Identification of calcium and integrin-binding protein 1 as a reprogrammed glucose metabolism mediator to restrict immune cell infiltration in the stromal compartment of pancreatic ductal adenocarcinoma

An increasing body of evidence has suggested that reprogrammed metabolism plays a critical role in the progression of pancreatic ductal adenocarcinoma (PDAC) by affecting the tumor and stromal cellular components in the tumor microenvironment (TME). By analyzing the KRAS pathway and metabolic pathways, we found that calcium and integrin-binding protein 1 (CIB1) corresponded with upregulation of glucose metabolism pathways and was associated with poor prognosis in patients with PDAC from The Cancer Genome Atlas (TCGA). Elevated CIB1 expression combined with upregulated glycolysis, oxidative phosphorylation (Oxphos), hypoxia pathway activation, and cell cycle promoted PDAC tumor growth and increased tumor cellular com-ponents. Furthermore, we confirmed the mRNA overexpression of CIB1 and co-expression of CIB1 and KRAS mutation in cell lines from the Expression Atlas. Subsequently, immunohistochemistry staining from the Human Protein Atlas (HPA) showed that high expression of CIB1 in tumor cells was associated with an increased tumor compartment and reduced stromal cellular abundance. Furthermore, using multiplexed immunohistochemistry (mIHC), we verified that low stromal abundance was correlated with low infiltration of CD8⁺ PD-1^- T cells which led to suppressed anti-tumor immunity. Overall, our findings identify CIB1 as a metabolic pathway-mediated factor for the restriction of immune cell infiltration in the stromal compartment of PDAC and highlight the potential value of CIB1 as a prognostic biomarker involved in metabolic reprogramming and immune modulation.

Strategies for targeting CIB1, a challenging drug target

Breast cancer is common malignancy in women which is diverse disease. In women, 287,850 and in male 2710 cases are reported in 2022 reported by WHO. Triple negative breast cancer (TNBC), a subtype of breast cancer that lacks expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), accounted for 10-20% of all new cases discovered in the United States in 2017. Because calcium integrin-binding protein1 lacks a suitable pocket that could be used to create a chemical inhibitor, and because the breast cancer-causing protein is nearly identical to its necessary wild-type counterpart, it was thought to be druggable. The structure and function of the newly discovered calcium integrin-binding protein1 have been improved, paving the way for the designing of several therapeutic candidates. Currently, no FDA-approved drugs are available for CIB1-driven cancer. CIB1 has proven to challenging drug target due to several factors, including the fact that the CIB1 protein is highly resistant to small inhibitors. This study aimed to present various ways for targeting calcium integrin-binding protein1, which is an important target that could be useful to scientists.

Optogenetic Control of Membrane Trafficking Using Light-Activated Reversible Inhibition by Assembly Trap of Intracellular Membranes (IM-LARIAT)

Intracellular membrane trafficking is a dynamic and complex cellular process. To study membrane trafficking with a high spatiotemporal resolution, we present an optogenetic method based on a blue-light inducible oligomerization of Rab GTPases, termed light-activated reversible inhibition by assembly trap of intracellular membranes (IM-LARIAT). In this chapter, we focus on the optical disruption of the dynamics and functions of previously studied intracellular membrane trafficking events, including transferrin recycling and growth cone regulation in relation to specific Rab GTPases. To aid general application, we provide a detailed description of transfection, imaging with a confocal microscope, and analysis of data.

