Proteomic Array Research Articles

Autoantibodies identify primary Sjögren’s syndrome in patients lacking serum IgG specific for Ro/SS-A and La/SS-B

ObjectiveIdentify autoantibodies in anti-Ro/SS-A negative primary Sjögren’s syndrome (SS).MethodsThis is a proof-of-concept, case-control study of SS, healthy (HC) and other disease (OD) controls. A discovery dataset of plasma samples (n=30...

Argonaute, Vault, and Ribosomal Proteins Targeted by Autoantibodies in Systemic Lupus Erythematosus.

To expand, in an unbiased manner, our knowledge of autoantigens and autoantibodies in patients with systemic lupus erythematosus (SLE) and evaluate their associations with serological and clinical variables. Human proteome arrays (> 21,000 proteins) were screened with serum from patients with SLE (n = 12) and healthy controls (n = 6) for IgG and IgA binding. Top hits were validated with 2 cohorts of patients with SLE (cohort 1, n = 49; cohort 2, n = 46) and other rheumatic diseases by ELISA. Clinical associations of the autoantibodies were tested. Ro60 was the top hit in the screen, and the 10 following proteins included 2 additional known SLE autoantigens plus 8 novel autoantigens involved in microRNA processing (Argonaute protein 1 [AGO1], AGO2, and AGO3), ribosomes (ribosomal protein lateral stalk subunit P2 and ovarian tumor deubiquitinase 5 [OTUD5]), RNA transport by the vault (major vault protein), and the immune proteasome (proteasome activator complex subunit 3). Patient serum contained IgG reactive with these proteins and IgA against the AGO proteins. Using the 95th percentile of healthy donor reactivity, 5-43% were positive for the novel antigens, with OTUD5 and AGO1 showing the highest percentages of positivity. Autoantibodies against AGO1 proteins were more prevalent in patients with oral ulcers in a statistically significant manner. IgG autoantibodies against AGO proteins were also seen in other rheumatic diseases. We discovered new autoantigens existing in cytosolic macromolecular protein assemblies containing RNA (except the proteasome) in cells. A more comprehensive list of autoantigens will allow for a better analysis of how proteins are targeted by the autoimmune response. Future research will also reveal whether specific autoantibodies have utility in the diagnosis or management of SLE.

Unmasking Arterial-resident Autoreactive B cells involved in Atherosclerosis and Peripheral Artery Disease Progression

Abstract Atherosclerosis activates the immune system, including B cells which secrete antibodies that bind antigens released by necrotic cells within plaques and may promote inflammation. To identify these antibodies, we isolated activated B cells from atherosclerotic ApoE-deficient mice aortas and human tibial arteries with peripheral artery disease post-amputation. Single-cell sequencing of the B cell receptors identified 35 mouse and 48 human overrepresented disease-relevant heavy and light chain pairings, which were sequentially expressed as antibody. Epitope determination was performed by human proteome array, and 14 mouse and 21 human protein targets were found with significant affinity and specificity. Mouse antigens were scrutinized by immunohistochemistry to confirm presence in inflamed plaques, and expression of these proteins were used to interrogate autoreactive antibody titers in diseased sera by ELISA. ApoE-deficient mice were immunized with the 6 most promising antigens. Serum antibody measurement showed strong, rapid, and early onset of antigen-specific antibody responses in the immunized mice compared to an adjuvant only control group. Strikingly, we saw decreased plaque accumulation in the immunized animals, suggesting antigen responses may clear pathogenic antigens before disease develops. Likewise, human antigen ELISAs comparing antigen-specific serum antibody titers to patient Framingham score for cardiovascular risk supported a role for two antigens in disease. To confirm these antigens as potential biomarkers, we will characterize the emergence of their antibody counterparts using a historical library of serum samples from individuals enrolled in the Baltimore Longitudinal Study on Aging. This work is directly funded by the National Institutes of Health – National Institute on Aging’s Intramural Research Program in the Lab of Molecular Biology and Immunology

Abstract 2535: Inhibition of oncogenic ASPP2kappa(k), a dominant-negative isoform of the tumorsuppressor ASPP2, results in reactivation of p53 in glioblastoma

