Session: 641. Chronic Lymphocytic Leukemias: Basic and Translational: Poster III
Hematology Disease Topics & Pathways:
Research, Lymphoid Leukemias, Translational Research, CLL, Diseases, Lymphoid Malignancies, Technology and Procedures, omics technologies
Proteomes and phosphoproteomes from all 105 samples were analyzed using a multiplexed isobaric-tagged (TMT) high resolution mass spectrometry (MS) workflow. Briefly, cells were lysed and proteins were digested into peptides with LysC and trypsin. Protein yield per sample ranged from 20 μg to 300 μg. Peptides were labeled with TMT-11 reagent and combined into 11 multiplexes while accounting for input material availability and randomizing for SF3B1 mutation, IGHV status and ATM/TP53 mutation. To enable cross TMT-plex comparison, we constructed a common reference consisting of 40 samples with highest protein amount and an equal representation between SF3B1wt and SF3B1mut samples. Each plex was fractionated into 24 fractions by high pH reversed phase separation and 500 ng protein per fraction were analyzed by MS (Orbitrap Exploris, Thermo Fisher Scientific). For phosphoproteome analysis, peptides were pooled into 12 fractions and enriched by IMAC prior to MS analysis. Spectra were analyzed by Spectrum Mill v7.1 (Broad Institute) and searched against a human reference proteome database supplemented with non-canonical ORFs supported by Riboseq evidence of translation (nuORFdb v1.0). Patient specific proteins containing single amino variants, indels, and splice isoforms, derived from WES and RNA-Seq, were included in the search database.
We obtained a total of 10,419 proteins, with a median of 8,882 proteins per TMT-plex and 6,969 proteins that were quantifiable across all samples. The phosphoproteome analysis identified 32,410 sites; while each TMT-plex yielded a median of 19,380 phosphosites per plex, 5,810 were quantifiable across all patients. We integrated proteome data with patient specific mutation calls, RNA-Seq and copy number alteration (CNA) data using Panoply, a cloud-based platform for proteogenomic data analysis (Broad Institute). We confirmed the impact of chr11 and chr13 deletion as well as chr12 amplification on protein expression.
We readily identified peptides spanning the SF3B1mut amino acid regions in corresponding samples. By unsupervised clustering, samples were grouped by SF3B1 status on the CNA and proteome level, a trend not observed based on RNA or phosphoproteome analysis. Gene set enrichment analysis revealed enrichment of TNFA and PI3K signaling in the SF3B1wt clusters, while the SF3B1mut associated clusters showed a strong association with metabolism changes. This analysis was highly concordant with a parallel interrogation comparing proteins expressed in SF3B1wt CLL versus SF3B1mut CLL. Here 1,955 proteins and 1,737 phosphosites were significantly altered (5% FDR). Proteins involved in B cell receptor and MAP kinase signaling were highly expressed in SF3B1wt samples, while again amino acid metabolism pathways as well as oxidative phosphorylation were upregulated in SF3B1mut samples.
To more deeply investigate the role of metabolism pathways in SF3B1mut CLL, we subjected 6 independent CLL samples to MS-based metabolomics analysis. Inosine (P=0.029) and guanosine (P=0.047) were lower in the SF3B1mut extracts (P=0.001), while acylcarnitines (P=0.0004) were increased, indicating fatty acid oxidation as a preferred energy source in SF3B1mut CLL.
Altogether, our study reveals fresh evidence of altered energy metabolism in SF3B1mut CLL. Ongoing studies focus on defining the mechanism by which SF3B1mut exerts these metabolic changes and novel therapeutic opportunities afforded by these findings.
Disclosures: Klaeger: Genentech, Inc.: Current Employment. Tausch: AstraZeneca: Honoraria, Speakers Bureau; Janssen-Cilag: Honoraria; BeiGene: Honoraria; Roche: Consultancy, Research Funding, Speakers Bureau; Abbvie: Consultancy, Research Funding, Speakers Bureau. Kipps: Gilead: Consultancy; Genentech-Roch: Consultancy, Research Funding; Pharmacyclics, LLC an AbbVie Company: Consultancy, Research Funding; Celgene: Consultancy; Oncternal: Research Funding; AbbVie: Consultancy, Research Funding. Fischer: Roche: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel Support; Astra Zeneca: Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria. Hallek: Bristol Myers Squibb: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; Roche, Janssen: Honoraria, Research Funding; Abbvie, AstraZeneca: Consultancy, Honoraria, Research Funding. Neuberg: Madrigal Pharmaceuticals: Current equity holder in publicly-traded company. Getz: MSMutSig: Patents & Royalties; MSMuTect: Patents & Royalties; SignatureAnalyzer-GPU: Patents & Royalties; MSIDetect: Patents & Royalties; Pharmacyclics: Research Funding; POLYSOLVER: Patents & Royalties; IBM: Research Funding; Scorpion Therapeutics: Consultancy, Current equity holder in publicly-traded company, Other: Founder. Stilgenbauer: Infinity: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Incyte: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Beigene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; AbbVIe: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Acerta: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Hoffmann-La Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; AstraZeneca: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Genentech: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Gilead: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; GSK: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Sunesis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Veristem: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Pharmacyclics: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. Wu: BioNTech: Current equity holder in publicly-traded company; Pharmacyclics: Research Funding. Carr: Seer, Inc.: Membership on an entity's Board of Directors or advisory committees; Kymera: Membership on an entity's Board of Directors or advisory committees; PTM BioLabs: Membership on an entity's Board of Directors or advisory committees.
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