Semi-In-Vivo Pull-Down Assay for Blue Light-Dependent Protein Interactions

Cryptochromes are photolyase-like blue-light receptors found in all major evolutionary lineages (Ahmad and Cashmore, Nature 366:162-166, 1993; Lin, Plant Physiol 110:1047, 1996; Cashmore, Cell 114:537-543, 2003; Partch and Sancar, Methods Enzymol 393:726-745, 2005). Arabidopsis cryptochrome 1 (CRY1) and cryptochrome 2 (CRY2) mediate primarily blue-light inhibition of hypocotyl elongation and photoperiodic control of floral initiation (Ahmad and Cashmore, Nature 366:162-166, 1993; Somers et al., Science, 282:1488-1490, 1998; Guo et al., Science 279 (5355):1360-1363, 1998; Yu et al., Arabidopsis Book 8:e0135, 2010). It has been proposed that phototransduction of cryptochromes involves the blue-light-dependent protein interactions, such as AtCRY2-CIB1 (CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1), AtCRY1-PIF4 (PHYTOCHROME INTERACTING FACTOR 4) modules, sequentially mediate gene expression and plant growth (Liu et al., Science 322 (5907):1535-1539, 2008; Ma et al., Proc Natl Acad Sci U S A 113 (1):224-229, 2016; Wang et al., Science 354:343-347, 2016). Cryptochromes also showed blue light response in vitro when expressed in Sf9 insect cells using the baculovirus expression system, thus the wavelength-specific CRY2-CIB1 interaction can also be observed in Semi-in-vivo pull-down assay (Li et al., Proc Natl Acad Sci U S A 108 (51):20844-20849, 2011; Liu et al., EMBO Reports, 2018). Here, we describe the detailed process of blue light-dependent CRY2-CIB1 interaction in Semi-in-vivo conditions.

The CIB1 transcription factor regulates light- and heat-inducible cell elongation via a two-step HLH/bHLH system

Light and high temperature promote plant cell elongation. PHYTOCHROME INTERACTING FACTOR4 (PIF4, a typical basic helix-loop-helix [bHLH] transcriptional activator) and the non-DNA binding atypical HLH inhibitors PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and LONG HYPOCOTYL IN FAR-RED 1 (HFR1) competitively regulate cell elongation in response to light conditions and high temperature. However, the underlying mechanisms have not been fully clarified. Here, we show that in Arabidopsis thaliana, the bHLH transcription factor CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1 (CIB1) positively regulates cell elongation under the control of PIF4, PAR1, and HFR1. Furthermore, PIF4 directly regulates CIB1 expression by interacting with its promoter, and PAR1 and HFR1 interfere with PIF4 binding to the CIB1 promoter. CIB1 activates genes that function in cell elongation, and PAR1 interferes with the DNA binding activity of CIB1, thus suppressing cell elongation. Hence, two antagonistic HLH/bHLH systems, the PIF4-PAR1/HFR1 and CIB1-PAR1 systems, regulate cell elongation in response to light and high temperature. We thus demonstrate the important role of non-DNA binding small HLH proteins in the transcriptional regulation of cell elongation in plants.

Integrative public data-mining pipeline for the validation of novel independent prognostic biomarkers for lung adenocarcinoma

Aim: We aimed to develop a candidate-based integrative public data mining strategy for validation of novel prognostic markers in lung adenocarcinoma. Materials & methods: An in silico approach integrating meta-analyses of publicly available clinical information linked RNA expression, gene copy number and mutation datasets combined with independent immunohistochemistry and survival datasets. Results: After validation of pipeline integrity utilizing data from the well-characterized prognostic factor Ki-67, prognostic impact of the calcium- and integrin-binding protein, CIB1, was analyzed. CIB1 was overexpressed in lung adenocarcinoma which correlated with pathological tumor and pathological lymph node status and impaired overall/progression-free survival. In multivariate analyses, CIB1 emerged as UICC stage-independent risk factor for impaired survival. Conclusion: Our pipeline holds promise to facilitate further identification and validation of novel lung cancer-associated prognostic markers.

