this study.

Objectives

1) To characterize biomarker changes (gene expression, circulating protein levels and immune cell phenotypes) following KZR-616 treatment. 2) To evaluate correlations between biomarker changes and treatment response to KZR-616.

Methods

The open-label Phase 1b MISSION Trial (NCT 03393013) was a 25-week trial of KZR- 616 administered subcutaneously once weekly at doses ranging from 30-75 mg for 13 weeks (W) with a 12 W follow-up. Forty-seven SLE pts with and without nephritis were enrolled with 35 completing all 25 W of study. Clinical response definitions at W13 or later were defined as either a >4 reduction of SLEDAI-2K or >50% drop in swollen joint counts (SJC) (baseline SJC>2). Biomarker samples included whole blood in RNA tubes (31 pts), cryopreserved PBMCs (15 pts), plasma (35 pts) and urine (2 pts). Whole blood RNA sequencing was performed using Illumina TruSeq. Differential expression was modelled using DESeq2. Fast pre-ranked gene set enrichment analysis (GSEA) was performed with gene sets derived from published literature. Cryopreserved PBMCs were analysed by flow cytometry to profile immune cell subtypes. Plasma protein was measured by Meso Scale Discovery (MSD) kits. Healthy volunteer (HV, N=12) samples were used to establish potential disease-related biomarker changes in patients at baseline (BL).

Results

Many gene modules were found to be altered at BL in SLE pts, relative to HV, including those representing interferon (IFN) response and B/plasma cells and changes were consistent with our prior report4. Comparisons of SLEDAI-2K responders (R) versus non-responders (NR) revealed enrichment of 193 gene modules (57 down and 136 up-regulated, padj,<0.1) at BL and 190 modules (105 down and 85 up) 4 weeks after treatment (W17). Expression of a 4-gene IFN module was enriched in SLEDAI-2K R vs NR at BL; expression of this module trended downward at W17 in R, whereas it increased over time in NR at W 5. Reduced numbers of circulating class-switched memory B cells and IgG-producing plasma cells were observed at W17 and/or W25. Plasma levels of BAFF were consistently increased at W5 but returned to BL levels by W17. Plasma levels of CD169/ SIGLEC-1, a monocyte activation marker, were higher at BL in SJC R vs. NR and were reduced after treatment in both groups. Two pts with active proliferative nephritis were enrolled into this study and both showed a reduction in levels of urine CD163 (uCD163), while plasma levels of this marker were stable.

Conclusion

Our integrative analysis indicates that KZR-616 elicits a potent effect on multiple immune pathways in SLE patients. Potential new biomarkers (gene, gene module, circulating protein) that may be useful for prediction of patient response were identified. Future biomarker studies in placebo-controlled trials may further our understanding of KZR-616 mechanism of action, patient selection and prediction of patient responses.

References

[1]Kirk, C.J. et al., Cells 2022, 11(1):9

[2]Muchamuel T, Arthritis Rheumatol. 2019; 71 (suppl 10).

[3]Furie R et al., Annals of the Rheumatic Diseases 2021;80:595-596,

[4]Fan R, et al., Arthritis Rheumatol. 2019; 71 (suppl 10).

Acknowledgements

Kezar Life Sciences acknowledges the support of site investigators and patient participants in the MISSION study.

Disclosure of Interests

Andrea Fan Shareholder of: Kezar, Employee of: Kezar, Brian Tuch Consultant of: Kezar, Tony Muchamuel Shareholder of: Kezar, Employee of: Kezar, Janet Anderl Shareholder of: Kezar, Employee of: Kezar, Richard Leff Consultant of: Kezar, Noreen Henig Shareholder of: Kezar, Employee of: Kezar, Christopher Kirk Shareholder of: Kezar, Employee of: Kezar

Abstract 323: Quantitative proteomic profiling of novel anti-cancer small molecule inhibitors of Sec61: Mechanistic investigation and biomarker discovery

Secreted and transmembrane (TM) proteins play key roles in malignant transformation and tumor growth. During translation, the majority of these proteins require translocation through the Sec61 protein complex into the endoplasmic reticulum (ER) for further processing. Thus, Sec61 represents a novel therapeutic target for cancer treatment through selective blockade of protein secretion. The structural analogs KZR-261 and KZR-834 were identified through a medicinal chemistry campaign and found to have broad in vitro anti-tumor activity and efficacy in mouse xenograft models. KZR-261 was nominated for clinical development and we describe here the proteomic assessment and in vitro pharmacodynamics of these novel anti-cancer agents.

