Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) provides unique opportunities for cancer target discovery using protein expression. Proteomics data from CPTAC tumor types have been primarily generated using a multiplex tandem mass tag (TMT) approach, which is designed to provide protein quantification relative to reference samples. However, relative protein expression data are suboptimal for prioritization of targets within a tissue type, which requires additional reprocessing of the original proteomics data to derive absolute quantitation estimation. We evaluated the feasibility of using differential protein analysis coupled with intensity-based absolute quantification (iBAQ) to identify tumor-enriched and highly expressed cell surface antigens, employing tandem mass tag (TMT) proteomics data from CPTAC. Absolute quantification derived from TMT proteomics data was highly correlated with that of label-free proteomics data from the CPTAC colon adenocarcinoma cohort, which contains proteomics data measured by both approaches. We validated the TMT-iBAQ approach by comparing the iBAQ value to the receptor density value of HER2 and TROP2 measured by flow cytometry in about 30 selected breast and lung cancer cell lines from the Cancer Cell Line Encyclopedia. Collections of these tumor-enriched and highly expressed cell surface antigens could serve as a valuable resource for the development of cancer therapeutics, including antibody-drug conjugates and immunotherapeutic agents.

Abstract 315: B7H3 is a potential therapeutic target in advanced metastatic prostate cancer

B7H3 is an immunomodulatory protein of the B7 family which inhibits T cell function. B7H3 mRNA is ubiquitously expressed in normal human tissues, but the protein is expressed at low levels, suggesting a tight post-transcriptional regulation. By contrast, B7H3 protein is overexpressed in several solid tumors and often correlates with poor survival, higher tumor grade, and metastasis independently of immune regulation. A few studies also have reported an association between B7H3 overexpression and therapy resistance. Since B7H3 protein is preferentially expressed on cancer cells and tumor vasculature, it is an attractive target for developing novel cancer therapies.

Here we analyzed the expression of B7H3 in 26 mCRPC organoid models and examined whether B7H3 can serve as a novel therapeutic target for advanced mPCa patients that fail current treatment regimens. The B7H3 protein expression in PDXOs of various lineages including adenocarcinoma (n=19), double-negative (DNPC, n= 2), and neuroendocrine (NE, n =5) lineages, was analyzed using simple western™ assay, immunofluorescence, and flow cytometry. We tested the ex-vivo drug response of PDXOs and performed PDX preclinical trials using humanized B7H3-ADC armed with a pyrrolobenzodiazepine (PBD) warhead. PBD dimers are DNA interstrand cross-linking agents and are a poor substrate of P-gp drug transporters.

Our results showed that B7-H3 was overexpressed in several PDX derived organoids of mPCa. Organoids with adenocarcinoma phenotype (n=19) demonstrated a range of B7H3 protein expression whereas RB1/TP53 mutated small cell neuroendocrine or double negative prostate cancer showed a relatively more uniform and low expression. Nonetheless, PDXOs of neuroendocrine, double negative or adenocarcinoma origin responded with maximum efficacy to B7H3-ADC ex vivo. Adenocarcinoma organoid models (n=19) displayed a wide range of responses, which was only partially correlated with B7H3 protein levels. Genetically-engineered loss of B7-H3 converted a responder to a non-responder phenotype. Our investigation for potential biomarkers of B7H3-PBD sensitivity suggested that RB1-deficiency induced replication stress and/or expression of SLFN11, an interferon pathway transcriptional target, to be the strong predictors of B7H3-PBD response, independent of tumor lineage. We further performed preclinical trials using four PDX models based on their RB1 and SLFN11 status, including a model of advanced adenocarcinoma lineage with low B7H3 expression. B7H3-PBD eradicated large established subcutaneous tumors and metastases and improved long-term overall survival in either RB1 deficient and/or SLFN11HIGH models, but showed no response in RB1+/SLFN11- tumors.

In conclusion, B7H3-PBD treatment has potential to produce complete and durable response in appropriately-selected, heavily-pretreated metastatic CRPC and NEPC.

Citation Format: Supreet Agarwal, Lei Fang, Juan Juan Yin, Elaine Hurt, Kathleen Kelly. B7H3 is a potential therapeutic target in advanced metastatic prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 315.

Abstract 1828: AZD8853: A novel antibody targeting GDF15 for immunotherapy refractory tumors

Immunotherapy has revolutionized patient care, however, the majority of patients with cancer still do not benefit from this treatment modality. This is due to many factors, including a complex tumor microenvironment (TME) that has too few functional effector cells and/or the presence of many inhibitory cells. Understanding how to remodel the TME to potentiate productive immunity against cancer cells is an active area of research. Growth and Differentiation Factor 15 (GDF-15) is a member of the TGF-beta superfamily that is overexpressed by many solid tumors and is implicated in dampening immune responses. The present study was aimed at understanding the role of GDF-15 in tumor immune biology. We show that GDF-15 can inhibit the differentiation and activation of human monocyte-derived dendritic cells (DCs) and prevent T cell activation. Furthermore blockade of GDF-15 by AZD8853, an anti-GDF15 monoclonal antibody, can restore these activities in vitro. Tumors derived from GDF15 knock-out syngeneic cell lines, Renca and MC-38, show 2-3 fold increases in T cells and activated DCs in the TME as compared to tumors derived from isogeneic parental cells. Treatment of mice with anti-GDF15 mAb leads to substantial anti-tumor activity in anti-PD-L1 refractory LL/2 and MBT2 syngeneic tumors with 50% of the animals showing complete tumor regressions. Coupled with this anti-tumor activity, we show that after 2 doses of anti-GDF15 mAb there is an increase in both activated T cells and DCs in the TME. Depletion of T cells, using anti-CD4 and anti-CD8, in mice ablates the anti-tumor activity observed with anti-GDF15 mAb treatment. These results suggest that inhibition of GDF15 by AZD8853 may be an attractive therapeutic strategy for patients with solid tumors that have high expression of GDF15.

Citation Format: Elaine Hurt, Suneetha Thomas, Kathy Mulgrew, Stephen Blackmore, James Moynihan, Fiona Cusdin, Roger Dodd, Peter Cariuk, Anna Sigurdardottir, Emily Brannigan, Claire Dobson, Rakesh Kumar, Mark Cobbold. AZD8853: A novel antibody targeting GDF15 for immunotherapy refractory tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1828.