Abstract GB is the most common, most aggressive primary brain tumor with a deleterious prognosis. Novel approaches to improve therapy are urgently needed. ASPP2 is a tumor suppressor, directly interacting with p53 to induce apoptosis. We recently identified a dominant-negative isoform of ASPP2, named ASPP2kappa(k), lacking the important p53 binding sites. We now show that ASPP2k is highly expressed and functionally active in high grade glioma and that silencing of ASPP2k reactivates induction of apoptosis via p53. Freshly resected glioma (n=76) were assessed for ASPP2k expression. Isogenic, p53wt cell models, stably suppressing or overexpressing ASPP2k were established in A-172 and U-251 cells and ex vivo from GB samples and the role of ASPP2k in induction of apoptosis, cellular proliferation, migration and invasion was assessed. A proteome array allowed to study pathways involved in ASPP2k signaling. An ASPP2k knock-down, NOD/SCID xenotransplant mouse model was established to study the role of ASPP2k in tumor engraftment and progression. Frequent overexpression of ASPP2k in glioma was confirmed in virtually all patients analyzed. Expression patterns varied widely (up to 40-fold compared to tumor-free tissue). Expression of ASPP2k thereby correlates with tumor biology - with highest levels found in aggressive grade IV GB. We further demonstrate that expression of ASPP2k results in impaired induction of apoptosis in all GB models - and knock down of ASPP2k renders cells more susceptible towards temozolamide (TMZ), γ-irradiation (avg. 25% TMZ, 40% irradiation) or combinational approaches compared to controls. Vice versa, overexpression of ASPP2κ further attenuates induction of apoptosis. Even more, ASPP2k directly affects other cellular functions in GB, rendering cells to a more aggressive phenotype with increased proliferation (approx. 25%), migration (approx. 65%) and invasion rates compared to the knock down strains. In line, silencing of ASPP2k resulted in strong upregulation of crucial p53 phosphorylation sites (S15/S46), as well as cell cycle regulators (p21, p27 and pRAD) in a proteome array, arguing for re-activation of crucial p53-mediated pathways in the ASPP2k silenced cells. Results were confirmed by western immunoblotting and FACS analyses. Ongoing xenotransplant mouse models confirm that silencing of ASPP2k in GB models attenuates tumor engraftment, development and progression in vivo. In summary, we here show that ASPP2k is highly expressed in GB and directly contributes to aggressiveness of the disease as well as resistance towards therapy. Silencing of ASPP2k thereby re-activates crucial p53 pathways, resulting in re-activation of p53-mediated apoptosis pathways as well as re-installation of cell cycle checkpoints. Future studies evaluating ASPP2k as a prognostic/predictive model and potential target for therapy are warranted. Citation Format: Marlon Hafner, Alessia Ruiba, Leonie Kampa, Vincent Kälin, Marian Neidert, Konrad Buchauer, Guido Henke, Ludwig Plasswilm, Marcus M. Schittenhelmn, Kerstin M. Kampa-Schittenhelm. Inhibition of oncogenic ASPP2kappa(k), a dominant-negative isoform of the tumorsuppressor ASPP2, results in reactivation of p53 in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2535.

Abstract 2560: Post-translational modification of focal adhesion kinase (FAK) protein increases in breast cancer cells upon exposure to conditioned medium derived from in vitro and in vivo adipocytes

Abstract Under obese conditions, dysregulation of the normal secretion of adipokines from fat cells has been shown to drive cancer progression. However, the role adipokine dysregulation plays in driving metastasis is still unclear. Recent studies have reported the activation of metastasis-associated cell signaling pathways. One such pathway involves Focal Adhesion Kinase (FAK), a non-receptor cytoplasmic protein that acts as a signal transducer between receptor activation by adipokines and downstream effector proteins that control the biological phenomenon of metastasis. Nevertheless, the association between obesity-induced changes in adipocyte secretory factors and the subsequent increase in the transactivation of FAK through phosphorylation is unknown. To elucidate the potential relationship of adipocyte-secreted factors towards activating FAK, breast cancer cells with low (MCF7) and high (MDA-MB-231) metastatic potential were exposed to in vitro and in vivo, murine adipocyte-derived, conditioned medium. For the in vitro adipocyte model, 3T3-L1 MBX cells differentiated to obesity, with fatty acids supplementation, were used. For the in vivo model, adipocyte-secreted factors from organ-cultured visceral fat harvested from C3H/HeJ female mice fed an either high fat (46%) or control (11%) diets, were collected in the medium. Adipocyte secretions from the in vitro and in vivo adipocyte samples were determined using a mouse adipokine proteomic profiler array and ELISA kit. Under obese conditions, both the 3T3-L1 MBX cells and C3H/HeJ visceral fat were found to have significant changes in their adipokine secretions in comparison to controls. Results showed that the breast cancer cells got increased FAK autophosphorylation when exposed to either in vitro or in vivo-derived obese adipocyte-conditioned medium in comparison to the untreated breast cancer cells. Citation Format: Noshin Mubtasim, Caleb Boren, Benjamin Barr, Lauren Gollahon. Post-translational modification of focal adhesion kinase (FAK) protein increases in breast cancer cells upon exposure to conditioned medium derived from in vitro and in vivo adipocytes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2560.

Abstract 6305: Bispecific claudin 18.2 and GPRC5D antibodies with potent cell-killing activity for cancer therapeutics

Abstract Tumor-associated antigens with little or no expression in healthy tissue are attractive targets for anti-tumor modalities including T cell-engaging bispecific antibodies. CLDN18.2 is a transmembrane adhesion protein undetectable in most healthy adult tissues but highly expressed in gastric, pancreatic, esophageal, and lung cancers. GPRC5D is a G protein-coupled receptor that is absent from most healthy tissues except for hair follicles but expressed on multiple myeloma cells. Both CLND18.2 and GPRC5D are novel oncology targets with no clinically approved therapies against them. Using our discovery platform tailored to complex transmembrane proteins, we have developed bispecific antibodies with the ability to potently kill CLDN18.2-positive or GPRC5D-positive cells. Multipass membrane proteins are valuable therapeutic targets in oncology and other disease areas but are largely inaccessible as antibody targets due to their poor expression, membrane-dependent structure, small extracellular regions, and poor immunogenicity due to sequence conservation. We developed an antibody discovery platform (MPS) that specifically addresses each of these challenges. This platform utilizes advanced immunization techniques including DNA, mRNA, and Lipoparticles (virus-like particles). It also employs chickens as an evolutionarily divergent host species for robust immune responses against conserved targets. Antibodies raised in chickens are directly humanized prior to isolation, reducing the need for downstream engineering. In two separate campaigns, we immunized chickens with CLDN18.2 and GPRC5D and obtained high-titer immune responses. We were successful in isolating high-affinity antibodies specific to each of these targets. Our CLDN18.2 antibodies showed specificity for their target and did not bind the closely related splice variant CLND18.1, which is highly expressed in healthy lung tissue. Additionally, the antibodies showed no binding to ~6,000 other proteins that were screened using a Membrane Proteome Array. A subset of antibodies from both discovery programs were configured as bispecific molecules using a CD3-targeting arm to bring tumor cells into close proximity with cytotoxic T cells that mediate cell killing. The panels of molecules encompassed multiple bispecific formats bearing different stoichiometries, geometries, and sizes to enable identification of lead molecules with favorable activities and safety profiles. Both CLDN18.2 and GPRC5D bispecifics showed potent T cell-mediated cytotoxicity with picomolar potency. They also showed good cytokine release and developability profiles. GPRC5D x CD3 and CLDN18.2 x CD3 bispecifics hold promise as potent and safe therapeutics for different cancer types. Citation Format: Ileine Sanchez, Hayley Roth, Brad Screnci, David Tucker, Nick Molino, Trevor Barnes, Paige Murphy, Kyle Guldner, Tim Phillips, Kristen Shema, Thomas Charpentier, Alyssa Cunningham, Janae Latta, Breanna Tyrell, Meghan Pitts, Carmen Navia, Charles Azuelos, Anna Lobley, Jawhara Karam, Valerie Fiers, Daniela Reyes, Kate Slovik, Alison Snyder, Marianne Assogba, Kai-Ti Chang, Riley Payne, Kyle Doolan, Ross Chambers, Joe Rucker, Benjamin Doranz. Bispecific claudin 18.2 and GPRC5D antibodies with potent cell-killing activity for cancer therapeutics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6305.