We utilized quantitative proteomic methods to study inhibition of protein secretion and global modulation of protein homeostasis across multiple tumor cell lines and peripheral blood mononuclear cells (PBMCs) from healthy donors. Cells were treated with KZR-834 or KZR-261 followed by subcellular fractionation of cytosolic and membrane/ER proteomes. The membrane/ER fraction was expected to be enriched for Sec61 client proteins. Subsequent proteomic profiling was performed with Tandem Mass Tag 6-plex (TMTsixplex™). Across tumor cell lines, a total of 2222 Sec61 client proteins were detected in the membrane/ER proteome, representing &gt;30% of the annotated Sec61 clientome. Of these proteins, 5-17% were inhibited by &gt;50% upon treatment, indicating that only a small portion of the total flux of secreted and TM proteins in cells was affected by our compounds. KZR-261 and KZR-834 preferentially targeted secreted and type 1 TM proteins relative to multi-pass TM proteins, which may be related to the smaller size of Sec61 targeting sequences in these proteins. Additionally, Ingenuity®Pathway Analysis (Qiagen) of the cytosolic proteome from tumor cell lines indicated that activation of the ER stress response was induced by KZR-834, which were further verified by gene expression and western blot analyses. In PBMCs treated with KZR-261, multiple type 1 TM proteins (IL-7 receptor, L-selectin, ICAM-1, HLA-DR) and the secreted protein beta-2-microglobulin were identified as sensitive cell surface targets. Flow cytometric analysis of PBMCs also showed a significant reduction in surface expression of those proteins in multiple cell populations.

Our results highlight quantitative proteomic profiling as a valuable tool towards elucidation of the mechanism of pleiotropically-acting molecules. By assessing global proteomic changes in non-transformed cells, pharmacodynamic markers were identified that will be employed in the Phase 1 trial of KZR-261 in solid tumors.

Citation Format: Yu Qian, Jennifer Whang, Janet Anderl, Henry W. Johnson, Christopher J. Kirk, Eric Lowe, Dustin McMinn, Beatriz Millare, Tony Muchamuel, Jinhai Wang. Quantitative proteomic profiling of novel anti-cancer small molecule inhibitors of Sec61: Mechanistic investigation and biomarker discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 323.

Analysis of autophagosome formation using lentiviral biosensors for live fluorescent cellular imaging

Autophagy, a highly regulated homeostatic degradative process, allows cells to reallocate nutrients from less important to more essential processes under extreme conditions of starvation. Autophagy also prevents the buildup of damaged proteins and organelles that cause chronic tissue damage and disease. Although a topic of great interest with involvement of multiple signaling pathways, there are limitations in real-time detection of the autophagic process. EMD Millipore has developed technologies where prepackaged, ready-to-use, high-titer lentiviral particles, "lentiviral biosensors," encoding GFP- or RFP-tagged proteins provide a convenient and robust solution for fluorescent imaging of cells undergoing autophagy. Compared to nonviral transfection methods, lentiviral transduction, in many cases, offers higher transfection efficiency and more homogeneous protein expression, particularly for traditionally hard-to-transfect primary cell types. Lentiviral biosensors are ideal for use with fixed and live cell fluorescent microscopy, and are nondisruptive towards cellular function. GFP- or RFP-protein localization matches well with antibody-based immunostaining and demonstrates altered patterns of expression upon treatment with modulators of cell function and phenotype. Lentiviral biosensors provide a broadly effective, convenient method for visualization of cell behavior under a variety of physiological and pathological treatment conditions, in both endpoint and real-time imaging modalities. In this study, we focus on lentiviral biosensors containing GFP-LC3 and RFP-LC3 to study the formation of autophagosomes.

Interferon-γ-induced upregulation of immunoproteasome subunit assembly overcomes bortezomib resistance in human hematological cell lines

Background

Despite encouraging results with the proteasome inhibitor bortezomib in the treatment of hematologic malignancies, emergence of resistance can limit its efficacy, hence calling for novel strategies to overcome bortezomib-resistance. We previously showed that bortezomib-resistant human leukemia cell lines expressed significantly lower levels of immunoproteasome at the expense of constitutive proteasomes, which harbored point mutations in exon 2 of the PSMB5 gene encoding the β5 subunit. Here we investigated whether up-regulation of immunoproteasomes by exposure to interferon-γ restores sensitivity to bortezomib in myeloma and leukemia cell lines with acquired resistance to bortezomib.