Expression of a TMC6-TMC8-CIB1 heterotrimeric complex in lymphocytes is regulated by each of the components

The TMC genes encode a set of homologous transmembrane proteins whose functions are not well understood. Biallelic mutations in either TMC6 or TMC8 are detected in more than half of cases of the pre-malignant skin disease epidermodysplasia verruciformis (EV). It is controversial whether EV induced by mutations in TMC6 or TMC8 originates from keratinocyte or lymphocyte defects. Quantification of TMC6 and TMC8 RNA levels in various organs revealed that lymphoid tissues have the highest levels of expression of both genes, and custom antibodies confirmed protein expression in mouse lymphocytes. To study the function of these proteins we generated mice with targeted deletion mutant alleles of Tmc6 or Tmc8 Either TMC6 or TMC8 deficiency induced a reduction in apparent molecular weight and/or amount of the other TMC molecule. Co-immunoprecipitation experiments indicated that TMC6 and TMC8 formed a protein complex in mouse and human T cells. MS and biochemical analysis demonstrated that TMC6 and TMC8 additionally interacted with the CIB1 protein to form TMC6-TMC8-CIB1 trimers. We demonstrated that TMC6 and TMC8 regulated CIB1 levels by protecting CIB1 from ubiquitination and proteasomal degradation. Reciprocally, CIB1 was needed for stabilizing TMC6 and TMC8 levels. These results suggest why inactivating mutations in any of the three human genes leads to similar clinical presentations. We also demonstrated that TMC6 and TMC8 levels are drastically lower and the proteins are less active in regulating CIB1 in keratinocytes than in T cells. Our study suggests that defects in lymphocytes may contribute to the etiology and pathogenesis of EV.

Calcium-induced dissociation of CIB1 from ASK1 regulates agonist-induced activation of the p38 MAPK pathway in platelets

Apoptosis signal-regulating kinase 1 (ASK1) is a mitogen-activated protein kinase kinase kinase (MAPKKK) that regulates activation of the c-Jun N-terminal kinase (JNK)- and p38-stress response pathways leading to apoptosis in nucleated cells. We have previously shown that ASK1 is expressed in platelets and regulates agonist-induced platelet activation and thrombosis. However, the mechanism by which platelet agonists cause activation of ASK1 is unknown. Here, we show that in platelets agonist-induced activation of p38 is exclusively dependent on ASK1. Both thrombin and collagen were able to activate ASK1/p38. Activation of ASK1/p38 was strongly dependent on thromboxane A2 (TxA2) and ADP. Agonist-induced ASK1 activation is blocked by inhibition of phospholipase C (PLC) β/γ activity or by chelating intracellular Ca2+. Furthermore, treatment of platelets with thapsigargin or Ca2+ ionophore robustly induced ASK1/p38 activation. In addition, calcium and integrin-binding protein 1 (CIB1), a Ca2+-dependent negative regulator of ASK1, associates with ASK1 in resting platelets and is dissociated upon platelet activation by thrombin. Dissociation of CIB1 corresponds with ASK1 binding to tumor necrosis factor (TNF) receptor associated factor 6 (TRAF6) and the autophosphorylation of ASK1 Thr838 within the catalytic domain results in full activation of ASK1. Furthermore, genetic ablation of Cib1 in mice augments agonist-induced Ask1/p38 activation. Together our results suggest that in resting platelets ASK1 is bound to CIB1 at low Ca2+ concentrations. Agonist-induced platelet activation causes an increase in intracellular Ca2+ concentration that leads to the dissociation of CIB1 from ASK1, allowing for proper dimerization through ASK1 N-terminal coiled-coil (NCC) domains.

Ca2+ functions as a molecular switch that controls the mutually exclusive complex formation of pyridoxal phosphatase with CIB1 or calmodulin

Pyridoxal 5'-phosphate (PLP) is an essential cofactor for neurotransmitter metabolism. Pyridoxal phosphatase (PDXP) deficiency in mice increases PLP and γ-aminobutyric acid levels in the brain, yet how PDXP is regulated is unclear. Here, we identify the Ca2+ - and integrin-binding protein 1 (CIB1) as a PDXP interactor by yeast two-hybrid screening and find a calmodulin (CaM)-binding motif that overlaps with the PDXP-CIB1 interaction site. Pulldown and crosslinking assays with purified proteins demonstrate that PDXP directly binds to CIB1 or CaM. CIB1 or CaM does not alter PDXP phosphatase activity. However, elevated Ca2+ concentrations promote CaM binding and, thereby, diminish CIB1 binding to PDXP, as both interactors bind in a mutually exclusive way. Hence, the PDXP-CIB1 complex may functionally differ from the PDXP-Ca2+ -CaM complex.