Abstract 6180: Antitumor activity of the ATR inhibitor Elimusertib in patient-derived xenograft models with DNA damage response pathway alterations

Abstract Introduction: The ataxia telangiectasia and RAD3-related (ATR) kinase is a key component of the DNA damage response (DDR) and functions in conjunction with ataxia telangiectasia mutated (ATM). ATM loss or functional deficiency may enhance reliance on ATR signaling. Preclinical and clinical studies have pointed to a potential synthetic lethality of ATR inhibition and ATM loss. In this study, we sought to further elaborate potential candidates for ATR inhibition by testing the anti-tumor effect of elimusertib (BAY 1895344) in patient-derived tumor xenograft (PDX) models with DDR alterations including ATM loss. Methods: Patient derived xenograft (PDX) models were implanted into athymic nu/nu mice. Once tumors reached an appropriate size of approximately 200-400mm3 treatments were started. Mice were randomized (N= 3-8) to different treatment arms for assessment of anti-tumor activity of elimusertib as monotherapy and in combination therapy with copanlisib. Monotherapy treatment was performed with 20 mg/kg and 40 mg/kg doses, applied twice daily for 3 days with 4 days treatment break (BID 3 days on/4 days off). Efficacy read-out was either Event-Free Survival (EFS-2), defined as time for doubling of tumor volume relative to baseline, or response based on RECIST criteria:(partial response [PR]= >30% decrease, stable disease [SD]= between 20% increase and 30% decrease, and progressive disease [PD]= >20% increase). For assessment of pharmacodynamic effects, tumors were harvested 10 days after treatment start and analyzed by immunohistochemistry (IHC) and RPPA (Reverse Phase Proteomics Array). Results: Elimusertib was tested in 21 PDX models with various DDR alterations. Of those 11 showed a statistically significant prolongation of event free survival compared to control. In 4 PDX models elimusertib reached a partial response (PR), and another 4 models showed stable disease (SD). Amongst the 5 models with ATM protein Ioss (IHC), one was PR and another one SD. In 3 of 5 PARP inhibitor resistant there was statistically significant prolongation of EFS upon elimusertib treatment vs control. We found an increase in DNA damage in tumors, as indicated by increased level of ƳH2AX (on IHC and RPPA). We also detected an increase in PI3K/mTOR pathway signaling as determined by p-MTOR and pS6 (RPPA) in 2 of 4 models (PR and PD model) with different sensitivity to ATRi and PARPi alone. We tested the combination of elimusertib with the PI3K inhibitor copanlisib achieved a statistically significant increase of EFS compared to monotherapy in 3 of 11 models tested. Conclusion ATR inhibition shows potent monotherapy activity in selected PDX models that harbor DDR defects, including models with intrinsic and acquired PARPi resistance. Further work is needed to identify markers predicting sensitivity or resistance that providing rationale for synergistic combination therapies. Citation Format: Kaushik Varadarajan, Christian X. Pico, Kurt Evans, Maria G. Raso, Yasmeen Rizvi, Xiaofeng Zheng, Timothy P. Diperi, Bailiang Wang, Stephen Scott, Ming Zhao, Argun Akcakanat, Antje M. Wengner, Timothy A. Yap, Funda Meric-Bernstam. Antitumor activity of the ATR inhibitor Elimusertib in patient-derived xenograft models with DNA damage response pathway alterations. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6180.