Methods

RPMI-8226 myeloma, THP1 monocytic/macrophage and CCRF-CEM (T) parental cells and sub lines with acquired resistance to bortezomib were exposed to Interferon-γ for 24-48 h where after the effects on proteasome subunit expression and activity were measured, next to sensitivity measurements to proteasome inhibitors bortezomib, carfilzomib, and the immunoproteasome selective inhibitor ONX 0914. At last, siRNA knockdown experiments of β5i and β1i were performed to identify the contribution of these subunits to sensitivity to proteasome inhibition. Statistical significance of the differences were determined using the Mann-Whitney U test.

Results

Interferon-γ exposure markedly increased immunoproteasome subunit mRNA to a significantly higher level in bortezomib-resistant cells (up to 30-fold, 10-fold, and 6-fold, in β1i, β5i, and β2i, respectively) than in parental cells. These increases were paralleled by elevated immunoproteasome protein levels and catalytic activity, as well as HLA class-I. Moreover, interferon-γ exposure reinforced sensitization of bortezomib-resistant tumor cells to bortezomib and carfilzomib, but most prominently to ONX 0914, as confirmed by cell growth inhibition studies, proteasome inhibitor-induced apoptosis, activation of PARP cleavage and accumulation of polyubiquitinated proteins. This sensitization was abrogated by siRNA silencing of β5i but not by β1i silencing, prior to pulse exposure to interferon-γ.

Conclusion

Downregulation of β5i subunit expression is a major determinant in acquisition of bortezomib-resistance and enhancement of its proteasomal assembly after induction by interferon-γ facilitates restoration of sensitivity in bortezomib-resistant leukemia cells towards bortezomib and next generation (immuno) proteasome inhibitors.

Higher ratio immune versus constitutive proteasome level as novel indicator of sensitivity of pediatric acute leukemia cells to proteasome inhibitors

The ex vivo sensitivity of pediatric leukemia cells to the proteasome inhibitor bortezomib was compared to 3 next generation proteasome inhibitors: the epoxyketone-based irreversible proteasome inhibitors carfilzomib, its orally bio-available analog ONX 0912, and the immunoproteasome inhibitor ONX 0914. LC50 values were determined by MTT cytotoxicity assays for 29 childhood acute lymphoblastic leukemia and 12 acute myeloid leukemia patient samples and correlated with protein expression levels of the constitutive proteasome subunits (β5, β1, β2) and their immunoproteasome counterparts (β5i, β1i, β2i). Acute lymphoblastic leukemia cells were up to 5.5-fold more sensitive to proteasome inhibitors than acute myeloid leukemia cells (P<0.001) and the combination of bortezomib and dexamethasone proved additive/synergistic in the majority of patient specimens. Although total proteasome levels in acute lymphoblastic leukemia and acute myeloid leukemia cells did not differ significantly, the ratio of immuno/constitutive proteasome was markedly higher in acute lymphoblastic leukemia cells over acute myeloid leukemia cells. In both acute lymphoblastic leukemia and acute myeloid leukemia, increased ratios of β5i/β5, β1i/β1 and β2i/β2 correlated with increased sensitivity to proteasome inhibitors. Together, differential expression levels of constitutive and immunoproteasomes in pediatric acute lymphoblastic leukemia and acute myeloid leukemia constitute an underlying mechanism of sensitivity to bortezomib and new generation proteasome inhibitors, which may further benefit from synergistic combination therapy with drugs including glucocorticoids.

Correction of cystathionine β-synthase deficiency in mice by treatment with proteasome inhibitors

Cystathionine beta-synthase (CBS) deficiency is an inborn error of metabolism characterized by extremely elevated levels of plasma total homocysteine. The vast majority of CBS-deficient patients have missense mutations located in the CBS gene that result in the production of either misfolded or unstable protein. Here, we examine the effect of proteasome inhibitors on mutant CBS function using two different mouse models of CBS deficiency. These mice lack mouse CBS and express a missense mutant human CBS enzyme (either p.I278T or p.S466L) that has less than 5% of normal liver CBS activity, resulting in a 10-30-fold elevation in plasma homocysteine levels. We show that treatment of these mice with two different proteasome inhibitors can induce liver Hsp70, Hsp40, and Hsp27, increase levels of active CBS, and lower plasma homocysteine levels to within the normal range. However, response rates varied, with 100% (8/8) of the p.S466L animals showing correction, but only 38% (10/26) of the p.I278T animals. In total, our data show that treatment with proteostasis modulators can restore significant enzymatic activity to mutant misfolded CBS enzymes and suggests that they may be useful in treating certain types of genetic diseases caused by missense mutations.

