Mangalaparthi, Kiran K.

Esophageal squamous cell carcinoma (ESCC) is a heterogeneous cancer associated with a poor prognosis in advanced stages. In India, it is the sixth most common cause of cancer-related mortality. In this study, we employed high-resolution mass spectrometry-based quantitative proteomics to characterize the differential protein expression pattern associated with ESCC. We identified several differentially expressed proteins including PDPN, TOP2A, POSTN and MMP2 that were overexpressed in ESCC. In addition, we identified downregulation of esophagus tissue-enriched proteins such as SLURP1, PADI1, CSTA, small proline-rich proteins such as SPRR3, SPRR2A, SPRR1A, KRT4, and KRT13, involved in squamous cell differentiation. We identified several overexpressed proteins mapped to the 3q24-29 chromosomal region, aligning with CNV alterations in this region reported in several published studies. Among these, we identified overexpression of SOX2, TP63, IGF2BP2 and RNF13 that are encoded by genes in the 3q26 region. Functional enrichment analysis revealed proteins involved in cell cycle pathways, DNA replication, spliceosome, and DNA repair pathways. We identified the overexpression of multiple proteins that play a major role in alleviating ER stress, including SYVN1 and SEL1L. The SYVN1/SEL1L complex is an essential part of the ER quality control machinery clearing misfolded proteins from the ER. SYVN1 is an E3 ubiquitin ligase that ubiquitinates ER-resident proteins. Interestingly, there are also other non-canonical substrates of SYVN1 which are known to play a crucial role in tumor progression. Thus, SYVN1 could be a potential therapeutic target in ESCC.

Abstract In response to diverse cellular cues, MAP3K1, a mitogen-activated protein kinase, participates in various cancer signaling networks including the NFκB, JNK, ERK, and p38 pathways. Functioning as a signaling kinase in these oncogenic pathways, MAP3K1 contributes to tumor growth and metastasis, thus making it an attractive therapeutic target for cancer. Structure-guided design using MAP3K1 AlphaFold and Schrödinger GLIDE led to the development of 51-106, a selective MAP3K1 small molecule inhibitor. Profiling using the KiNativTM platform in a cellular matrix revealed 51-106 as a selective ATP-competitive MAP3K1 inhibitor. 51-106 blocked TNFα-induced MAP3K1-IKKβ-mediated NFκB activity. Phosphoproteomics analysis following MAP3K1 inhibition by 51-106 showed a dose dependent decrease in NPM1 T199 phosphorylation indicating NPM1 as a novel substrate of MAP3K1. NPM1 plays a critical role in DNA damage repair; consistently we observed a dose dependent S-phase arrest upon MAP3K1 inhibition by 51-106, suggesting a dysfunctional DNA damage response. Higher MAP3K1 transcript level in pancreatic cancer patients is associated with poorer (50% vs. 15%) 5-year survival. Treatment of pancreatic cancer cell lines with the MAP3K1 inhibitor 51-106 inhibited cell growth and migration. In combination studies, 51-106 synergistically inhibited growth with gemcitabine in LSL-KrasG12D/+, LSL-Trp53R172H/+, Pdx1-Cre (KPC) cell lines in vitro and in KPC syngeneic orthotopic implantation mouse model of pancreatic cancer in vivo. Our study is the first to identify NPM1 as a potential substrate of MAP3K1, and these results warrant the investigation of MAP3K1 inhibition as a therapeutic option in cancer. Citation Format: Lidia Boghean, Sarbjit Singh, Kiran Mangalaparthi, Surendra K. Shukla, Smitha Kizhake, Amritha Kizhake, Donn Wishka, Jayapal Reddy Mallareddy, Joel Morris, Paul Grothaus, Pankaj K. Singh, Akhilesh Pandey, Amarnath Natarajan. Phosphoproteomic profiling following MAP3K1 kinase inhibition identifies NPM1 as a novel substrate [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 2025.

AbstractPurposeThis pilot study aimed to use proteomic profiling of sonicate fluid samples to compare host response during Staphylococcus aureus‐associated periprosthetic joint infection (PJI) and non‐infected arthroplasty failure (NIAF) and identify potential novel biomarkers differentiating the two.Experimental designIn this pilot study, eight sonicate fluid samples (four from NIAF and four from S. aureus PJI) were studied. Samples were reduced, alkylated, and trypsinized overnight, followed by analysis using liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) on a high‐resolution Orbitrap Eclipse mass spectrometer. MaxQuant software suite was used for protein identification, filtering, and label‐free quantitation.ResultsPrincipal component analysis of the identified proteins clearly separated S. aureus PJI and NIAF samples. Overall, 810 proteins were identified based on their detection in at least three out of four samples from each group; 35 statistically significant differentially abundant proteins (DAPs) were found (two‐sample t‐test p‐values ≤0.05 and log2fold‐change values ≥2 or ≤−2). Gene ontology pathway analysis found that microbial defense responses, specifically those related to neutrophil activation, to be increased in S. aureus PJI compared to NIAF samples.Conclusion and clinical relevanceProteomic profiling of sonicate fluid using LC‐MS/MS differentiated S. aureus PJI and NIAF in this pilot study. Further work is needed using a larger sample size and including non‐S. aureus PJI and a diversty of NIAF‐types.

Pancreatic ductal adenocarcinoma is a recalcitrant tumor with minimal response to conventional chemotherapeutic approaches. Oncogenic signaling by activated tyrosine kinases has been implicated in cancers resulting in activation of diverse effector signaling pathways. Thus, the discovery of aberrantly activated tyrosine kinases is of great interest in developing novel therapeutic strategies in the treatment and management of pancreatic cancer. Patient-derived tumor xenografts (PDXs) in mice serve as potentially valuable preclinical models as they maintain the histological and molecular heterogeneity of the original human tumor. Here, we employed high-resolution mass spectrometry combined with immunoaffinity purification using anti-phosphotyrosine antibodies to profile tyrosine phosphoproteome across 13 pancreatic ductal adenocarcinoma PDX models. This analysis resulted in the identification of 1199 tyrosine-phosphorylated sites mapping to 704 proteins. The mass spectrometric analysis revealed widespread and heterogeneous activation of both receptor and non-receptor tyrosine kinases. Preclinical studies confirmed ephrin type-B receptor 4 (EphB4) as a potential therapeutic target based on the efficacy of human serum albumin-conjugated soluble EphB4 in mice bearing orthotopic xenografts. Immunohistochemistry-based validation using tissue microarrays from 346 patients with PDAC showed significant expression of EphB4 in >70% of patients. In summary, we present a comprehensive landscape of tyrosine phosphoproteome with EphB4 as a promising therapeutic target in pancreatic ductal adenocarcinoma.