Abstract 2646: Screening the membrane proteome to determine antibody specificity and de-risk CAR-T cell development

Abstract Rigorous specificity analysis is critical for the development of antibody-based therapies, as even minimal off-target binding can lead to toxicity and clinical failures. Long believed to be exquisitely specific, recent preclinical data and our own work indicate that monoclonal antibodies (MAbs) frequently (~25%) display cross-reactivity. In many cases, off-target interactions occur with unrelated proteins that cannot be predicted by protein sequence homology. Cross-reactivity can lead to serious or even life-threatening consequences especially when MAbs are configured as bispecifics, antibody-drug conjugates (ADC) or CAR-T cell therapies, and IND applications for biotherapeutics require cross-reactivity assessment to prevent adverse events. Tissue cross-reactivity (TCR) studies have traditionally been used to screen for off-target binding, however, with poor predictive value for in vivo safety and toxicity. We developed the Membrane Proteome Array (MPA) platform to de-risk MAb-based therapeutics by testing for specificity across 6,000 human membrane proteins expressed in live cells. In contrast to TCR studies, proteins in the MPA exist in their native conformations and are not altered by fixation. The MPA assesses binding interactions by high-throughput flow cytometry allowing for high sensitivity detection and rapid analysis. We will discuss the importance of early-stage specificity testing to expose possible toxicities and present case studies for antibody and cell therapy profiling. MPA data have been used in numerous successful regulatory applications and may be used to replace or complement other cross-reactivity studies. In particular, MPA profiling has been used in IND applications for CAR-T and cell-therapies where conventional immunohistochemical binding assays did not suffice. Citation Format: Joseph Rucker, Rachel H. Fong, Tabb Sullivan, Carmen Navia, Brad Screnci, Rona Wilf, Benjamin J. Doranz. Screening the membrane proteome to determine antibody specificity and de-risk CAR-T cell development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2646.

Abstract 2658: ZW251, a novel glypican-3-targeting antibody drug conjugate bearing a topoisomerase 1 inhibitor payload

Abstract Background: Glypican-3 (GPC3) is a cell-surface oncofetal glycoprotein frequently expressed in hepatocellular carcinoma (HCC) with minimal presence in normal adult tissues. ZW251 is an antibody-drug conjugate (ADC) targeting human GPC3, composed of a humanized IgG1 antibody conjugated to a novel camptothecin-based topoisomerase 1 inhibitor, ZD06519, via a maleimide anchor and a glycyl glycyl phenylalanyl glycine (GGFG)-aminomethyl (AM) cleavable linker. Materials and Methods: Extensive functional characterization was performed to assess the mechanism of action and therapeutic potential of the ZW251 ADC. Antibody binding to human and cynomolgus monkey GPC3 was assessed by surface plasmon resonance and flow cytometry. A screen of off-target binding and target specificity was conducted using a membrane proteome array. ZW251 antibody internalization in GPC3-expressing tumor cell lines was assessed by flow cytometry. In vitro ADC cytotoxicity against tumor monolayers and spheroids was assessed in a panel of HCC cell lines. Tumor cell co-culture assays were also performed to assess bystander-mediated cell killing by ZW251. The pharmacokinetic (PK) profile of the ZW251 antibody was assessed in Tg32 mice expressing human FcRn. Anti-tumor activity of ZW251 was investigated in a large panel of cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) mouse models representing a range of GPC3 expression. Results: The ZW251 antibody backbone demonstrated nanomolar binding affinity to both human and cynomolgus monkey GPC3, and strong binding to target-expressing cancer cell lines. Rapid internalization of ZW251 antibody was observed in GPC3-expressing HCC cell lines. ZW251 exhibited potent and target-specific cytotoxicity in a panel of HCC cells cultured either in monolayer or as 3D spheroids. ZW251 showed effective bystander-mediated killing of GPC3 negative cancer cells when in co-culture with GPC3 positive cancer cells. The ZW251 antibody demonstrated a favorable PK profile in Tg32 mice. A single administration of ZW251 resulted in robust tumor growth inhibition of a large panel of CDX and PDX models representing a range of GPC3-expression. Overall, these results support the potential of ZW251 as a novel therapeutic agent against GPC3-bearing cancers. Citation Format: Laurence Madera, Andrea Hernández Rojas, Raffaele Colombo, Alex Wu, Chayne L. Piscitelli, Dunja Urosev, Allysha Bissessur, Chi Wing Cheng, Renee Duan, Catrina Kim, Kevin Yin, Vincent Fung, Kaylee Wu, Winnie Cheung, Diego A. Alonzo, Mark E. Petersen, Stuart D. Barnscher, Jamie R. Rich. ZW251, a novel glypican-3-targeting antibody drug conjugate bearing a topoisomerase 1 inhibitor payload [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2658.

Abstract 5498: SHP2 inhibition enhances antitumor effect of mirdametinib in a pediatric brain tumor model bearing CDC42SE2BRAF fusion by rewiring the proteome and phosphoproteome landscape

