CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma

Diffuse large B-cell lymphoma (DLBCL) exhibits significant genetic heterogeneity which contributes to drug resistance, necessitating development of novel therapeutic approaches. Pharmacological inhibitors of cyclin-dependent kinases (CDK) demonstrated pre-clinical activity in DLBCL, however many stalled in clinical development. Here we show that AZD4573, a selective inhibitor of CDK9, restricted growth of DLBCL cells. CDK9 inhibition (CDK9i) resulted in rapid changes in the transcriptome and proteome, with downmodulation of multiple oncoproteins (eg, MYC, Mcl-1, JunB, PIM3) and deregulation of phosphoinotiside-3 kinase (PI3K) and senescence pathways. Following initial transcriptional repression due to RNAPII pausing, we observed transcriptional recovery of several oncogenes, including MYC and PIM3. ATAC-Seq and ChIP-Seq experiments revealed that CDK9i induced epigenetic remodeling with bi-directional changes in chromatin accessibility, suppressed promoter activation and led to sustained reprograming of the super-enhancer landscape. A CRISPR library screen suggested that SE-associated genes in the Mediator complex, as well as AKT1, confer resistance to CDK9i. Consistent with this, sgRNA-mediated knockout of MED12 sensitized cells to CDK9i. Informed by our mechanistic findings, we combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro as well as resulted in delayed tumor progression and extended survival of mice xenografted with DLBCL in vivo. Thus, CDK9i induces reprogramming of the epigenetic landscape, and super-enhancer driven recovery of select oncogenes may contribute to resistance to CDK9i. PIM and PI3K represent potential targets to circumvent resistance to CDK9i in the heterogeneous landscape of DLBCL.

Generation of a humanized afucosylated BAFF-R antibody with broad activity against human B-cell malignancies

B-cell activating factor receptor (BAFF-R) is a mature B-cell survival receptor, which is highly expressed in a wide variety of B-cell malignancies but with minimal expression in immature B cells. These properties make BAFF-R an attractive target for therapy of B-cell lymphomas. We generated a novel humanized anti BAFF-R monoclonal antibody (mAb) with high specificity and potent in vitro and in vivo activity against B-cell lymphomas and leukemias. The humanized variants of an original chimeric BAFF-R mAb retained BAFF-R binding affinity and antibody-dependent cellular cytotoxicity (ADCC) against a panel of human cell lines and primary lymphoma samples. Furthermore, 1 humanized BAFF-R mAb clone and its afucosylated version, glycoengineered to optimize the primary mechanism of action, prolonged survival of immunodeficient mice bearing human tumor cell lines or patient-derived lymphoma xenografts in 3 separate models, compared with controls. Finally, the tissue specificity of this humanized mAb was confirmed against a broad panel of normal human tissues. Taken together, we have identified a robust lead-candidate BAFF-R mAb for clinical development.

Abstract A06: Strategies to circumvent resistance to cyclin-dependent kinase-9 inhibition (CDK9i) in non-Hodgkin lymphoma (NHL)

Introduction Oncogenic programs are facilitated by activators of transcriptional machinery, including certain CDKs. CDK9, a component of the positive transcription elongation factor b (pTEFb) complex, has arisen as an attractive target due to its regulation of MYC and MCL1 transcription (Hashiguchi et al, 2019). Nevertheless, we and others have observed resistance to CDK9i in vitro and in vivo. Here we studied the effects of CDK9 inhibition using the novel selective CDK9 inhibitor AZD4573, currently under evaluation in clinical trials. Methods A panel of NHL cell lines (OCI-LY3/19, SUDHL4/10/16, VAL, U2932) and primary NHL cells were employed. Response to CDK9i was characterized using LC-MS proteomic analysis, RNA-Seq, and CRISPR-Cas9 Screening. Results NHL cells treated with AZD4573 for 6h exhibited a dose dependent reduction in phospho-RNAPIISer2, as well as loss of MYC and Mcl-1. CDK9i potently inhibited proliferation and induced apoptosis in a panel of NHL cell lines (IC50 range 5-30 nM). Two DLBCL cell lines underwent LC-MS proteomic analysis following AZD4573 treatment (30 nM, 3h). Treated cells exhibited rapid loss of MYC, Mcl-1, PIM3 and JUNB protein levels. We observed broad transcriptional repression via RNA-seq, including downregulation of PIM3 and JUNB (30 nM, 3h). However, a subset of genes, including MYC, PIM1 and JUNB underwent early transcriptional recovery, confirmed by immunoblotting, thus identifying candidate genes which may account for resistance to CDK9i. PIM kinases cooperate with the PI3K/ATK signaling pathway, and have been proposed as therapeutic targets in cancer. We next used SGI1776 (PIM1 specific) and AZD1208 (pan-PIM) in combination with AZD4573, and found synergy between them in a panel of 4 cell lines and primary samples. OCI-LY3 xenograft mice treated with a combination of AZD4573 (15 mg/kg; IP; once weekly) and AZD1208 (30 mg/kg; oral gavage, twice weekly) demonstrated restricted tumor growth and increased survival compared to control. To further understand pathways mediating resistance to CDK9i, we carried out a genome-wide loss of function CRISPR-Cas9 library screen. Two Cas9-expressing NHL cell lines were transduced with a CRISPR library comprised of ~5 unique sgRNA per gene. Loss of AKT, RPTOR, or mTOR, among others, sensitized cells to AZD4573. Concurrent treatment with PI3K inhibitors synergistically suppressed proliferation of NHL cell lines and primary cells treated with AZD4573 in vitro. OCI-LY3 xenograft mice were treated with AZD4573 (15 mg/kg; IP; once weekly), Copanlisib (15 mg/kg; IP; twice weekly), or a combination of both. Combo treatment restricted tumor growth and prolonged survival to a greater extent than either drug alone. Conclusions CDK9i with AZD4573 downregulated numerous oncoproteins. However, a subset of genes including MYC and PIM3 recovered transcription. PI3K/AKT pathway was implicated in resistance to CDK9i in CRISPR library screens. Concurrent targeting of pro-survival pathways (e.g., PIM, PI3K) partially reversed resistance to CDK9i.