CIB1 depletion with docetaxel or TRAIL enhances triple-negative breast cancer cell death

Background

Patients diagnosed with triple negative breast cancer (TNBC) have limited treatment options and often suffer from resistance and toxicity due to chemotherapy. We previously found that depleting calcium and integrin-binding protein 1 (CIB1) induces cell death selectively in TNBC cells, while sparing normal cells. Therefore, we asked whether CIB1 depletion further enhances tumor-specific killing when combined with either the commonly used chemotherapeutic, docetaxel, or the cell death-inducing ligand, TRAIL.

Methods

We targeted CIB1 by RNA interference in MDA-MB-436, MDA-MB-231, MDA-MB-468, docetaxel-resistant MDA-MB-436 TNBC cells and ME16C normal breast epithelial cells alone or combination with docetaxel or TRAIL. Cell death was quantified via trypan blue exclusion using flow cytometry and cell death mechanisms were analyzed by Western blotting. Cell surface levels of TRAIL receptors were measured by flow cytometry analysis.

Results

CIB1 depletion combined with docetaxel significantly enhanced tumor-specific cell death relative to each treatment alone. The enhanced cell death strongly correlated with caspase-8 activation, a hallmark of death receptor-mediated apoptosis. The death receptor TRAIL-R2 was upregulated in response to CIB1 depletion, which sensitized TNBC cells to the ligand TRAIL, resulting in a synergistic increase in cell death. In addition to death receptor-mediated apoptosis, both combination treatments activated a non-apoptotic mechanism, called paraptosis. Interestingly, these combination treatments also induced nearly complete death of docetaxel-resistant MDA-MB-436 cells, again via apoptosis and paraptosis. In contrast, neither combination treatment induced cell death in normal ME16C cells.

Conclusion

Novel combinations of CIB1 depletion with docetaxel or TRAIL selectively enhance naive and docetaxel-resistant TNBC cell death while sparing normal cell. Therefore, combination therapies that target CIB1 could prove to be a safe and durable strategy for treatment of TNBC and potentially other cancers.

Electronic supplementary material

The online version of this article (10.1186/s12935-019-0740-2) contains supplementary material, which is available to authorized users.

CIB1 and CO interact to mediate CRY2-dependent regulation of flowering

Cryptochromes are photolyase-like photoreceptors. Arabidopsis CRY2 (cryptochrome 2) primarily mediates the photoperiodic regulation of floral initiation. CRY2 has been shown to promote FT (FLOWERING LOCUS T) mRNA expression in response to blue light by suppressing the degradation of the CO (CONSTANS) protein and activating CIB1 (CRY2-interacting bHLH1). Although CIB1 and CO are both transcriptional activators of FT, their relationship is unknown. Here, we show that CIB1 physically interacts with CO and promotes FT transcription in a CO-dependent manner. CRY2, CIB1, and CO form a protein complex in response to blue light to activate FT transcription, and the complex is regulated by the photoperiod and peaks at dusk along with higher FT expression. We also determined that CRY2 was recruited to the FT chromatin by CIB1 and CO and that all three proteins are bound to the same region within the FT promoter. Therefore, there is crosstalk between the CRY2-CO and CRY2-CIBs pathways, and CIB1 and CO act together to regulate FT transcription and flowering.

