bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S2 from Prediction of Response to Lenvatinib Monotherapy for Unresectable Hepatocellular Carcinoma by Machine Learning Radiomics: A Multicenter Cohort Study
Authors: Bo Zhiyuan , Chen Bo , Zhao Zhengxiao , He Qikuan , Mao Yicheng , Yang Yunjun , Yao Fei , Yang Yi , Chen Ziyan , Yang Jinhuan , Yu Haitao , Ma Jun , Wu Lijun , Chen Kaiyu , Wang Luhui , Wang Mingxun , Shi Zhehao , Yao Xinfei , Dong Yulong , Shi Xintong , Shan Yunfeng , Yu Zhengping , Wang Yi , Chen Gang
Published: April 2023

Representative segmentation of ROIs and primary CECT images of HCC patients that exhibited PR and PD. (A) Primary image and ROI (red region) marked image from a patient with PR; (B) Primary image and ROI (blue region) marked image from a patient with PD; (C) pretreatment and post-treatment CECT images from a patient who shows PR; (D) pretreatment and post-treatment CECT images from a patient who shows PD. Abbreviations: HCC, hepatocellular carcinoma; ROI, region of interest; CECT, contrast enhanced computed tomography; PR, partial response; PD, progressive disease.
Supplementary Table S3 from Beneficial Effects of Mifepristone Treatment in Patients with Breast Cancer Selected by the Progesterone Receptor Isoform Ratio: Results from the MIPRA Trial
Authors: Elía Andrés , Saldain Leo , Vanzulli Silvia I. , Helguero Luisa A. , Lamb Caroline A. , Fabris Victoria , Pataccini Gabriela , Martínez-Vazquez Paula , Burruchaga Javier , Caillet-Bois Ines , Spengler Eunice , Acosta Haab Gabriela , Liguori Marcos , Castets Alejandra , Lovisi Silvia , Abascal María F. , Novaro Virginia , Sánchez Jana , Muñoz Javier , Belizán José M. , Abba Martín C. , Gass Hugo , Rojas Paola , Lanari Claudia
Published: April 2023

Morphological features of tumors before and after mifepristone treatment
Supplementary Methods from Beneficial Effects of Mifepristone Treatment in Patients with Breast Cancer Selected by the Progesterone Receptor Isoform Ratio: Results from the MIPRA Trial
Authors: Elía Andrés , Saldain Leo , Vanzulli Silvia I. , Helguero Luisa A. , Lamb Caroline A. , Fabris Victoria , Pataccini Gabriela , Martínez-Vazquez Paula , Burruchaga Javier , Caillet-Bois Ines , Spengler Eunice , Acosta Haab Gabriela , Liguori Marcos , Castets Alejandra , Lovisi Silvia , Abascal María F. , Novaro Virginia , Sánchez Jana , Muñoz Javier , Belizán José M. , Abba Martín C. , Gass Hugo , Rojas Paola , Lanari Claudia
Published: April 2023

Morphological evaluation of CNBs and matched surgical samples; RNA-Seq analysis; Proteomics
Figure FS5 from Allogeneic CAR T Cells Targeting DLL3 Are Efficacious and Safe in Preclinical Models of Small Cell Lung Cancer
Authors: Zhang Yi , Tacheva-Grigorova Silvia K. , Sutton Janette , Melton Zea , Mak Yvonne S.L. , Lay Cecilia , Smith Bryan A. , Sai Tao , Van Blarcom Thomas , Sasu Barbra J. , Panowski Siler H.
Published: April 2023

Fig. S5. Clone 4 showed pancreatic membrane staining in one of three TCR studies but other derisking studies suggest the staining may be artifactual.
Supplementary Table S2 from A Phase II Window of Opportunity Study of Neoadjuvant PD-L1 versus PD-L1 plus CTLA-4 Blockade for Patients with Malignant Pleural Mesothelioma
Authors: Lee Hyun-Sung , Jang Hee-Jin , Ramineni Maheshwari , Wang Daniel Y. , Ramos Daniela , Choi Jong Min , Splawn Taylor , Espinoza Monica , Almarez Michelle , Hosey Leandria , Jo Eunji , Hilsenbeck Susan , Amos Christopher I. , Ripley R. Taylor , Burt Bryan M.
Published: April 2023

Supplementary Table 2. Preoperative adverse events, defined as AEs observed after ICB and before surgery
Supplementary Figure S9 from A Phase II Window of Opportunity Study of Neoadjuvant PD-L1 versus PD-L1 plus CTLA-4 Blockade for Patients with Malignant Pleural Mesothelioma
Authors: Lee Hyun-Sung , Jang Hee-Jin , Ramineni Maheshwari , Wang Daniel Y. , Ramos Daniela , Choi Jong Min , Splawn Taylor , Espinoza Monica , Almarez Michelle , Hosey Leandria , Jo Eunji , Hilsenbeck Susan , Amos Christopher I. , Ripley R. Taylor , Burt Bryan M.
Published: April 2023

Supplementary Figure 9. Alteration of naïve T (Tnaive) and stem cell-like memory T (Tscm)
cells in PBMCs and BMMCs.
Supplementary Figure S7 from Elucidating the Genetic Landscape of Oral Leukoplakia to Predict Malignant Transformation
Authors: Wils Leon J. , Poell Jos B. , Brink Arjen , Evren Ilkay , Brouns Elisabeth R. , de Visscher Jan G.A.M. , Bloemena Elisabeth , Brakenhoff Ruud H.
Published: April 2023