Citation Format: Elana Thieme, Duanchen Sun, Nur Bruss, Geeta Sharma, Tingting Liu, Daniel Coleman, Tamilla Nechiporuk, Daniel Bottomly, Shannon McWeeney, Patrick Pirrotte, Zheng Xia, Alexey Danilov. Strategies to circumvent resistance to cyclin-dependent kinase-9 inhibition (CDK9i) in non-Hodgkin lymphoma (NHL) [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A06.

Pharmacologic Targeting of Mcl-1 Induces Mitochondrial Dysfunction and Apoptosis in B-Cell Lymphoma Cells in a TP53- and BAX-Dependent Manner

PURPOSE

Bcl-2 has been effectively targeted in lymphoid malignancies. However, resistance is inevitable, and novel approaches to target mitochondrial apoptosis are necessary. AZD5991, a selective BH3-mimetic in clinical trials, inhibits Mcl-1 with high potency.

EXPERIMENTAL DESIGN

We explored the preclinical activity of AZD5991 in diffuse large B-cell lymphoma (DLBCL) and ibrutinib-resistant mantle cell lymphoma (MCL) cell lines, MCL patient samples, and mice bearing DLBCL and MCL xenografts using flow cytometry, immunoblotting, and Seahorse respirometry assay. Cas9 gene editing and ex vivo functional drug screen assays helped identify mechanisms of resistance to Mcl-1 inhibition.

RESULTS

Mcl-1 was expressed in DLBCL and MCL cell lines and primary tumors. Treatment with AZD5991 restricted growth of DLBCL cells independent of cell of origin and overcame ibrutinib resistance in MCL cells. Mcl-1 inhibition led to mitochondrial dysfunction as manifested by mitochondrial membrane depolarization, decreased mitochondrial mass, and induction of mitophagy. This was accompanied by impairment of oxidative phosphorylation. TP53 and BAX were essential for sensitivity to Mcl-1, and oxidative phosphorylation was implicated in resistance to Mcl-1 inhibition. Induction of prosurvival proteins (e.g., Bcl-xL) in stromal conditions that mimic the tumor microenvironment rendered protection of primary MCL cells from Mcl-1 inhibition, while BH3-mimetics targeting Bcl-2/xL sensitized lymphoid cells to AZD5991. Treatment with AZD5991 reduced tumor growth in murine lymphoma models and prolonged survival of MCL PDX mice.

CONCLUSIONS

Selective targeting Mcl-1 is a promising therapeutic approach in lymphoid malignancies. TP53 apoptotic network and metabolic reprogramming underlie susceptibility to Mcl-1 inhibition.

Abstract 938: Pharmacologic targeting Mcl-1 with AZD5991 induces apoptosis, suppresses mitochondrial respiration and overcomes ibrutinib resistance in non-Hodgkin lymphoma cells