Insight into the Roles of E3 Ubiquitin Ligase c-Cbl, ESCRT Machinery, and Host Cell Signaling in Kaposi's Sarcoma-Associated Herpesvirus Entry and Trafficking

Kaposi's sarcoma-associated herpesvirus (KSHV) in vitro infection of dermal endothelial cells begins with its binding to host cell surface receptor molecules such as heparan sulfate (HS), integrins (α3β1, αVβ3, and αVβ5), xCT, and EphA2 receptor tyrosine kinase (EphA2R). These initial events initiate dynamic host protein-protein interactions involving a multimolecular complex of receptors, signal molecules (focal adhesion kinase [FAK], Src, phosphatidylinositol 3-kinase [PI3-K], and RhoA-GTPase), adaptors (c-Cbl, CIB1, Crk, p130Cas, and GEF-C3G), actin, and myosin II light chain that lead to virus entry via macropinocytosis. Here we discuss how KSHV hijacks c-Cbl, an E3 ubiquitin ligase, to monoubiquitinate the receptors and actin, which acts like a marker for trafficking (similar to zip codes), resulting in the recruitment of the members of the host endosomal sorting complexes required for transport (ESCRT) Hrs, Tsg101, EAP45, and the CHMP5 and -6 proteins (zip code readers) recognizing the ubiquitinated protein and adaptor machinery to traffic through the different endosomal compartments in the cytoplasm to initiate the macropinocytic process and infection.

Cytosolic interaction of type III human CD38 with CIB1 modulates cellular cyclic ADP-ribose levels

CD38 catalyzes the synthesis of the Ca²⁺ messenger, cyclic ADP-ribose (cADPR). It is generally considered to be a type II protein with the catalytic domain facing outside. How it can catalyze the synthesis of intracellular cADPR that targets the endoplasmic Ca²⁺ stores has not been resolved. We have proposed that CD38 can also exist in an opposite type III orientation with its catalytic domain facing the cytosol. Here, we developed a method using specific nanobodies to immunotarget two different epitopes simultaneously on the catalytic domain of the type III CD38 and firmly established that it is naturally occurring in human multiple myeloma cells. Because type III CD38 is topologically amenable to cytosolic regulation, we used yeast-two-hybrid screening to identify cytosolic Ca²⁺ and integrin-binding protein 1 (CIB1), as its interacting partner. The results from immunoprecipitation, ELISA, and bimolecular fluorescence complementation confirmed that CIB1 binds specifically to the catalytic domain of CD38, in vivo and in vitro. Mutational studies established that the N terminus of CIB1 is the interacting domain. Using shRNA to knock down and Cas9/guide RNA to knock out CIB1, a direct correlation between the cellular cADPR and CIB1 levels was demonstrated. The results indicate that the type III CD38 is functionally active in producing cellular cADPR and that the activity is specifically modulated through interaction with cytosolic CIB1.

Protein Inactivation by Optogenetic Trapping in Living Cells

Optogenetic modules that use genetically encoded elements to control protein function in response to light allow for precise spatiotemporal modulation of signaling pathways. As one of optical approaches, LARIAT (Light-Activated Reversible Inhibition by Assembled Trap) is a unique light-inducible inhibition system that reversibly sequesters target proteins into clusters, generated by multimeric proteins and a blue light-induced heterodimerization module. Here we present a method based on LARIAT for optical inhibition of targets in living mammalian cells. In the protocol, we focus on the inhibition of proteins that modulate cytoskeleton and cell cycle, and describe how to transfect, conduct a photo-stimulation, and analyze the data.

Quantitative real-time kinetics of optogenetic proteins CRY2 and CIB1/N using single-molecule tools

In this work we evaluate the interaction of two optogenetic protein variants (CIB1, CIBN) with their complementary protein CRY2 by single-molecule tools in cell-free extracts. After validating the blue light induced co-localization of CRY2 and CIB1/N by Förster resonance energy transfer (FRET) in live cells, a fluorescence correlation spectroscopy (FCS) based method was developed to quantitatively determine the in vitro association of the extracted proteins. Our experiments suggest that CIB1, in comparison with CIBN, possesses a better coupling efficiency with CRY2 due to its intact protein structure and lower diffusion rate within 300s detection window.