Abstract 375: Integrin β4-targeted cancer immunotherapies

Integrins are heterodimeric cell surface receptors that mediate interaction of cells with extracellular matrix components. Integrin β4 (ITGB4) has been reported by other investigators as a marker of cancer stem cells (CSCs). Immunological targeting of CSCs utilizing ITGB4 as a biomarker represnets a novel therapeutic opportunity to improve the efficacy of current cancer treatment. We previously reported the use of ALDH as a marker to isolate CSCs from multiple tumor types, including both human and animal tumors. In this study, we used two murine tumor models: triple-negative breast cancer (TNBC) 4T1 tumor syngeneic to Balb/c mice and SCC7 tumor which is a spontaneously arising head and neck squamous cell cancer syngeneic to C3H mice. 4T1 cells highly express ITGB4 (about 90%) in unsorted, ALDHhigh and ALDHlow cell populations. In contrast, SCC7 cells preferentially express ITGB4 on ALDHhigh CSCs because ITGB4 cell-surface abundance on ALDHhigh SCC7 cells is approximately 2-fold higher than that on ALDHlow SCC7 cells. We tested two different approaches for ITGB4-targeted immunotherapy: using ITGB4 protein as antigen to pulse dendritic cells (DC) to prepare ITGB4-DC for vaccination, or coating tumor-draining lymph node (TDLN) T cells with anti-CD3 x anti-ITGB4 bispecific antibody (ITGB4BiAb) to prepare ITGB4BiAb-T cells for adoptive transfer. We found that for the tumor which expresses ITGB4 on all the tumor cells at high level (4T1), ITGB4-targeted immunotherapies could inhibit both local tumor growth and metastasis; for the tumor which preferentially expresses ITGB4 on ALDHhigh CSCs (SCC7), ITGB4-targeted immunotherapies inhibited the tumor growth in the lung, with partial effect on local tumor. Co-current administration of anti-PD-L1 mAb significantly enhanced the therapeutic effectiveness of both approches. Our immune monitoring studies in vitro revealed that splenetic T cells harvested from mice treated with ITGB4-DC vaccine or ITGB4BiAb armed T cells mediated significant cytotoxicity against 4T1 cells and SCC7 cells, especially to ALDHhigh CSCs. In addition, ITGB4-DC vaccine or ITGB4BiAb armed T cells conferred significant host anti-ITGB4 humoral immunity as evident by produced antibodies that specifically bind and kill 4T1 cells and SCC7 cells, especially the ALDHhigh CSC population. As a result, both immunotherapeutic approaches significantly reduced the number of ALDHhigh CSCs in the residual tumor subjected to immunotherapies. In conclusion, ITGB4-targeted immunotherapies alone or combined with PD-L1 blockade demonstrated significant antitumor immunity via targeting CSCs. This may provide novel therapeutic strategies for the treatment of ITGB4-positive cancers, such as breast cancer, head and neck squamous cell carcinoma and other soilid tumors.

Citation Format: Shasha Ruan, Ming Lin, Yongshun Chen, Elaine Hurt, Alfred E. Chang, Max S. Wicha, Qiao Li. Integrin β4-targeted cancer immunotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 375.

Abstract 1676: Involvement of B cells in the efficacy of anti-PD-L1 antibodies: Suppression of B cells by cancer stem cells

We reported that adoptive transfer of tumor reactive B cells could mediate tumor regression, and that anti-PD-L1 administration significantly augments the therapeutic efficacy of cancer stem cell (CSC) vaccine. However, whether B cells are involved in the anti-tumor immunity mediated by anti-PD-L1 has not been identified. In the present study, we used two murine models: breast tumor 4T1 and colon cancer CT26. Tumor-bearing mice were administered with anti-CD20 mAb (MB20.11) to deplete B cells prior to anti-PD-L1 mAb administration. Depletion of B cells as compared to the control resulted in more aggressive tumor growth, and the anti-tumor efficacy of anti-PD-L1 was significantly reduced (p=0.041 and p=0.0011 for 4T1 and CT26 respectively), indicating the involvement of host B cells in the function of anti-PD-L1. Mechanistically, the administration of anti-PD-L1 partially recovered the humoral immune response, suggesting that the blockage of PD-L1/PD1 pathway could contribute to the rescue of B cell immune function. We detected higher PD-L1 expression on ALDHhigh CSCs than on ALDHlow non-CSCs or on unsorted tumor cells. On the other hand, we detected elevated expression of PD-1 on activated B cells. While the suppressive effect of CSCs on T cells has well been recognized, the interactions between CSCs and B cells is unknown. We hypothesize that CSCs may suppress B cells either directly via the PD-L1/PD1 immune check point interaction or indirectly via CSC suppression on Th cells. To test this hypothesis, we co-cultured purified B cells with ALDHhigh CSCs with or without the addition of anti-PD-L1 mAb. We found that the reduction of IgG secretion of B cells suppressed by CSCs could be rescued by anti-PD-L1 in a dose-dependent manner. These experiments indicate that CSCs can directly suppress the IgG production by B cells via PD-L1/PD-1 interaction. Moreover, when we co-cultured purified B cells plus purified CD4+ Th cells with ALDHhigh CSCs with or without the addition of anti-PD-L1 mAb, we found that the IgG production was further and significantly (p=0.0155) reduced as compared to the co-culture of CSCs and B cells alone. The addition of anti-PD-L1 to the cultures rescued IgG production by T/B/CSC co-cultures to a greater (p=0.0429) extent than in just B/CSC co-culture. These results indicate that CSCs can also indirectly suppress IgG production by B cells via the PD-L1/PD-1 interaction with Th cells. Together, this study demonstrates that the anti-tumor function of anti-PD-L1 mAb involves host B cells, and that CSCs can both directly and indirectly inhibit B cell function through the PD-L1/PD-1 axis on both B cells and Th cells, respectively.

Citation Format: Leiming Xia, FEI LIAO, Jing Zhang, Ming Lin, Ronald Herbst, Elaine Hurt, Alfred Chang, Max Wicha, Qiao Li. Involvement of B cells in the efficacy of anti-PD-L1 antibodies: Suppression of B cells by cancer stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1676.

Effective combination therapies in preclinical endocrine resistant breast cancer models harboring ER mutations

Although endocrine therapy is successfully used to treat patients with estrogen receptor (ER) positive breast cancer, a substantial proportion of this population will relapse. Several mechanisms of acquired resistance have been described including activation of the mTOR pathway, increased activity of CDK4 and activating mutations in ER. Using a patient derived xenograft model harboring a common activating ER ligand binding domain mutation (D538G), we evaluated several combinatorial strategies using the selective estrogen receptor degrader (SERD) fulvestrant in combination with chromatin modifying agents, and CDK4/6 and mTOR inhibitors. In this model, fulvestrant binds WT and MT ER, reduces ER protein levels, and downregulated ER target gene expression. Addition of JQ1 or vorinostat to fulvestrant resulted in tumor regression (41% and 22% regression, respectively) though no efficacy was seen when either agent was given alone. Interestingly, although the CDK4/6 inhibitor palbociclib and mTOR inhibitor everolimus were efficacious as monotherapies, long-term delayed tumor growth was only observed when co-administered with fulvestrant. This observation was consistent with a greater inhibition of compensatory signaling when palbociclib and everolimus were co-dosed with fulvestrant. The addition of fulvestrant to JQ1, vorinostat, everolimus and palbociclib also significantly reduced lung metastatic burden as compared to monotherapy. The combination potential of fulvestrant with palbociclib or everolimus were confirmed in an MCF7 CRISPR model harboring the Y537S ER activating mutation. Taken together, these data suggest that fulvestrant may have an important role in the treatment of ER positive breast cancer with acquired ER mutations.

Abstract 1903: Cancer stem cell vaccine significantly reduces local tumor relapse and prolongs survival in the adjuvant setting

Although surgical resection has been a standard treatment for solid malignancies, therapeutic efficacy is limited by both local and distant recurrence. Effectively preventing local tumor recurrence remains a significant challenge. The existence of micro metastasis at the time of tumor resection represents an even greater therapeutic challenge, since 90% of tumor deaths are due to tumor metastasis. There is increasing evidence that many cancers are driven and maintained by a subpopulation of cells that display stem cell properties. Cancer stem cells (CSCs) can self-renew, mediate tumor growth and contribute to tumor recurrence and metastasis. Targeting CSCs may thus increase the therapeutic efficacy of current cancer treatment. We previously described a strategy to target CSCs using CSC-dendritic cell (DC) vaccination. However, the efficacy of CSC targeted therapeutics may be greatest when they are deployed in the adjuvant setting. In this study, two mouse models were utilized: SCC7 subcutaneous (s.c.) tumors, and a D5 melanoma model. Established s.c. SCC7 tumors were surgically removed from mice followed by treatment using ALDHhigh SCC7 CSC-DC vaccine, which significantly reduced local tumor relapse and prolonged animal survival. This effect was significantly augmented by simultaneous administration of anti-PD-L1 mAb. In the minimal disease setting of D5, ALDHhigh CSC-DC vaccination significantly inhibited tumor growth, reduced spontaneous lung metastases resulting in increased survival. CCR10 and its ligands were down-regulated on ALDHhigh D5 CSCs and in lung tissues respectively in animals subjected to ALDHhigh D5 CSC-DC vaccination. Down-regulation of CCR10 by siRNA significantly blocked tumor cell migration in vitro and metastasis in vivo. T cells harvested from ALDHhigh D5 CSC-DC vaccinated animals selectively killed the ALDHhigh D5 CSCs. There was also evidence of humoral immunological targeting of CSCs. As a result, CSC-DC vaccination significantly decreased the percentage of ALDHhigh cells in residual tumors. These data indicate that, when used in an adjuvant setting, ALDHhigh CSC-DC vaccines effectively inhibit local tumor recurrence, reduce spontaneous lung metastasis, and prolong animal survival; compared with traditional DC vaccines and that simultaneous PD-L1 blockade can significantly enhance this effect.