Bcl-2 family proteins determine cell fate and comprise pro-apoptotic “initiators” (Noxa, Bim, Puma), anti-apoptotic “guardians” (Bcl-2, Mcl-1, Bcl-xL) and pro-apoptotic effectors (Bax/Bak). Venetoclax, a Bcl-2 inhibitor, received regulatory approval in the therapy of chronic lymphocytic leukemia and acute myeloid leukemia. However, venetoclax is modestly effective in non-Hodgkin lymphoma (NHL). Mcl-1 is a short-lived pro-survival protein that is frequently overexpressed in NHL, leading to increased cell survival and drug resistance. Mcl-1 transgenic mice develop aggressive lymphoma. Thus, selective targeting Mcl-1 represents a promising pharmacologic strategy in NHL. AZD5991 is a selective small-molecule inhibitor with high potency against Mcl-1 which has entered clinical trials. Here we explored its pre-clinical activity in NHL. We detected Mcl-1 expression in ten diffuse large B-cell lymphoma (DLBCL) as well as in parental/ibrutinib-resistant JeKo-1 and Mino mantle cell lymphoma (MCL) cell lines. AZD5991 suppressed proliferation and induced apoptosis in DLBCL cells in a dose-dependent manner, as well as in parental/ibrutinib-resistant MCL cells. Mcl-1 inhibition led to mitochondrial dysfunction, including mitochondrial membrane depolarization, decreased mitochondrial mass, increased mitophagy, and increased levels of reactive oxygen species in both DLBCL and parental/ibrutinib-resistant MCL cells. Mcl-1 inhibition downmodulated basal and maximal respiratory capacity in sensitive, but not in resistant cells, as determined by the Seahorse assay, further indicating mitochondria compromise as a mechanism of susceptibility to Mcl-1 inhibition. An inhibitors screening assay identifies that AZD5991 demonstrated synergy with other BH3-mimetics. Co-treatment of DLBCL cells with Bcl-2/xL inhibitors AZD4320, venetoclax and navitoclax overcame resistance to AZD5991. Finally, Primary MCL cells were co-cultured with control, CD40L- or BAFF-expressing stroma which partially mimics the lymph node microenvironment and induces resistance to spontaneous and drug-induced apoptosis. Mcl-1 inhibition induced apoptosis of primary MCL cells in both control and BAFF-expressing conditions, accompanied by decreased mitochondrial respiration. Meanwhile, CD40L stroma rendered protection from AZD5991 which was partially overcome by co-treatment with venetoclax. In summary, Mcl-1 inhibition using selective BH3-mimetic AZD5991 restricts cell proliferation and induces apoptosis in a subset of DLBCL, parental/ibrutinib-resistant MCL cells and primary neoplastic B cells. Mcl-1 inhibition leads to mitochondrial dysfunction and inhibition of cellular respiration. Resistance to Mcl-1 inhibition may be overcome by concurrent targeting of alternative anti-apoptotic proteins (Bcl-2/xL) in NHL.

Citation Format: Tingting Liu, Vi Lam, Elana Thieme, Xiaoguang Wang, Fei Xu, Steve Kurtz, Jeff Tyner, Olga V. Danilova, Alexey Danilov. Pharmacologic targeting Mcl-1 with AZD5991 induces apoptosis, suppresses mitochondrial respiration and overcomes ibrutinib resistance in non-Hodgkin lymphoma cells [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 938.

[Relations between disordered exocrine pancreas function, alcohol consumption and age in alcoholics]

During clinical withdrawal treatment, a disturbed exocrine pancreas function was found in 28 per cent of 72 alcohol addicts, which occurred in connection with an alcohol-induced pancreatitis. The clinical course was mainly quiescent. Altered bicarbonate concentrations and enzyme dissociations were found as a result of the secretin pancreozymin test. In alcohol addicts, the maximum activity of the amylase output was reached as early as 20 minutes and that of bicarbonate, trypsin and chemotrypsin not until 40 minutes post stimulationem. The sums of the logarithmically transformed 40-minute output of bicarbonate, amylase and trypsin displayed significant differences between the alcohol-addict and control groups. The degree of severity of the disturbed exocrine pancreas function was essentially a function of the daily amount of alcohol taken by the addict and of the age of the patient. The dysfunction was most evident in the 30-to-50-year-old patients. Chronic consumption of alcohol is assumed to give rise to a selective effect on the hydro-kinetic and ecbolic pancreas function.

[Endangering the water-electrolyte balance in gastrointestinal diseases in the aged]

In old people the range of operation, as well as the adaptability of the electrolyte and water metabolism, is reduced by the involutive reduction of the renal, pulmonary and endocrinic functions, as well as by a reduced feeling of thirst, a reduction of the buffer mechanisms, and a dwindling amount of body water. The threat to the maintenance of the requisite amount of body-water and to a normal electrolysis, caused by gastro-intestinal illnesses, is discussed from the point of view of geriatrics. Hydro-mineral upsets occurring in gastroenterology are primarily caused either by an inadequate supply, inadequate absorption, or by an extra-ordinary loss of intestinal secretions, as well as by interference with the normal electrolyte and water metabolism due to medical treatment. Situations in which such hydro-mineral disturbances wright occur are indicated and therapeutic measures suggested. We assert and prove that in old people the danger of extreme reduction of body-water and electrolysis frequently presents a greater threat to life than the illness from which it proceeds, and we maintain that a due consideration of this problem can in many cases literally save the life of the old patient.

[Use of anamnestic questionnaires in gastrointestinal diseases in the aged]

The authors relate their experiences in using questionnaires for taking the history of patients with gastroenterological enterological ailments. They have found that the older the patient, the more the results of the questionnaire diverge from those obtained by conventional methods of history-taking. Consequently the authors advise a cautious approach to the use of questionnaires when dealing with elderly patients.