Proteomics Profiling of CLL Versus Healthy B-cells Identifies Putative Therapeutic Targets and a Subtype-independent Signature of Spliceosome Dysregulation

Johnston, Harvey E.; Carter, Matthew; Larráyoz, Marta; Clarke, James; Garbis, Spiros D.; Oscier, David; Strefford, Jonathan C.; Steele, Andrew J.; Walewska, Renata; Cragg, Mark S.

doi:10.1074/mcp.ra117.000539

Cited by 47 publications

(54 citation statements)

References 66 publications

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“…All four datasets showed consistent results, indicating that CKAP4 mRNA levels were significantly higher in tumor tissues compared with adjacent liver tissues. These results confirm the upregulation of CKAP4 in tumor tissues in accordance with previous results found in HCC (19) and other types of cancer, including cervical cancer, bladder cancer, lung cancer, pancreatic cancer, ESCC, CLL, PDAC and intrahepatic cholangiocellular carcinoma (12)(13)(14)(15)(16)(17)(18)27).…”

Section: Discussionsupporting

confidence: 92%

“…As a novel DKK1 receptor that stimulates tumor cell proliferation, CKAP4 is frequently upregulated in pancreatic cancer, lung cancer and esophageal squamous cell carcinoma (ESCC), and blocking CKAP4 activity via knockdown or anti-CKAP4 antibodies can prevent xenograft tumor formation (14)(15)(16). CKAP4 has also been demonstrated to be upregulated in chronic lymphocytic leukemia (CLL) (17). Recently, exosomal CKAP4 was reported to be a promising biomarker for pancreatic ductal adenocarcinoma (PDAC) (18).…”

Section: Cytoskeleton-associated Membrane Protein 4 Is Upregulated Inmentioning

confidence: 99%

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Cytoskeleton-associated membrane protein�4 is upregulated in tumor tissues and is associated with clinicopathological characteristics and prognosis in hepatocellular carcinoma

et al. 2020

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The role of cytoskeleton-associated membrane protein 4 (CKAP4) in hepatocellular carcinoma (HCC) is controversial. The present study aimed to investigate the association between tumor CKAP4 mRNA expression and clinicopathological characteristics and prognosis in patients with HCC. Data relating to CKAP4 mRNA expression in HCC tumor and normal adjacent liver tissues, and clinicopathological characteristics, were downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas databases. The CKAP4 mRNA levels in tumor tissues were compared with those in normal adjacent liver tissues, their association with clinicopathological parameters was analyzed, and diagnostic and prognostic values were evaluated in patients with HCC. In all 4 datasets (total samples, n=693), CKAP4 mRNA levels were significantly higher in tumor tissues compared with adjacent tissues (all P<0.001), with the area under the receiver operating characteristic curve ranging from 0.799-0.898 for HCC diagnosis. In patients with HCC with available clinical data (n=361), the low-level CKAP4 mRNA group exhibited a lower body mass index (P=0.005), higher α-fetoprotein level (P<0.001), more frequent adjacent liver tissue inflammation (P<0.001), poorer tumor histological grade (P<0.001), higher Ishak fibrosis score (P= 0.035) and a more advanced tumor node metastasis (TNM) stage (P=0.014) compared with the high-level CKAP4 mRNA group. Patients stratified by all the above parameters, except for TNM stage, exhibited significantly different expression of tissue CKAP4 mRNA (P<0.05-0.001). Furthermore, higher CKAP4 mRNA levels were observed in patients who died within one year following diagnosis compared with those who survived >3 years (P=0.003). The high-level CKAP4 mRNA group also exhibited lower overall survival (OS) and disease-free survival (DFS) rates compared with the low-level group [hazard ratio (HR)=1.494; 95% confidence interval (CI), 1.044-2.138; P=0.028] for OS and (HR=1.616; 95% CI, 1.022-2.555; P=0.040) for DFS. The results of the present study suggest that CKAP4 mRNA is upregulated in HCC tumor tissues compared with normal adjacent tissues, and is associated with poor clinical prognosis, pathological features and survival in patients with HCC. Thus, CKAP4 is a potential biomarker for HCC diagnosis and prognosis.

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Section: Discussionsupporting

confidence: 92%

Section: Cytoskeleton-associated Membrane Protein 4 Is Upregulated Inmentioning

confidence: 99%

Cytoskeleton-associated membrane protein�4 is upregulated in tumor tissues and is associated with clinicopathological characteristics and prognosis in hepatocellular carcinoma

et al. 2020

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“…Several signalling pathways were identified in the bioinformatics analysis, including growth factor signalling (EGF, FGF, VEGF), PI3 kinase and FAS signalling. In agreement with a recently published study looking at protein differences between healthy B cells and CLL cells, we also identified several differentially expressed proteins that mapped to the spliceosome (Johnston et al , ).…”

Section: Discussionsupporting

confidence: 91%

“…The availability of mass spectrometry (MS) late last century led to studies investigating the CLL proteome. These analyses identified a limited number of differentially expressed proteins not only between M-and UM-CLL (Cochran et al, 2003;Barnidge et al, 2005;Scielzo et al, 2005;Rees-Unwin et al, 2010;Alsagaby et al, 2014;Eagle et al, 2015), but also between healthy B cells and B-CLL cells (Johnston et al, 2018;Mayer et al, et al 2018). This is most likely not an accurate representation of the true proteomic differences between these cell types, given their vastly divergent lifespans and functions in the body.…”