Citation Format: Fei Liao, Yang yang Hu, Xin Chen, Alfed E Chang, Robert E Hollingsworth, Elaine Hurt, John Owen, Jeffrey S Moyer, Mark E.P Prince, Joel Whitfield, Yuxin Chu, Qibin Song, Max S Wicha, Qiao Li. Cancer stem cell vaccine significantly reduces local tumor relapse and prolongs survival in the adjuvant setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1903. doi:10.1158/1538-7445.AM2017-1903

Targeting ADAM17 inhibits human colorectal adenocarcinoma progression and tumor-initiating cell frequency

ADAM17 (a disintegrin and metalloproteinase 17)/TACE (TNFα converting enzyme) has emerged as a potential therapeutic target in colorectal cancer (CRC) and other cancers, due in part to its role in regulating various tumor cell surface proteins and growth factors and cytokines in the tumor microenvironment. The emergence of MEDI3622, a highly potent and specific antibody-based ADAM17 inhibitor, has allowed testing of the concept that targeting ADAM17 may be an important new therapeutic approach for CRC patients. We demonstrate that MEDI3622 is highly efficacious on tumor growth in multiple human CRC PDX models, resulting in improved survival of animals bearing tumor xenografts. MEDI3622 was further found to impact Notch pathway activity and tumor-initiating cells. The promising preclinical activity seen here supports further clinical investigation of this treatment approach to improve therapeutic outcome for patients diagnosed with metastatic CRC, including patients with KRAS-mutant tumors for whom other therapeutic options are currently limited.

Abstract 1717: Circulating tumor cells from in vitro 3D culture systems have tumor-initiating capacity in vivo

Circulating tumor cells (CTCs) are cells that have detached from the primary tumor and entered the bloodstream with the potential to seed metastatic tumors in distal sites. High CTC numbers correlate with aggressive disease, increased metastasis, and decreased time to relapse. It has also been shown that cancer stem cells (CSCs) represent a proportion of the CTCs present in patients. Given that CSCs are resistant to chemotherapy and are responsible for tumor initiation, it is posited that the CSCs are the seeds of metastasis. However, direct evidence for this hypothesis is limited because there are few methods for culturing and studying these rare cells. We are using a 3D culture chamber system (RealBio D4™) to establish long-term cultures of human-derived breast and pancreatic tumors. We observed that the system's 3D matrix supported culture development and incorporation of tissue organization and microenvironment. Further, the chamber design allowed CTCs generated within the cultures to migrate out of the cell mass into the circulating nutrient medium where they were collected for characterization. The isolated CTCs displayed CSC properties via CellSearch® (CD44+,CD24-; CD44+,CD24+ for breast and pancreas respectively). In addition, these isolated CTCs displayed tumor-initiating capacity when implanted into mice. Future studies will compare CTCs isolated from 3D culture with cells from tumors, blood, and tissue grown on scaffold through RT-PCR, histology, and gene expression assays.

Citation Format: Marina C. Cabrera, Elaine Hurt, Xiaoru Chen, Shi Xiaoqing, Haifeng Bao. Circulating tumor cells from in vitro 3D culture systems have tumor-initiating capacity in vivo. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1717.

Abstract 540: Adjuvant effect of anti-PD-L1 in boosting HER2-targeted T cell adoptive immunotherapy

In a phase I clinical trial, we used anti-CD3 x anti-HER2 bispecific antibody (HER2Bi) armed T cells. Utilizing HER2-directed T cells benefitted both HER2+ patients and patients with 1 or 2+ HER2 expression, ones that would be considered “HER2-negative” by classical criteria. We have also shown that the level of cancer stem cell (CSC) marker ALDH in HER2+ breast cancer cells (ALDHhighHER2+) is much higher than that in HER2- breast cancer cells (ALDHlowHER2-), and that in luminal breast cancers that are considered HER2-, HER2 is actually selectively expressed in the ALDHhigh CSC population. These observations might account for the surprising result that HER2Bi-armed T cells, while intended to target HER2, seemed to benefit HER2- patients after adoptive transfer. In this study, we found that the HER2Bi-armed T cells used in the clinical trial killed ALDHhigh human breast CSCs isolated from MCF7 (HER2-) tumor significantly more than ALDHlow MCF7 cells in vitro, while the same HER2Bi-armed T cells killed ALDHhigh human breast CSCs (ALDHhighHER2+) isolated from BT474 (HER2+) tumor equally to ALDHlow BT474 cells (ALDHlowHER2+). We then tested the “mouse HER2” (neu) expression on ALDHhigh vs. ALDHlow 4T1 cells (mouse TNBC), and found that mHER2 was selectively expressed in the ALDHhigh 4T1 CSC population. These results replicated our findings in human breast cancers that HER2 is selectively expressed on CSCs, even in HER2- murine tumors, such as 4T1. For mHER2 targeting in animal models, we generated anti-mouse HER2-CD3 bispecific (mHER2Bi) that binds to mouse HER2 and mouse CD3. In vitro, the mHER2Bi-armed T cells killed ALDHhigh 4T1 CSCs significantly more than ALDHlow 4T1 cells. In vivo, adoptive transfer of mHER2Bi-armed T cells for HER2 targeted therapy showed antitumor effect in mHER2- 4T1-bearing host. To boost the therapeutic efficacy of mHER2-targeted T cells, we administrated anti-mouse PD-L1 during mHER2Bi-armed T cell adoptive transfer. This combination decreased metastases significantly more than the use of either strategy alone. Collectively, these studies have generated evidence providing proofs of principle that due to the selective expression of HER2 on CSCs, HER2-targeted T cell therapy could benefit HER2- host as well as HER2+ hosts via immune destruction of HER2+ CSCs, and use of anti-PD-L1 as an adjuvant could significantly boost the efficacy of HER2-targeted T cell therapy.

Citation Format: Yang Xia, Yangyang Hu, Yi Wang, Yangyi Bao, Fu Dai, Shiang Huang, Elaine Hurt, Robert E. Hollingsworth, Archana Thakur, Lawrence Lum, Alfred E. Chang, Max S. Wicha, Qiao Li. Adjuvant effect of anti-PD-L1 in boosting HER2-targeted T cell adoptive immunotherapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 540.