Abstract Pediatric gliomas are the most common type of pediatric brain tumors representing wide range of molecularly and clinically heterogenous subtypes. The hyperactivity of mitogen-activated protein kinases (MAPK) pathway has been identified in the majority of pediatric glioma suggesting its therapeutic potential. However, pharmacologic targeting single MAPK pathway’s component is limited due to the development of drug resistance and differential response associated with tumor molecular landscape. Therefore, effective combination strategy in the framework of precision medicine is needed. Here we report combination benefit and molecular underpinning therapeutic response of brain penetrant MEK inhibitor (mirdametinib) and SHP2 inhibitor (SHP099) in a pediatric patient derived xenograft (PDX) and xenoline developed at our institution. Our model was derived from a pediatric patient who was diagnosed with rare high-grade subtype of glioma, anaplastic pleomorphic xanthoastrocytoma, and did not respond to MEK inhibitor, trametinib. Integrative multi-omics revealed molecular fidelity between our model and its patient tumor counterpart including the presence of 7q35 fusion, CDC52SE2-BRAF, CDKN2A/B loss, and MAPK pathway hyperactivation. In vitro studies using our xenoline IU-X128 demonstrated synergy between SHP099 and mirdametinib to curtail cell proliferation (p<0.05). Moreover, this combination was well tolerated in our PDX, IU-RHT128, and potentiated anti-tumor effect of the single agent within clinically achievable doses. Reverse Phase Proteome Array (RPPA) identified MAPK reactivation via Mushasi RNA binding protein-PI3K-AKT crosstalk as a potential innate resistance mechanism to single agent MEK inhibitor in the PDX tumor. Further, tandem mass tags (TMT)-LC-MS/MS profiling on tumor treated with single agent SHP099 or mirdametinib and their combination revealed that combination therapy does not only revert certain proteome and phosphoproteome reprogramming from single agent treatment but also created a novel landscape which can be associated with anti-tumor effect. In this case, kinase network reprograming leading to MAPK reactivation was identified in mirdametinib treated tumor which was attenuated in the combination treatment. In summary, our results demonstrated that combination SHP099 and mirdametinib is superior to single agent alone in the pediatric A-PXA brain tumor model with proteome and phosphoproteome reprogramming of multiple networks as potential molecular mechanisms underlying therapeutic benefit of combination therapy. Ultimately, clinical translation of this finding will potentially benefit patient of this malignant rare pediatric glioma subset which currently does not have standard therapy. Citation Format: Nur P. Damayanti, Anthony Alfonso, Josue D. Ordaz, Erika Dobrota, M. Reza Saadatzadeh, Pankita Pandya, Barbara J. Bailey, Khadijeh Bijangi-Vishehsaraei, Harlan E. Shannon, Kathy Coy, Melissa Trowbridge, Anthony L. Sinn, Rosa Gallager, Julia Wulfkuhle, Emanuel Petricoin, Amber Mosley, Mark S. Marshall, Alex Lion, Michael J. Fergusson, Karl Balsara, Karen E. Pollok. SHP2 inhibition enhances antitumor effect of mirdametinib in a pediatric brain tumor model bearing CDC42SE2BRAF fusion by rewiring the proteome and phosphoproteome landscape. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5498.

Comparative Analysis of the Humoral Immune Response to the EBV Proteome across EBV-Related Malignancies.

Epstein-Barr virus (EBV) is linked to multiple cancers, including classical Hodgkin lymphoma (cHL), endemic Burkitt lymphoma (eBL), nasopharyngeal carcinoma (NPC), and extranodal natural killer/T-cell lymphoma (NKTCL). Anti-EBV IgG and IgA antibody responses targeting 202 sequences from 86 EBV proteins were measured using the same EBV whole proteome array across four case-control studies investigating EBV-positive cHL, eBL, NPC, and NKTCL (407 cases/620 controls). We grouped EBV-targeted antibodies into pathways by immunoglobulin type (IgA and IgG) and life-cycle stage (latent, immediate early lytic, early lytic, late lytic, and glycoprotein) and evaluated their association with each cancer type. In an additional analysis, we focused on the subset of 46 individual antibodies representing the top candidates for each cancer and compared their associations across the four cancer types using multivariable linear regression models. IgA antibody responses targeting all EBV life-cycle stages were associated with NPC but limited to anti-early lytic stage for cHL. NPC and eBL were associated with IgG antibodies across the viral life cycle; cHL with antibodies in the early lytic, late lytic and glycoprotein stages; and NKTCL with antibodies in the latent, immediate early lytic and early lytic phases. EBNA3A, BBLF1, BDLF4, and BLRF2 IgG antibodies were associated with all cancer types. Our observed similarities and differences across four EBV-associated cancers may inform EBV-related oncogenesis. Understanding the comparative humoral immune response across EBV-related cancers may aid in identifying shared etiologic roles of EBV proteins and inform unique pathogenic processes for each cancer.

Transcriptomic and Functional Evidence That miRNA193a-3p Inhibits Lymphatic Endothelial Cell (LEC) and LEC + MCF-7 Spheroid Growth Directly and by Altering MCF-7 Secretome.

MicroRNA 193a-3p (miR193a-3p) is a short non-coding RNA with tumor suppressor properties. Breast cancer (BC) progression is governed by active interaction between breast cancer cells, vascular (V)/lymphatic (L) endothelial cells (ECs), and BC secretome. We have recently shown that miR193a-3p, a tumor suppressor miRNA, inhibits MCF-7 BC cell-driven growth of VECs via direct antimitogenic actions and alters MCF-7 secretome. Since LEC-BC cross-talk plays a key role in BC progression, we investigated the effects of miR193a-3p on MCF-7 secretome and estradiol-mediated growth effects in LECs and LEC + MCF-7 spheroids, and delineated the underlying mechanisms. Transfection of LECs with miR193a-3p, as well as secretome from MCF-7 transfected cells, inhibited LEC growth, and these effects were mimicked in LEC + MCF-7 spheroids. Moreover, miR193a-3p inhibited ERK1/2 and Akt phosphorylation in LECs and LEC + MCF-7 spheroids, which are importantly involved in promoting cancer development and metastasis. Treatment of LECs and LEC + MCF-7 spheroids with estradiol (E2)-induced growth, as well as ERK1/2 and Akt phosphorylation, and was abrogated by miR193a-3p and secretome from MCF-7 transfected cells. Gene expression analysis (GEA) in LEC + MCF-7 spheroids transfected with miR193a-3p showed significant upregulation of 54 genes and downregulation of 73 genes. Pathway enrichment analysis of regulated genes showed significant modulation of several pathways, including interferon, interleukin/cytokine-mediated signaling, innate immune system, ERK1/2 cascade, apoptosis, and estrogen receptor signaling. Transcriptomic analysis showed downregulation in interferon and anti-apoptotic and pro-growth molecules, such as IFI6, IFIT1, OSA1/2, IFITM1, HLA-A/B, PSMB8/9, and PARP9, which are known to regulate BC progression. The cytokine proteome array of miR193a-3p transfected MCF secretome and confirmed the upregulation of several growth inhibitory cytokines, including IFNγ, Il-1a, IL-1ra, IL-32, IL-33, IL-24, IL-27, cystatin, C-reactive protein, Fas ligand, MIG, and sTIM3. Moreover, miR193a-3p alters factors in MCF-7 secretome, which represses ERK1/2 and Akt phosphorylation, induces pro-apoptotic protein and apoptosis in LECs, and downregulates interferon-associated proteins known to promote cancer growth and metastasis. In conclusion, miR193a-3p can potentially modify the tumor microenvironment by altering pro-growth BC secretome and inhibiting LEC growth, and may represent a therapeutic molecule to target breast tumors/cancer.