Abstract 1022: Carfilzomib demonstrates broad antitumor activity in preclinical lung cancer models

Carfilzomib (CFZ), is an irreversible inhibitor of the chymotrypsin-like activity of the proteasome that was recently FDA approved for treatment of refractory and relapsed multiple myeloma. Early Phase 1B studies of CFZ showed signs of clinical activity in a number of solid tumors, including non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). We investigated the anti-tumor activity of CFZ monotherapy and in combination with cisplatin in NSCLC and SCLC cell lines and xenograft models. CFZ showed marked anti-proliferative activity in A549, H1993, H520, H460, H1299 NSCLC cell lines, with IC50 values after 96 hours of treatment ranging from 1.0 nM to 27 nM. CFZ + cisplatin resulted in antagonistic anti-proliferative activity in the NSCLC A549, H1993, and H520 cells, independent of sequence of drug administration. In vivo, CFZ monotherapy resulted in tumor growth inhibition in an A549 NSCLC murine xenograft model. In contrast, the SCLC cell lines SHP77 and H69 were more resistant to the anti-proliferative effects of CFZ, with IC50 values at 96 hours of 0.917 μM and &gt;30 μM, respectively. In vitro, in the SHP-77 SCLC cell line CFZ + Cisplatin showed synergistic activity. In vivo, in a SHP-77 SCLC SCID murine xenograft model CFZ monotherapy resulted in an 8-day tumor growth delay to reach 1500 mm3. No additive or synergistic anti-tumor efficacy was observed for CFZ + cisplatin in this model. Western blot analysis from SHP-77 cell lines grown in vitro and treated with CFZ showed an increase in cleaved PARP and p53, supporting activation of apoptosis. We will report on inhibition of the chymotrypsin-like proteasome activity in CFZ-treated lung cancer cell lines. Together, these pre-clinical studies support further preclinical and clinical investigations of CFZ in NSCLC and SCLC, including novel CFZ + anti-cancer drug combinations.

Citation Format: Amanda F. Baker, Barbara Sands, Lilliana Carbajal, Janet Anderl, Elena T. Chan, Christopher J. Kirk, Linda L. Garland. Carfilzomib demonstrates broad antitumor activity in preclinical lung cancer models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1022. doi:10.1158/1538-7445.AM2013-1022

Abstract 4105: Assessment of autophagosome formation in primary cells by lentiviral delivery of fluorescent protein-tagged LC3

Assessment of autophagosome formation has been greatly facilitated by monitoring redistribution of LC3-fluorescent protein fusions. The sensitivity of the technique and capability for real-time analysis of autophagosome formation are advantageous over detection of endogenous LC3 redistribution in many experimental settings. However, the necessity for transfection can be an impediment to analysis of autophagosome formation in difficult-to-transfect cells, particularly primary cultures. We have developed lentiviral vectors (employing 3rd generation technology for optimal biosafety) encoding monomeric TagGFP2 and TagRFP fused at the N-termini of wild-type LC3 and LC3G120A as tools for analysis of autophagy in a wide variety of cell types. In immortalized cell lines and in primary cells (HUVEC and human mesenchymal stem cells) transduced with the GFP- and RFP-LC3 lentiviruses, amino acid deprivation in the presence of a lysosome inhibitor induced redistribution of the fluorescence from a diffuse cytoplasmic pattern to a punctate distribution. Minimal background of punctae in fed cells was observed. 3-Methyladenine blocked the starvation-induced redistribution, and the G120A mutant did not undergo detectable redistribution upon amino acid deprivation. In addition, we demonstrate effectiveness of lentiviral GFP-LC3 in HUVECs by flow cytometry, in which the plasma membrane is selectively permeabilized such that free cytosolic fluorescent protein-tagged LC3 is released while autophagosome-bound LC3 fusion protein is retained. We anticipate that these lentiviral autophagy biosensors will facilitate analysis of autophagosome formation in physiologically relevant primary cells.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4105. doi:1538-7445.AM2012-4105