Abstract 3329: Increasing the efficacy of cancer stem cell-based vaccine in the PD-L1/PD-1 blockade

We have previously reported the development of a strategy to target the cancer stem cell (CSC) populations in melanoma and squamous cell carcinoma using CSC lysate-pulsed dendritic cells (DCs). Using mouse models we demonstrated that DCs pulsed with CSCs enriched by virtue of their expression of the CSC marker ALDH (termed CSC-DC) significantly inhibited tumor growth. However, CSC-DC vaccine therapy alone may not be sufficient to overcome the immunosuppressive components of the tumor microenvironment. CSC-mediated suppression of T cells has been reported in a process involving the PD-L1/PD-1 axis. Immunologically targeting CSCs while simultaneously blocking PD-L1/PD-1-mendiated immune suppression may significantly enhance the outcome of current immunotherapies of cancer. To test this hypothesis, we investigated the effect of using anti-PD-L1 to block the immunosuppression during the CSC-DC vaccination to augment the therapeutic efficacy of using each regimen alone. We used 4T1 cell line, a mammary carcinoma syngeneic to BALB/c mice, and found that 4T1 tumors contain approx. 6-10% ALDEFLUOR+/ALDHhigh cells, and that these cells are enriched for tumor initiating capacity compared to bulk or ALDEFLUOR-/ALDHlow cells. Inoculating 4T1 cells into the mammary fat pad induces the development of spontaneous pulmonary metastases. ALDHhigh 4T1 CSCs expressed PD-L1. 4T1 ALDHhigh CSC-DC vaccine + anti-PD-L1 administration significantly reduced pulmonary metastases and prolonged survival compared with 4T1 ALDHhigh CSC-DC vaccine or anti-PD-L1 administration alone. Anti-PD-L1 administration increased systematic anti-4T1 CSC immunity induced by CSC-DC vaccine. This is evident by the increased production of total IgG in the serum samples collected from the 4T1-bearing animals subjected to 4T1 CSC-DC vaccination with anti-PD-L1 administration. The CSC-reactivity/specificity of the immune sera was demonstrated by their specific binding to the ALDHhigh vs. ALDHlow 4T1 cells in flow cytometry. Importantly, the immunological consequence of such binding was Ab-mediated ALDHhigh 4T1 CSC lysis via complement dependent cytotoxicity. In addition, CTLs generated from the splenocytes harvested from the hosts subjected to 4T1 CSC-DC vaccination with anti-PD-L1 administration killed ALDHhigh 4T1 CSCs significantly more than ALDHlow 4T1 cells. These results are supportive of the conclusion that administration of anti-PD-L1 as an adjuvant could significantly boost the therapeutic efficacy of the CSC-DC vaccine, and that this effect was due to both antibody and T cell-mediated anti-CSC immunity.

Citation Format: Yangyang Hu, Yang Xia, Xin Chen, Li Zhou, Yangyi Bao, Shiang Huang, Xiubao Ren, Elaine Hurt, Robert E. Hollingsworth, Alfred E. Chang, Max S. Wicha, Qiao Li. Increasing the efficacy of cancer stem cell-based vaccine in the PD-L1/PD-1 blockade. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3329.

Therapeutic Efficacy of Cancer Stem Cell Vaccines in the Adjuvant Setting

Dendritic cell (DC)-based vaccine strategies aimed at targeting cancer stem-like cells (CSC) may be most efficacious if deployed in the adjuvant setting. In this study, we offer preclinical evidence that this is the case for a CSC-DC vaccine as tested in murine models of SCC7 squamous cell cancer and D5 melanoma. Vaccination of mice with an ALDH(high) SCC7 CSC-DC vaccine after surgical excision of established SCC7 tumors reduced local tumor relapse and prolonged host survival. This effect was augmented significantly by simultaneous administration of anti-PD-L1, an immune checkpoint inhibitor. In the minimal disease setting of D5 melanoma, treatment of mice with ALDH(high) CSC-DC vaccination inhibited primary tumor growth, reduced spontaneous lung metastases, and increased host survival. In this setting, CCR10 and its ligands were downregulated on ALDH(high) D5 CSCs and in lung tissues, respectively, after vaccination with ALDH(high) D5 CSC-DC. RNAi-mediated attenuation of CCR10 blocked tumor cell migration in vitro and metastasis in vivo T cells harvested from mice vaccinated with ALDH(high) D5 CSC-DC selectively killed ALDH(high) D5 CSCs, with additional evidence of humoral immunologic engagement and a reduction in ALDH(high) cells in residual tumors. Overall, our results offered a preclinical proof of concept for the use of ALDH(high) CSC-DC vaccines in the adjuvant setting to more effectively limit local tumor recurrence and spontaneous pulmonary metastasis, as compared with traditional DC vaccines, with increased host survival further accentuated by simultaneous PD-L1 blockade. Cancer Res; 76(16); 4661-72. ©2016 AACR.

A Novel IL6 Antibody Sensitizes Multiple Tumor Types to Chemotherapy Including Trastuzumab-Resistant Tumors

Elevated levels of the proinflammatory cytokine IL6 are associated with poor survival outcomes in many cancers. Antibodies targeting IL6 and its receptor have been developed for chronic inflammatory disease, but they have not yet been shown to clearly benefit cancer patients, possibly due to antibody potency or the settings in which they have been tested. In this study, we describe the development of a novel high-affinity anti-IL6 antibody, MEDI5117, which features an extended half-life and potent inhibitory effects on IL6 biologic activity. MEDI5117 inhibited IL6-mediated activation of STAT3, suppressing the growth of several tumor types driven by IL6 autocrine signaling. In the same models, MEDI5117 displayed superior preclinical activity relative to a previously developed anti-IL6 antibody. Consistent with roles for IL6 in promoting tumor angiogenesis, we found that MEDI5117 inhibited the growth of endothelial cells, which can produce IL6 and support tumorigenesis. Notably, in tumor xenograft assays in mice, we documented the ability of MEDI5117 to enhance the antitumor activities of chemotherapy or gefitinib in combination treatment regimens. MEDI5117 also displayed robust activity on its own against trastuzumab-resistant HER2(+) tumor cells by targeting the CD44(+)CD24(-) cancer stem cell population. Collectively, our findings extend the evidence of important pleiotropic roles of IL6 in tumorigenesis and drug resistance, and offer a preclinical proof of concept for the use of IL6 antibodies in combination regimens to heighten therapeutic responses and overcome drug resistance.

Abstract 975: Monoclonal antibody targeting of ADAM17 is an effective treatment for metastatic colorectal cancer resulting in tumor growth control and reductions of cancer stem cells

ADAM17/TACE (TNFα converting enzyme) has been implicated to play a role in the drug resistance of colorectal cancers. The present study addresses the hypothesis that MEDI3622, a specific ADAM17 monoclonal antibody known to possess both human and mouse cross reactivity, represents a viable therapeutic strategy to improve outcome in the treatment of metastatic colorectal cancer (mCRC). We have generated both in vitro and in vivo data in patient-derived CRC models to provide compelling support for further exploration of this treatment strategy. A heterogeneous panel of low passage colorectal patient-derived xenografts (PDX) has been established from biospecimens procured during patient surgeries conducted at University of Michigan. All xenograft models have been genomically profiled and their histologies mimicked those observed in the original samples. As anticipated, approximately half of these models harbor an oncogenic KRAS mutation and exhibit widely differing histologies, consistent with the heterogeneity encountered in the clinic. Efficacy testing of MEDI3622 has shown that this agent significantly impaired tumor growth in 3 of the 5 PDX models examined, including one model that is KRASMT. Furthermore, cancer stem cell function in these CRC models is negatively impacted by MEDI3622, reducing tumor initiation frequencies in tumor re-implantation studies at the conclusion of treatment. Therefore our results suggest that a monoclonal antibody approach that targets ADAM17 may provide an attractive therapeutic strategy for the treatment of metastatic colorectal cancer both by reducing tumor growth and inhibiting cancer stem cells.