Precision targeting of autoantigen-specific B cells in muscle-specific tyrosine kinase myasthenia gravis with chimeric autoantibody receptor T cells.

Muscle-specific tyrosine kinase myasthenia gravis (MuSK MG) is an autoimmune disease that causes life-threatening muscle weakness due to anti-MuSK autoantibodies that disrupt neuromuscular junction signaling. To avoid chronic immunosuppression from current therapies, we engineered T cells to express a MuSK chimeric autoantibody receptor with CD137-CD3ζ signaling domains (MuSK-CAART) for precision targeting of B cells expressing anti-MuSK autoantibodies. MuSK-CAART demonstrated similar efficacy as anti-CD19 chimeric antigen receptor T cells for depletion of anti-MuSK B cells and retained cytolytic activity in the presence of soluble anti-MuSK antibodies. In an experimental autoimmune MG mouse model, MuSK-CAART reduced anti-MuSK IgG without decreasing B cells or total IgG levels, reflecting MuSK-specific B cell depletion. Specific off-target interactions of MuSK-CAART were not identified in vivo, in primary human cell screens or by high-throughput human membrane proteome array. These data contributed to an investigational new drug application and phase 1 clinical study design for MuSK-CAART for the treatment of MuSK autoantibody-positive MG.

Combination of IL-17A/F and TNF-α uniquely alters the bronchial epithelial cell proteome to enhance proteins that augment neutrophil migration

BackgroundThe heterodimer interleukin (IL)-17A/F is elevated in the lungs in chronic respiratory disease such as severe asthma, along with the pro-inflammatory cytokine tumor necrosis factor-α (TNF-α). Although IL-17A/F and TNF-α are known to functionally cooperate to exacerbate airway inflammation, proteins altered by their interaction in the lungs are not fully elucidated.ResultsWe used Slow Off-rate Modified Aptamer-based proteomic array to identify proteins that are uniquely and/or synergistically enhanced by concurrent stimulation with IL-17A/F and TNF-α in human bronchial epithelial cells (HBEC). The abundance of 38 proteins was significantly enhanced by the combination of IL-17A/F and TNF-α, compared to either cytokine alone. Four out of seven proteins that were increased > 2-fold were those that promote neutrophil migration; host defence peptides (HDP; Lipocalin-2 (LCN-2) and Elafin) and chemokines (IL-8, GROα). We independently confirmed the synergistic increase of these four proteins by western blots and ELISA. We also functionally confirmed that factors secreted by HBEC stimulated with the combination of IL-17A/F and TNF-α uniquely enhances neutrophil migration. We further showed that PI3K and PKC pathways selectively control IL-17A/F + TNF-α-mediated synergistic production of HDPs LCN-2 and Elafin, but not chemokines IL-8 and GROα. Using a murine model of airway inflammation, we demonstrated enhancement of IL-17A/F, TNF-α, LCN-2 and neutrophil chemokine KC in the lungs, thus corroborating our findings in-vivo.ConclusionThis study identifies proteins and signaling mediated by concurrent IL-17A/F and TNF-α exposure in the lungs, relevant to respiratory diseases characterized by chronic inflammation, especially neutrophilic airway inflammation such as severe asthma.

A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer.

Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer. The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease. The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.

Haploinsufficiency of Calreticulin Causes Dysregulation of Hematopoiesis and Results in a Myeloproliferative Phenotype in an in-Vivo Mouse Model