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confidence: 99%

Altered expression of metabolic pathways in CLL detected by unlabelled quantitative mass spectrometry analysis

et al. 2019

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Summary Chronic lymphocytic leukaemia (CLL) remains the most common incurable malignancy of B cells in the western world. Patient outcomes are heterogeneous and can be difficult to predict with current prognostic markers. Here, we used a quantitative label‐free proteomic technique to ascertain differences in the B‐cell proteome from healthy donors and CLL patients with either mutated (M‐CLL) or unmutated (UM‐CLL) IGHV to identify new prognostic markers. In peripheral B‐CLL cells, 349 (22%) proteins were differentially expressed between normal B cells and B‐CLL cells and 189 (12%) were differentially expressed between M‐CLL and UM‐CLL. We also examined the proteome of proliferating CLL cells in the lymph nodes, and identified 76 (~8%) differentially expressed proteins between healthy and CLL lymph nodes. B‐CLL cells show over‐expression of proteins involved in lipid and cholesterol metabolism. A comprehensive lipidomic analysis highlighted large differences in glycolipids and sphingolipids. A shift was observed from the pro‐apoptotic lipid ceramide towards the anti‐apoptotic/chemoresistant lipid, glucosylceramide, which was more evident in patients with aggressive disease (UM‐CLL). This study details a novel quantitative proteomic technique applied for the first time to primary patient samples in CLL and highlights that primary CLL lymphocytes display markers of a metabolic shift towards lipid synthesis and breakdown.

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“…Alternatively, MS is an emerging technology, in terms of CLL, used so far to investigate malignant biology and severity. [42][43][44] Although this has provided a global view of protein expression in CLL cells, it has not been useful to understand signaling changes, either in response to receptor activation, or following receipt of therapy. In our approach we combined MS with a kinobead-based protocol to examine changes to signaling in CLL cells following sIgM activation.…”

Section: Discussionmentioning

confidence: 99%

Kinobead Profiling Reveals Reprogramming of B-cell Receptor Signaling in Response to Therapy Within Primary Chronic Lymphocytic Leukemia Cells

Linley

Griffin

Cicconi

et al. 2019

Preprint

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+44(0)151 794 5310 Running head: Therapy brings about BCR signal changes. Key points1. sIgM signaling patterns alter following in vivo therapy using either chemoimmunotherapy or ibrutinib. Kinobeads provide a novel method for high-resolution investigation of signaling in primary CLL cells. AbstractInduction of signaling via cell surface receptor activation is a critical driver of CLL pathobiology, especially via the B-cell receptor (BCR), which promotes tumor survival and progression. The vital nature of BCR signaling has been recognized through the development of kinase inhibitors (KI), most notably ibrutinib, that target key nodes within this pathway. Current efforts to monitor signaling investigate expression of a highly confined series of kinases and phosphoproteins. While generating key insights, full appreciation of their wider significance to malignant pathology and therapy response remains an unresolved issue. Here, we describe a kinobead-based protocol, used in conjunction with mass-spectrometry (MS) or immunoblotting, to study surface-IgM (sIgM) signaling within primary CLL cells. Employing this approach, we isolated a 'fingerprint' of over 30 kinases which displayed unique, patient-specific response to sIgM stimulation, and which displayed greater activation change in CLL cells from patients who had undergone prior chemoimmunotherapy (CIT) compared to those from untreated/treatment-naïve patients. Matched sample analysis of ARCTIC/AdMIRe clinical trial patients revealed the unique nature of the kinome response was present at the intra-patient level, while longitudinal profiling of IcICLLe trial patients supported this as well as showing our finding related to ibrutinib therapy. Refinement of the kinome fingerprint determined 4 kinases linked to proliferation found to be present to a significantly higher level within previously treated patient cells. Proliferation assays confirmed that these patients possess higher proliferative capacity, implying alterations of signaling resulting in promoting of biological processes critical to malignant cells. Collectively, these data represent the first comprehensive investigation into BCR signaling response within CLL, where our probing of kinase active sites reveals unique evidence of adaptive reprogramming in response to therapy.

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Proteomics Profiling of CLL Versus Healthy B-cells Identifies Putative Therapeutic Targets and a Subtype-independent Signature of Spliceosome Dysregulation

Cited by 47 publications

References 66 publications

Cytoskeleton-associated membrane protein�4 is upregulated in tumor tissues and is associated with clinicopathological characteristics and prognosis in hepatocellular carcinoma

Cytoskeleton-associated membrane protein�4 is upregulated in tumor tissues and is associated with clinicopathological characteristics and prognosis in hepatocellular carcinoma

Altered expression of metabolic pathways in CLL detected by unlabelled quantitative mass spectrometry analysis

Kinobead Profiling Reveals Reprogramming of B-cell Receptor Signaling in Response to Therapy Within Primary Chronic Lymphocytic Leukemia Cells

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