Citation Format: Joseph Dosch, Elizabeth Ziemke, Theodore Welling, Karin Hardiman, Juidth Sebolt-Leopold, Emil Michelotti, Robert Hollingsworth, Elaine Hurt. Monoclonal antibody targeting of ADAM17 is an effective treatment for metastatic colorectal cancer resulting in tumor growth control and reductions of cancer stem cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 975. doi:10.1158/1538-7445.AM2015-975

Abstract 4587: In vitro and In vivo characterization of circulating tumor cells from breast cancer patients

Circulating tumor cells (CTCs) are an independent prognostic marker associated with poor clinical outcome in patients with metastatic diseases. However, CTC biology, especially the tumorigenic and metastatic activity of CTCs, is not yet well understood. In this study, we hypothesized that CTCs contain a population of cancer stem cells (CSCs) that are the seed cells responsible for metastases. To test this hypothesis, we sought to assess subpopulations of CTCs in breast cancer patients and to characterize CTCs for CSC properties and tumorigenic potential. For assessment of CTC subsets, blood samples from breast cancer patients were enriched for CTCs by magnetic separation. The enriched CTC samples were immunostained for various cell surface markers and then analyzed by FACS. The phenotypes of CTCs were further confirmed by imaging analysis. To evaluate tumorigenicity of CTCs, CTC samples from patients were cultured in vitro and then implanted into immunodeficient mice by orthotopic injection. Different phenotypes of CTCs were found in breast cancer patients, including EpCAM+CD44−CD24−/dimCD45−, EpCAM+CD44+CD24−/dimCD45−, EpCAM+CD44+CD24+CD45−, and EpCAM+CD44+CD24+CD45dim. Of these phenotypes, EpCAM+CD44+CD24−/dim cells have been reported as CSCs in breast cancer. This subset of CSC-like CTCs constituted 4.6% to 71% of the total CTC population. In vitro culture of CTCs resulted in the generation of mammospheres, as is typical of CSCs. During in vitro culture, some of CTCs showed staining positive for Ki-67, indicating that these cells were proliferating. To assess tumorigenic potential of CTCs, cultured CTCs were injected into the mouse mammary fat pads of immunodeficient mice. Human tumors were developed in these mice. Further analysis of the CTC-derived tumor xenografts demonstrated a heterogenous phenotype where EpCAM+CD44+CD24dim/− CSCs accounted for less than 3% of the total tumor cells. Only this subset of cells isolated from CTC-derived xenograft tumors could form secondary tumors after being reimplanted into mice. Our results support the hypothesis that CTCs contain a CSC-like population that may initiate new tumors. As a result, CTCs may be a potential therapeutic target for the prevention of metastasis in addition to serving as a readily accessible source for biomarker evaluation of new therapies in cancer patients.

Citation Format: Sanjoo Jalla, Xiaoru Chen, Patricia Burke, Xiaoqing Shi, Meggan Czapiga, Vivekananda Datta, Philip Brohawn, Jiaqi Huang, Charles Brown, Elaine Hurt, Laura Richman, Robert Hollingsworth, Theresa LaVallee, Haifeng Bao. In vitro and In vivo characterization of circulating tumor cells from breast cancer patients. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4587. doi:10.1158/1538-7445.AM2013-4587

TGFBR3 is lost in prostate cancer, contributing to malignant transformation

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Background: Resistance to transforming growth factor-beta (TGF-beta) is common in solid tumors. Alterations of TGF-beta biology in prostate cancer are complex, with a downregulation of this cytokine reported in early disease and upregulation of TGF-beta in advanced disease. Mechanisms of TGF-beta resistance in early disease are not well understood. We have investigated the function of TGF-beta receptor 3 (TGFBR3) to determine its role in prostate cancer. Methods: We undertook an analysis of the data in seven published DNA microarray studies of nonneoplastic prostate tissue versus prostate cancer specimens using oncomine. Of the genes we identified as known to be directly involved in the TGF-beta pathway, loss of TGFBR3 was most significantly associated with prostate cancer. We determined TGFBR3 expression in prostate cancer cell lines and the immortalized prostate epithelial cell line RWPE-1. To assess the consequences of loss of TGFBR3 expression, we created an shRNA construct and stably infected RWPE-1 cells. We analyzed gene expression changes by DNA microarray analysis and confirmed changes by Western Blot. We then searched TGFBR3 regulated genes based on our knockdown studies in the data set from the seven previously published studies. Furthermore, we evaluated the phenotypic consequences of TGFBR3 knockdown. Results: TGFBR3 expression was significantly lost in 6 of 7 microarray studies. TGFBR3 was downregulated in 3 of 4 of prostate cancer cell lines, compared with RWPE-1. DNA microarray analysis of TGFBR3 knockdown in RWPE-1 cells showed that expression of DPYSL3, Vimentin, COCH, SERPINF1, PMP22, LTBP1 and BMP4 were decreased both with TGFBR3 knockdown and in the transition to prostate cancer. Of these genes, vimentin expression was most dramatically downregulated in TGFBR3 knockdown cells and we showed that vimentin protein expression was completely lost. The phenotypic consequence of TGFBR3 knockdown in RWPE-1 cells was formation of colonies that appear to reflect loss of contact inhibition. Conclusions: TGFBR3 is lost in prostate cancer. TGFBR3 knockdown leads to colony formation by immortalized prostate epithelial cells. Our data suggests that loss of TGFBR3 contributes to malignant transformation of the prostate.

No significant financial relationships to disclose.

Pus1p-dependent tRNA pseudouridinylation becomes essential when tRNA biogenesis is compromised in yeast

Yeast Pus1p catalyzes the formation of pseudouridine (psi) at specific sites of several tRNAs, but its function is not essential for cell viability. We show here that Pus1p becomes essential when another tRNA:pseudouridine synthase, Pus4p, or the essential minor tRNA for glutamine are mutated. Strikingly, this mutant tRNA, which carries a mismatch in the T psi C arm, displays a nuclear export defect. Furthermore, nuclear export of at least one wild-type tRNA species becomes defective in the absence of Pus1p. Our data, thus, show that the modifications formed by Pus1p are essential when other aspects of tRNA biogenesis or function are compromised and suggest that impairment of nuclear tRNA export in the absence of Pus1p might contribute to this phenotype.

The nucle(ol)ar Tif6p and Efl1p are required for a late cytoplasmic step of ribosome synthesis

Deletion of elongation factor-like 1 (Efl1p), a cytoplasmic GTPase homologous to the ribosomal translocases EF-G/EF-2, results in nucle(ol)ar pre-rRNA processing and pre-60S subunits export defects. Efl1p interacts genetically with Tif6p, a nucle(ol)ar protein stably associated with pre-60S subunits and required for their synthesis and nuclear exit. In the absence of Efl1p, 50% of Tif6p is relocated to the cytoplasm. In vitro, the GTPase activity of Efl1p is stimulated by 60S, and Efl1p promotes the dissociation of Tif6p-60S complexes. We propose that Tif6p binds to the pre-60S subunits in the nucle(ol)us and escorts them to the cytoplasm where the GTPase activity of Efl1p triggers a late structural rearrangement, which facilitates the release of Tif6p and its recycling to the nucle(ol)us.