Background.JAK2V617F, MPLW515K/L and CALR exon9 mutations drive the development of Philadelphia negative Myeloproliferative Neoplasms (MPN). While JAK2 and MPL knock out (KO) leads to severe defects of hematopoiesis, the role of Calreticulin (CALR) deregulation is not fully understood, however recent reports demonstrated that CALR deletion leads to neoplastic transformation (Shide K et al Blood, 2020; Balliu M et al Blood Adv., 2021). Aim. To investigate the role of CALR in hematopoiesis and MPN development, we generated and characterized a Calr KO mouse model. Methods. We developed a Calr+/- mouse model by crossing mice carrying a floxed allele targeting Calr intron 3 and 7 (Calr+/flx) with Vav-Cre mice. The phenotypic characterization was performed by blood counts analysis, bone marrow (BM) and spleen histology, flow-cytometry and clonogenic assay by plating 2x104 cells for CFU-GEMM, CFU-GM and BFU-E and 2.5x105 for CFU-Mk. Proteome profiler membrane-based array and RNA-sequencing were employed to profiling BM protein and gene expression. Results. Sanger sequencing of BM cells of Calr+/- mice confirmed the deletion of Calr exons 4-7, resulting in the downregulation of Calr mRNA (-0.56-fold ±0.1) and decreased protein content (-0.47-fold ±0.21) compared to Calr+/flx mice (hence, controls). The productivity, body weight and lifespan were comparable between Calr+/- and controls. Calr+/- mice showed increased platelet count (median: 1360, range: 1156-1986 x109/L), 1.2 to 1.5-fold compared to controls, starting from month 4 (p=0.007) up to the latest time point available at 12 months (p=0.03). Erythrocytes count of Calr+/- increased after month 6 up to month 12 (median:10.3, range:9.9-10.6 x1012/L)(P=0.004) paralleled by an upward trend of hematocrit (median:47%, range:42-51%) and hemoglobin (median:18.3, range:14.2-20.1 g/L) levels. The spleen index (spleen:body weight ratio x100) resulted increased in Calr+/- (mean: 0.38±0.09) compared to controls (mean: 0.3±0.08) (P=0.039). Histology revealed an augmented number of poly-lobulated megakaryocytes, most of which found in clusters, in BM of Calr+/- mice. Most Calr+/- mice showed a progressive loss of spleen architecture with resulting loss of clear demarcation between red and white pulp combined with focal fibrosis, especially in aged mice. Calr haploinsufficiency conferred an augmented clonogenic capacity to BM and, to a lesser extent, splenic progenitors, in semisolid culture assay. BM Calr+/- CFU-GEMM, CFU-GM and CFU-Mk were in median 8.9 (5-15), 102.7 (49-157) and 16 (9.7-13.6) and 5.7 (3 -10) (P=0.007), 80.2 (33-159) (P=0.0031) and 11.9 (12.7-22) (P=0.048) in Calr+/flx, respectively. Of note, BM BFU-E count was 1.3-fold higher in Calr +/- than controls (P=0.009). Calr+/- splenic progenitors showed an enhanced clonogenic potential, strikingly for CFU-GEMM (P=0.0064). We observed that Calr+/- myeloid progenitors were significantly expanded when compared to controls: BM Mk precursors (FcγRlow/cKIT+/CD41+) and both BM and spleen LSK (Lin-/Sca1+/cKIT+) were, respectively, +1.6-fold (P=0.048), +1.4-fold (P=0.042) and +2-fold (P=0.008) than controls. Proteomic array performed on BM cells identified a set of deregulated proteins, mainly represented by cytokines (IL1α, IL4, IL6), chemokines (CXCL5, CXCL12, C1qR, VEGF, Endoglin) and cell adhesion molecules (VCAM, ICAM). These observations were strengthened by the result of transcriptomics analysis on bulk RNA-sequencing from Calr+/- and Calr+/flx mice BM cells highlighting a number of differentially expressed RNAs (increased n=385, decreased n=350) that resulted enriched in signaling pathways regulating chemokines and cell adhesion molecules, including "cell chemotaxis” (GO:0060326), "leukocyte migration” (GO:0050900), "regulation of cell-cell adhesion” (GO:0022407); cytokines, as determined by "Cytokine-cytokine receptor interaction” (KEGG:mmu04060); and Ca2+ homeostasis, including "cellular calcium ion homeostasis” (GO:0006874), "regulation of cytosolic calcium ion concentration” (GO:0051480 ). Conclusion. Finding from this in-vivo model suggest that haploinsufficiency of Calr induces dysregulation of hematopoiesis, ultimately resulting in a mild-ET phenotype. These findings will be validated in larger series and integrated with ongoing experiments to outline the molecular mechanisms underlying the CALR-driven MPN phenotype.

Analysis of CRSsNP Proteome Using a Highly Multiplexed Approach in Nasal Mucus.

Chronic rhinosinusitis without nasal polyps (CRSsNP) represents a phenotype of CRS, whose immunological mechanisms are still unclear. So far there are neither suitable biomarkers to determine the course of the disease nor an individual therapy. The purpose of this study was to characterize the CRSsNP endotype by identifying and validating non-invasive proteomic biomarkers. A highly-multiplexed proteomic array consisting of antibodies against 2000 proteins was used to identify proteins that are differentially expressed in the nasal mucus of the CRSsNP and control groups (n = 7 per group). The proteins identified to be most differentially expressed were validated in matched nasal mucus samples using western blots and enzyme-linked immunosorbent assay (ELISA). Validation was also done in a second cohort using western blots (CRSsNP n = 25, control n = 23) and ELISA (n = 30 per group). Additionally, immunohistochemistry in CRSsNP and control tissue samples was performed to characterize the selected proteins further. Out of the 2000 proteins examined, 7 from the most differentially expressed proteins were chosen to be validated. The validation results showed that 4 proteins were significantly upregulated in CRSsNP mucus, including macrophage inflammatory protein-1beta (MIP-1β), resistin, high mobility group box 1 (HMGB1), and forkhead box protein 3 (FOXP3). Cartilage acidic protein 1 (CRTAC1) was not significantly upregulated. Two proteins were significantly downregulated including scavenger receptor class F member 2 (SCARF2) and P-selectin. All proteins selected are mainly associated with inflammation, cell proliferation/differentiation, apoptosis and cell-cell or cell-matrix interaction. Proteomic analysis of CRSsNP and control mucus has confirmed known and revealed novel disease-associated proteins that could potentially serve as a new biosignature for CRSsNP. Analysis of the associated pathways will specify endotypes of CRSsNP and will lead to an improved understanding of the pathophysiology of CRSsNP. Furthermore, our data contribute to the development of a reproducible, non-invasive, and quantitative "liquid biopsy" for rhinosinusitis.

Micro-RNA193a-3p Inhibits Breast Cancer Cell Driven Growth of Vascular Endothelial Cells by Altering Secretome and Inhibiting Mitogenesis: Transcriptomic and Functional Evidence.

Breast cancer (BC) cell secretome in the tumor microenvironment (TME) facilitates neo-angiogenesis by promoting vascular endothelial cell (VEC) growth. Drugs that block BC cell growth or angiogenesis can restrict tumor growth and are of clinical relevance. Molecules that can target both BC cell and VEC growth as well as BC secretome may be more effective in treating BC. Since small non-coding microRNAs (miRs) regulate cell growth and miR193a-3p has onco-suppressor activity, we investigated whether miR193a-3p inhibits MCF-7-driven growth (proliferation, migration, capillary formation, signal transduction) of VECs. Using BC cells and VECs grown in monolayers or 3D spheroids and gene microarrays, we demonstrate that: pro-growth effects of MCF-7 and MDA-MB231 conditioned medium (CM) are lost in CM collected from MCF-7/MDA-MB231 cells pre-transfected with miR193a-3p (miR193a-CM). Moreover, miR193a-CM inhibited MAPK and Akt phosphorylation in VECs. In microarray gene expression studies, miR193a-CM upregulated 553 genes and downregulated 543 genes in VECs. Transcriptomic and pathway enrichment analysis of differentially regulated genes revealed downregulation of interferon-associated genes and pathways that induce angiogenesis and BC/tumor growth. An angiogenesis proteome array confirmed the downregulation of 20 pro-angiogenesis proteins by miR193a-CM in VECs. Additionally, in MCF-7 cells and VECs, estradiol (E2) downregulated miR193a-3p expression and induced growth. Ectopic expression of miR193a-3p abrogated the growth stimulatory effects of estradiol E2 and serum in MCF-7 cells and VECs, as well as in MCF-7 and MCF-7+VEC 3D spheroids. Immunostaining of MCF-7+VEC spheroid sections with ki67 showed miR193a-3p inhibits cell proliferation. Taken together, our findings provide first evidence that miR193a-3p abrogates MCF-7-driven growth of VECs by altering MCF-7 secretome and downregulating pro-growth interferon signals and proangiogenic proteins. Additionally, miR193a-3p inhibits serum and E2-induced growth of MCF-7, VECs, and MCF-7+VEC spheroids. In conclusion, miRNA193a-3p can potentially target/inhibit BC tumor angiogenesis via a dual mechanism: (1) altering proangiogenic BC secretome/TME and (2) inhibiting VEC growth. It may represent a therapeutic molecule to target breast tumor growth.

ADSCs stimulated by resistin promote breast cancer cell malignancy via CXCL5 in a breast cancer coculture model

The tumor microenvironment represents one of the main obstacles in breast cancer treatment owing to the presence of heterogeneous stromal cells, such as adipose-derived stem cells (ADSCs), that may interact with breast cancer cells and promote cancer development. Resistin is an adipocytokine associated with adverse breast cancer progression; however, its underlying mechanisms in the context of the breast tumor microenvironment remain largely unidentified. Here, we utilized a transwell co-culture model containing patient-derived ADSCs and breast cancer cell lines to investigate their potential interaction, and observed that breast cancer cells co-cultured with resistin-treated ADSCs (R-ADSCs) showed enhanced cancer cell growth and metastatic ability. Screening by proteome arrays revealed that C-X-C motif chemokine ligand 5 (CXCL5) was released in the conditioned medium of the co-culture system, and phosphorylated ERK was increased in breast cancer cells after co-culture with R-ADSCs. Breast cancer cells treated with the recombinant proteins of CXCL5 showed similarly enhanced cell migration and invasion ability as occurred in the co-culture model, whereas application of neutralizing antibodies against CXCL5 reversed these phenomena. The orthotopic xenograft in mice by breast cancer cells after co-culture with R-ADSCs had a larger tumor growth and more CXCL5 expression than control. In addition, clinical analysis revealed a positive correlation between the expression of resistin and CXCL5 in both tumor tissues and serum specimens of breast cancer patients. The current study suggests that resistin-stimulated ADSCs may interact with breast cancer cells in the tumor microenvironment via CXCL5 secretion, leading to breast cancer cell malignancy.

In Vitro Evidence of Statins' Protective Role against COVID-19 Hallmarks.

Despite the progressions in COVID-19 understanding, the optimization of patient-specific therapies remains a challenge. Statins, the most widely prescribed lipid-lowering drugs, received considerable attention due to their pleiotropic effects, encompassing lipid metabolism control and immunomodulatory and anti-thrombotic effects. In COVID-19 patients, statins improve clinical outcomes, reducing Intensive Care Unit admission, the onset of ARDS, and in-hospital death. However, the safety of statins in COVID-19 patients has been debated, mainly for statins’ ability to induce the expression of the ACE2 receptor, the main entry route of SARS-CoV-2. Unfortunately, the dynamic of statins’ mechanism in COVID-19 disease and prevention remains elusive. Using different in vitro models expressing different levels of ACE2 receptor, we investigated the role of lipophilic and hydrophilic statins on ACE2 receptor expression and subcellular localization. We demonstrated that the statin-mediated increase of ACE2 receptor expression does not necessarily coincide with its localization in lipid rafts domains, particularly after treatments with the lipophilic atorvastatin that disrupt lipid rafts’ integrity. Through a proteomic array, we analyzed the cytokine patterns demonstrating that statins inhibit the release of cytokines and factors involved in mild to severe COVID-19 cases. The results obtained provide additional information to dissect the mechanism underlying the protective effects of statin use in COVID-19.