The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport

Nucleoporin Nsp1p, which has four predicted coiled-coil regions (coils 1 to 4) in the essential carboxy-terminal domain, is unique in that it is part of two distinct nuclear pore complex (NPC) subcomplexes, Nsp1p-Nup57p-Nup49p-Nic96p and Nsp1p-Nup82p-Nup159p. As shown by in vitro reconstitution, coiled-coil region 2 (residues 673 to 738) is sufficient to form heterotrimeric core complexes and can bind either Nup57p or Nup82p. Accordingly, interaction of Nup82p with Nsp1p coil 2 is competed by excess Nup57p. Strikingly, coil 3 and 4 mutants are still assembled into the core Nsp1p-Nup57p-Nup49p complex but no longer associate with Nic96p. Consistently, the Nsp1p-Nup57p-Nup49p core complex dissociates from the nuclear pores in nsp1 coil 3 and 4 mutant cells, and as a consequence, defects in nuclear protein import are observed. Finally, the nsp1-L640S temperature-sensitive mutation, which maps in coil 1, leads to a strong nuclear mRNA export defect. Thus, distinct coiled-coil regions within Nsp1p-C have separate functions that are related to the assembly of different NPC subcomplexes, nucleocytoplasmic transport, and incorporation into the nuclear pores.

Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p

The yeast nuclear protein Yra1p is an essential export factor for mRNA. Yra1p interacts directly with the mRNA transport factor Mex67p/Mtr2p, which is associated with the nuclear pore. Here, we report a genetic interaction between YRA1 and SUB2, the gene for a DEAD box helicase involved in splicing. Mutation of SUB2 as well as its overexpression leads to a defect in mRNA export. Moreover, Yra1p and Sub2p bind directly to each other both in vivo and in vitro. Significantly, Sub2p and Mex67p/Mtr2p bind to the same domains of Yra1p, and the proteins compete for binding to Yra1p. Together, these data indicate that the spliceosomal component Sub2p is also important in mRNA export and may function to recruit Yra1p to the mRNA. Sub2p may then be displaced from Yra1p by the binding of Mex67p/Mtr2p, which participates in the export of mRNA through the nuclear pores.

Targeting of Ran: variation on a common theme?

The Ran GTPase plays a key role in nucleocytoplasmic transport. In its GTP-bound form, it directly interacts with members of the importin β family of nuclear transport receptors and modulates their association with cargo. Work in cell-free higher-eukaryote systems has demonstrated additional roles for Ran in spindle and nuclear envelope formation during mitosis. However, until recently, no Ran-target proteins in these cellular processes were known. Several groups have now identified importin β as one important target of Ran during mitotic spindle formation. This finding suggests that Ran uses the same effectors to regulate different cellular processes.

Identification of a 60S preribosomal particle that is closely linked to nuclear export

A nuclear GTPase, Nug1p, was identified in a genetic screen for components linked to 60S ribosomal subunit export. Nug1p cosedimented with nuclear 60S preribosomes and was required for subunit export to the cytoplasm. Tagged Nug1p coprecipitated with proteins of the 60S subunit, late precursors to the 25S and 5.8S rRNAs, and at least 21 nonribosomal proteins. These included a homologous nuclear GTPase, Nug2p, the Noc2p/Noc3p heterodimer, Rix1p, and Rlp7p, each of which was implicated in 60S subunit export. Other known ribosome synthesis factors and proteins of previously unknown function, including the 559 kDa protein Ylr106p, also copurified. Eight of these proteins were copurified with nuclear pore complexes, suggesting that this complex represents the transport intermediate for 60S subunit export.

Maturation and intranuclear transport of pre-ribosomes requires Noc proteins

How pre-ribosomes temporally and spatially mature during intranuclear biogenesis is not known. Here, we report three nucleolar proteins, Noc1p to Noc3p, that are required for ribosome maturation and transport. They can be isolated in two distinct complexes: Noc1p/Noc2p associates with 90S and 66S pre-ribosomes and is enriched in the nucleolus, and Noc2p/Noc3p associates with 66S pre-ribosomes and is mainly nucleoplasmic. Mutation of each Noc protein impairs intranuclear transport of 60S subunits at different stages and inhibits pre-rRNA processing. Overexpression of a conserved domain common to Noc1p and Noc3p is dominant-negative for cell growth, with a defect in nuclear 60S subunit transport, but no inhibition of pre-rRNA processing. We propose that the dynamic interaction of Noc proteins is crucial for intranuclear movement of ribosomal precursor particles, and, thereby represent a prerequisite for proper maturation.

Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a nuclear export sequence-containing factor, Nmd3p, that associates with the large subunit protein Rpl10p

Nuclear export of ribosomes requires a subset of nucleoporins and the Ran system, but specific transport factors have not been identified. Using a large subunit reporter (Rpl25p-eGFP), we have isolated several temperature-sensitive ribosomal export (rix) mutants. One of these corresponds to the ribosomal protein Rpl10p, which interacts directly with Nmd3p, a conserved and essential protein associated with 60S subunits. We find that thermosensitive nmd3 mutants are impaired in large subunit export. Strikingly, Nmd3p shuttles between the nucleus and cytoplasm and is exported by the nuclear export receptor Xpo1p. Moreover, we show that export of 60S subunits is Xpo1p dependent. We conclude that nuclear export of 60S subunits requires the nuclear export sequence-containing nonribosomal protein Nmd3p, which directly binds to the large subunit protein Rpl10p.

Mutations in the YRB1 gene encoding yeast ran-binding-protein-1 that impair nucleocytoplasmic transport and suppress yeast mating defects

We identified two temperature-sensitive (ts) mutations in the essential gene, YRB1, which encodes the yeast homolog of Ran-binding-protein-1 (RanBP1), a known coregulator of the Ran GTPase cycle. Both mutations result in single amino acid substitutions of evolutionarily conserved residues (A91D and R127K, respectively) in the Ran-binding domain of Yrb1. The altered proteins have reduced affinity for Ran (Gsp1) in vivo. After shift to restrictive temperature, both mutants display impaired nuclear protein import and one also reduces poly(A)+ RNA export, suggesting a primary defect in nucleocytoplasmic trafficking. Consistent with this conclusion, both yrb1ts mutations display deleterious genetic interactions with mutations in many other genes involved in nucleocytoplasmic transport, including SRP1 (alpha-importin) and several beta-importin family members. These yrb1ts alleles were isolated by their ability to suppress two different types of mating-defective mutants (respectively, fus1Delta and ste5ts), indicating that reduction in nucleocytoplasmic transport enhances mating proficiency. Indeed, in both yrb1ts mutants, Ste5 (scaffold protein for the pheromone response MAPK cascade) is mislocalized to the cytosol, even in the absence of pheromone. Also, both yrb1ts mutations suppress the mating defect of a null mutation in MSN5, which encodes the receptor for pheromone-stimulated nuclear export of Ste5. Our results suggest that reimport of Ste5 into the nucleus is important in downregulating mating response.

Cloning and characterization of the Schizosaccharomyces pombe tRNA:pseudouridine synthase Pus1p

Saccharomyces cerevisiae cells that carry deletions in both the LOS1 (a tRNA export receptor) and the PUS1 (a tRNA:pseudouridine synthase) genes exhibit a thermosensitive growth defect. A Schizosaccharomyces pombe gene, named spPUS1, was cloned from a cDNA library by complementation of this conditional lethal phenotype. The corresponding protein, spPus1p, shows sequence similarity to S. cerevisiae and murine Pus1p as well as other known members of the pseudouridine synthase family. Accordingly, recombinant spPus1p can catalyze in vitro the formation of pseudouridines at positions 27, 28, 34, 35 and 36 of yeast tRNA transcripts. The sequence and functional conservation of the Pus1p proteins in fungi and mammalian species and their notable absence from prokaryotes suggest that this family of pseudouridine synthases is required for a eukaryote-specific step of tRNA biogenesis, such as nuclear export.

Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction

Assembly of nuclear pore complexes (NPCs) is a critical yet poorly understood cellular function. One approach to studying NPC assembly is to identify yeast mutants defective in this process. This requires robust assays for NPC assembly that can be used for phenotypic analysis. We have previously reconstructed yeast nuclei from electron micrographs of serially sectioned cells to precisely determine the number of NPCs (Winey et al., 1997). Here we report the analysis of strains mutant in either of two nucleoporin-encoding genes, NIC96 (Zabel et al., 1996) and NUP192 (Kosova et al., 1999). Using conditional alleles of either gene, we have found that the NPC number falls significantly following shift to the restrictive temperature. We conclude that the drop in NPC number results from the failure to assemble new NPCs during cell divisions, leading to the dilution of NPCs that existed when the cells were shifted to the restrictive temperature. We are also able to document a subtle defect in NPC numbers in nup192-15 cells at their permissive temperature. The data presented here quantitatively demonstrate that NPC numbers fall in nic96-1 and nup192-15 strains upon shifting to the restrictive temperature, indicating that these gene products are required for NPC assembly.

The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans

In metazoans, most pre-messenger RNAs contain introns that are removed by splicing. The spliced mRNAs are then exported to the cytoplasm. Recent studies showed that splicing promotes efficient mRNA export, but the mechanism for coupling these two processes is not known. Here we show that Aly, the metazoan homologue of the yeast mRNA export factor Yralp (ref. 2), is recruited to messenger ribonucleoprotein (mRNP) complexes generated by splicing. In contrast, Aly does not associate with mRNPs assembled on identical mRNAs that already have no introns or with heterogenous nuclear RNP (hnRNP) complexes. Aly is recruited during spliceosome assembly, and then becomes tightly associated with the spliced mRNP. Aly shuttles between the nucleus and cytoplasm, and excess recombinant Aly increases both the rate and efficiency of mRNA export in vivo. Consistent with its splicing-dependent recruitment, Aly co-localizes with splicing factors in the nucleus. We conclude that splicing is required for efficient mRNA export as a result of coupling between the splicing and the mRNA export machineries.

Nup116p associates with the Nup82p-Nsp1p-Nup159p nucleoporin complex

Nup116p is a GLFG nucleoporin involved in RNA export processes. We show here that Nup116p physically interacts with the Nup82p-Nsp1p-Nup159p nuclear pore subcomplex, which plays a central role in nuclear mRNA export. For this association, a sequence within the C-terminal domain of Nup116p that includes the conserved nucleoporin RNA-binding motif was sufficient and necessary. Consistent with this biochemical interaction, protein A-Nup116p and the protein A-tagged Nup116p C-terminal domain, like the members of the Nup82p complex, localized to the cytoplasmic side of the nuclear pore complex, as revealed by immunogold labeling. Finally, synthetic lethal interactions were found between mutant alleles of NUP116 and all members of the Nup82p complex. Thus, Nup116p consists of three independent functional domains: 1) the C-terminal part interacts with the Nup82p complex; 2) the Gle2p-binding sequence interacts with Gle2p/Rae1p; and 3) the GLFG domain interacts with shuttling transport receptors such as karyopherin-beta family members.

Yeast Ran-binding protein 1 (Yrb1) shuttles between the nucleus and cytoplasm and is exported from the nucleus via a CRM1 (XPO1)-dependent pathway

The RanGTP-binding protein RanBP1, which is located in the cytoplasm, has been implicated in release of nuclear export complexes from the cytoplasmic side of the nuclear pore complex. Here we show that Yrb1 (the yeast homolog of RanBP1) shuttles between the nucleus and the cytoplasm. Nuclear import of Yrb1 is a facilitated process that requires a short basic sequence within the Ran-binding domain (RBD). By contrast, nuclear export of Yrb1 requires an intact RBD, which forms a ternary complex with the Xpo1 (Crm1) NES receptor in the presence of RanGTP. Nuclear export of Yrb1, however, is insensitive towards leptomycin B, suggesting a novel type of substrate recognition between Yrb1 and Xpo1. Taken together, these data suggest that ongoing nuclear import and export is an important feature of Yrb1 function in vivo.

Review: transport of tRNA out of the nucleus-direct channeling to the ribosome?

Although tRNA was the first substrate whose export from the nuclei of eukaryotic cells had been shown to be carrier-mediated and active, it has only been in the last 2 years that the first mechanistic details of this nucleocytoplasmic transport pathway have begun to emerge. A member of the importin/karyopherin beta superfamily, Los1p in yeast and Xpo-t in vertebrates, has been shown to export tRNA in cooperation with the small GTPase Ran (Gsp1p) from the nucleus into the cytoplasm, where tRNA becomes available for translation. However, Los1p is not essential for viability in yeast cells, suggesting that alternative tRNA export pathways exist. Recent results show that aminoacylation and a translation factor are also required for efficient nuclear tRNA export. Thus, protein translation and nuclear export of tRNA appear to be coupled processes.

An aminoacylation-dependent nuclear tRNA export pathway in yeast

Yeast Los1p, the homolog of human exportin-t, mediates nuclear export of tRNA. Using fluorescence in situ hybridization, we could show that the export of some intronless tRNA species is not detectably affected by the disruption of LOS1. To find other factors that facilitate tRNA export, we performed a suppressor screen of a synthetically lethal los1 mutant and identified the essential translation elongation factor eEF-1A. Mutations in eEF-1A impaired nuclear export of all tRNAs tested, which included both spliced and intronless species. An even stronger defect in nuclear exit of tRNA was observed under conditions that inhibited tRNA aminoacylation. In all cases, inhibition of tRNA export led to nucleolar accumulation of mature tRNAs. Our data show that tRNA aminoacylation and eEF-1A are required for efficient nuclear tRNA export in yeast and suggest coordination between the protein translation and the nuclear tRNA processing and transport machineries.

Mex67p mediates nuclear export of a variety of RNA polymerase II transcripts

Mex67p is essential for nuclear poly(A)(+) RNA export in yeast, but which specific transcripts are transported by Mex67p is not known. We observed that thermosensitive mex67-5 cells do not produce a heat shock response at 37 degrees C but will induce heat shock proteins (Hsp) (e.g. Hsp104p and Hsp70p) when shifted back from the restrictive to permissive temperature (30 degrees C). This memory of a previous heat stress in mex67-5 cells could be explained if HSP mRNAs accumulated inside the nucleus during heat shock and were exported and translated in the cytoplasm on return to the permissive temperature. To test this hypothesis, nuclear export of heat shock mRNAs was directly analyzed by in situ hybridization using fluorescent-labeled oligonucleotide probes specific for SSA transcripts. This revealed that Mex67p is required for nuclear export of heat shock mRNAs. Furthermore, other polymerase II transcripts encoding the transcriptional repressor ASH1 and the glycolytic enzyme PGK1 are shown to require Mex67p for their export into the cytoplasm. Thus, Mex67p is an mRNA export factor for a broad range of polymerase II transcripts.

Yra1p, a conserved nuclear RNA-binding protein, interacts directly with Mex67p and is required for mRNA export

Mex67p and Mtr2p constitute an essential mRNA export complex that interacts with poly(A)+ RNA and nuclear pore proteins. We have identified Yra1p, an intranuclear protein with in vitro RNA-RNA annealing activity, which directly binds to Mex67p. The complex between Yra1p and Mex67p was reconstituted in vitro and shown by UV-crosslinking to bind directly to RNA. Mutants of YRA1 are impaired in nuclear poly(A)+ RNA export at restrictive growth conditions. ALY, the mouse homologue of Yra1p and a transcriptional coactivator, can bind in vitro to yeast and human Mex67p and partly complements the otherwise non-viable yra1 null mutant. Thus, Yra1p is the first RNA-binding protein characterized, which bridges the shuttling Mex67p/Mtr2p exporter to intranuclear mRNA transport cargoes.

Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p

A fraction of the yeast nucleoporin Nic96p is localized at the terminal ring of the nuclear basket. When Nic96p was affinity purified from glutaraldehyde-treated spheroplasts, it was found to be associated with Mlp2p. Mlp2p, together with Mlp1p, are the yeast Tpr homologues, which form the nuclear pore-attached intranuclear filaments (Strambio-de-Castillia, C., Blobel, G., and Rout, M. P. (1999) J. Cell Biol. 144, 839-855). Double disruption mutants of MLP1 and MLP2 are viable and apparently not impaired in nucleocytoplasmic transport. However, overproduction of MLP1 causes nuclear accumulation of poly(A)(+) RNA in a chromatin-free area of the nucleus.

Purification of protein A-tagged yeast ran reveals association with a novel karyopherin beta family member, Pdr6p

The small GTPase Ran (encoded by GSP1 and GSP2 in yeast) plays a central role in nucleocytoplasmic transport. GSP1 and GSP2 were tagged with protein A and functionally expressed in a gsp1 null mutant. After affinity purification of protein A-tagged Gsp1p or Gsp2p by IgG-Sepharose chromatography, known karyopherin beta transport receptors (e.g. Kap121p and Kap123p) and a novel member of this protein family, Pdr6p, were found to be associated with yeast Ran. Subsequent tagging of Pdr6p with green fluorescent protein revealed association with the nuclear pore complexes in vivo. Thus, functional tagging of yeast Ran allowed the study of its in vivo distribution and interaction with known and novel Ran-binding proteins.

Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane

Human Nup93, the homologue of yeast Nic96p, is associated with a 205-kDa protein whose intracellular location and function is unknown. We show here that the yeast open reading frame YJL039c, which is homologous to this human p205, encodes the so far largest yeast nucleoporin. Accordingly, green fluorescent protein (GFP)-tagged YJL039c was localized to the nuclear pores and therefore named Nup192p. Affinity purification of ProtA-Nic96p from glutaraldehyde-fixed spheroplasts reveals association with Nup192p. NUP192 is essential for cell growth. A temperature-sensitive mutant nup192-15 is neither impaired in nuclear import of a SV40 nuclear localization sequence-containing reporter protein nor in mRNA export, but association of Nup49-GFP with nuclear pores is inhibited at the non-permissive temperature. By immunoelectron microscopy, Nup192p-ProtA is seen at the inner site of the nuclear pores, at a distance of 60 +/- 15 nm from the central plane of the pore. This suggests that Nup192p is an evolutionarily conserved structural component of the nuclear pore complex with a preferential location at the inner site of the nuclear membrane.

Nuclear RNA export in yeast

Eukaryotic cells massively exchange macromolecules (proteins and RNAs) between the nucleus and cytoplasm through the nuclear pore complexes. Whereas a mechanistic picture emerges of how proteins are imported into and exported from the nucleus, less is known about nuclear exit of the different classes of RNAs. However, the yeast Saccharomyces cerevisiae offers an experimental system to study nuclear RNA export in vivo and thus to genetically dissect the different RNA export machineries. In this review, we summarize our current knowledge and recent progress in identifying components involved in nuclear RNA export in yeast.

The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human

Human TAP is an orthologue of the yeast mRNA export factor Mex67p. In mammalian cells, TAP has a preferential intranuclear localization, but can also be detected at the nuclear pores and shuttles between the nucleus and the cytoplasm. TAP directly associates with mRNA in vivo, as it can be UV-crosslinked to poly(A)+ RNA in HeLa cells. Both the FG-repeat domain of nucleoporin CAN/Nup214 and a novel human 15 kDa protein (p15) with homology to NTF2 (a nuclear transport factor which associates with RanGDP), directly bind to TAP. When green fluorescent protein (GFP)-tagged TAP and p15 are expressed in yeast, they localize to the nuclear pores. Strikingly, co-expression of human TAP and p15 restores growth of the otherwise lethal mex67::HIS3/mtr2::HIS3 double knockout strain. Thus, the human TAP-p15 complex can functionally replace the Mex67p-Mtr2p complex in yeast and thus performs a conserved role in nuclear mRNA export.

Transfer RNA biogenesis: A visa to leave the nucleus

Only correctly folded and mature tRNAs can leave the nucleus and enter the cytoplasm. Surprisingly, tRNA-aminoacylation has been found to occur, not only in the cytosol, but also inside the nucleus, where it may act as an additional proofreading step and facilitate the export of 'ready-to-function' aminoacyl-tRNAs.

A novel in vivo assay reveals inhibition of ribosomal nuclear export in ran-cycle and nucleoporin mutants

To identify components involved in the nuclear export of ribosomes in yeast, we developed an in vivo assay exploiting a green fluorescent protein (GFP)-tagged version of ribosomal protein L25. After its import into the nucleolus, L25-GFP assembles with 60S ribosomal subunits that are subsequently exported into the cytoplasm. In wild-type cells, GFP-labeled ribosomes are only detected by fluorescence in the cytoplasm. However, thermosensitive rna1-1 (Ran-GAP), prp20-1 (Ran-GEF), and nucleoporin nup49 and nsp1 mutants are impaired in ribosomal export as revealed by nuclear accumulation of L25-GFP. Furthermore, overexpression of dominant-negative RanGTP (Gsp1-G21V) and the tRNA exportin Los1p inhibits ribosomal export. The pattern of subnuclear accumulation of L25-GFP observed in different mutants is not identical, suggesting that transport can be blocked at different steps. Thus, nuclear export of ribosomes requires the nuclear/cytoplasmic Ran-cycle and distinct nucleoporins. This assay can be used to identify soluble transport factors required for nuclear exit of ribosomes.

A novel complex of membrane proteins required for formation of a spherical nucleus

Two membrane proteins were identified through their genetic interaction with the nucleoporin Nup84p and shown to participate in nuclear envelope morphogenesis in yeast. One component is a known sporulation factor Spo7p, and the other, Nem1p, a novel protein whose C-terminal domain is conserved during eukaryotic evolution. Spo7p and Nem1p localize to the nuclear/ER membrane and behave biochemically as integral membrane proteins. Nem1p binds to Spo7p via its conserved C-terminal domain. Although cells without Spo7p or Nem1p are viable, they exhibit a drastically altered nuclear morphology with long, pore-containing double nuclear membrane extensions. These protrusions emanate from a core nucleus which contains the DNA, and penetrate deeply into the cytoplasm. Interestingly, not only Spo7(-) and Nem1(-), but also several nucleoporin mutants are defective in sporulation. Thus, Spo7p and Nem1p, which exhibit a strong genetic link to nucleoporins of the Nup84p complex, fulfil an essential role in formation of a spherical nucleus and meiotic division.

Yeast Los1p has properties of an exportin-like nucleocytoplasmic transport factor for tRNA

Saccharomyces cerevisiae Los1p, which is genetically linked to the nuclear pore protein Nsp1p and several tRNA biogenesis factors, was recently grouped into the family of importin/karyopherin-beta-like proteins on the basis of its sequence similarity. In a two-hybrid screen, we identified Nup2p as a nucleoporin interacting with Los1p. Subsequent purification of Los1p from yeast demonstrates its physical association not only with Nup2p but also with Nsp1p. By the use of the Gsp1p-G21V mutant, Los1p was shown to preferentially bind to the GTP-bound form of yeast Ran. Furthermore, overexpression of full-length or N-terminally truncated Los1p was shown to have dominant-negative effects on cell growth and different nuclear export pathways. Finally, Los1p could interact with Gsp1p-GTP, but only in the presence of tRNA, as revealed in an indirect in vitro binding assay. These data confirm the homology between Los1p and the recently identified human exportin for tRNA and reinforce the possibility of a role for Los1p in nuclear export of tRNA in yeast.