Overview of type of changes found in 12 target genes in 89 OL samples. Top: In the left graph the distribution of the classes of mutations is depicted. In the middle graph the type of variants is shown. In the right graph the nucleotide changes are indicated. Bottom: In the left graph the number of mutations per sample is indicated. In the middle graph the number of variant classes found per sample is shown. In the right graph the top 10 mutated genes are depicted. Del = deletion. Ins = insert. SNP = single nucleotide polymorphism. SNV = Single nucleotide variant.
Supplementary Figure S6 from Elucidating the Genetic Landscape of Oral Leukoplakia to Predict Malignant Transformation
Authors: Wils Leon J. , Poell Jos B. , Brink Arjen , Evren Ilkay , Brouns Elisabeth R. , de Visscher Jan G.A.M. , Bloemena Elisabeth , Brakenhoff Ruud H.
Published: April 2023

Copy number profiles and mutations for biopsies from the oral leukoplakia and the tumor from two patients that have a different origin. For each lesion the location, the copy number profile and the mutations are shown. For each mutation the gene, the variant allele frequency (VAF) and amino acid change is indicated.
Supplementary Data DS1 from LAMC2 Regulates Key Transcriptional and Targetable Effectors to Support Pancreatic Cancer Growth
Authors: Erice Oihane , Narayanan Shruthi , Feliu Iker , Entrialgo-Cadierno Rodrigo , Malinova Antonia , Vicentini Caterina , Guruceaga Elizabeth , Delfino Pietro , Trajkovic-Arsic Marija , Moreno Haritz , Valencia Karmele , Blanco Ester , Macaya Irati , Öhlund Daniel , Khatri Purvesh , Lecanda Fernando , Scarpa Aldo , Siveke Jens T. , Corbo Vincenzo , Ponz-Sarvise Mariano , Vicent Silve
Published: April 2023

This file includes the Suppl. Methods, Table (1) and References
Table S4 from Dynamic Mutational Landscape of Cerebrospinal Fluid Circulating Tumor DNA and Predictors of Survival after Proton Craniospinal Irradiation for Leptomeningeal Metastases
Authors: Wijetunga N. Ari , Goglia Alexander G. , Weinhold Nils , Berger Michael F. , Cislo Michael , Higginson Daniel S. , Chabot Kiana , Osman Ahmed M. , Schaff Lauren , Pentsova Elena , Miller Alexandra M. , Powell Simon N. , Boire Adrienne , Yang Jonathan T.
Published: April 2023

Gene set enrichment analysis
Supplementary Data Table 6 from Bolus versus Continuous Intravenous Delivery of Doxorubicin in Soft-Tissue Sarcomas: Post Hoc Analysis of a Prospective Randomized Trial (SARC021/TH CR-406)
Authors: Cranmer Lee D. , Lu Yao , Heise Rachel S. , Ballman Karla V. , Loggers Elizabeth T. , Pollack Seth M. , Wagner Michael J. , Reinke Denise K. , Schöffski Patrick , Tap William D.
Published: April 2023

Univariable logistic regression of objective response (partial and complete).
Table S1 from Dynamic Mutational Landscape of Cerebrospinal Fluid Circulating Tumor DNA and Predictors of Survival after Proton Craniospinal Irradiation for Leptomeningeal Metastases
Authors: Wijetunga N. Ari , Goglia Alexander G. , Weinhold Nils , Berger Michael F. , Cislo Michael , Higginson Daniel S. , Chabot Kiana , Osman Ahmed M. , Schaff Lauren , Pentsova Elena , Miller Alexandra M. , Powell Simon N. , Boire Adrienne , Yang Jonathan T.
Published: April 2023

Read sequencing depth by sample
Supplementary Table S3 from Impact of RNA Signatures on pCR and Survival after 12-Week Neoadjuvant Pertuzumab plus Trastuzumab with or without Paclitaxel in the WSG-ADAPT HER2+/HR− Trial
Authors: Graeser Monika , Gluz Oleg , Biehl Claudia , Ulbrich-Gebauer Daniel , Christgen Matthias , Palatty Jenci , Kuemmel Sherko , Grischke Eva-Maria , Augustin Doris , Braun Michael , Potenberg Jochem , Wuerstlein Rachel , Krauss Katja , Schumacher Claudia , Forstbauer Helmut , Reimer Toralf , Stefek Andrea , Fischer Hans Holger , Pelz Enrico , zu Eulenburg Christine , Kates Ronald , Ni Hua , Kolberg-Liedtke Cornelia , Feuerhake Friedrich , Kreipe Hans Heinrich , Nitz Ulrike , Harbeck Nadia
Published: April 2023

Supplementary Table 3 shows associations between the genes in ER signaling signature and pCR
Supplementary Table S4 from Loss of CDKN2A Cooperates with WWTR1(TAZ)–CAMTA1 Gene Fusion to Promote Tumor Progression in Epithelioid Hemangioendothelioma
Authors: Seavey Caleb N. , Hallett Andrea , Li Shuo , Che Kepeng , Pobbati Ajaybabu V. , Ma Shuang , Burtscher Ashley , Kanai Ryan , Lamar John M. , Rubin Brian P.
Published: April 2023

Supplemental Table 4. Bulk RNA sequencing of EHE cell lines
Differential gene expression between EHE cell lines and endothelial cells via DESEQ2. Overlap in transcripts that are overexpressed by EHE cells (LogFC2>2 and FDR<0.05) are listed. These overlaps were used to generate the Venn diagram in Figure 4G.
Supplementary Data S3 from Exploring the Immunogenicity of Noncanonical HLA-I Tumor Ligands Identified through Proteogenomics
Authors: Lozano-Rabella Maria , Garcia-Garijo Andrea , Palomero Jara , Yuste-Estevanez Anna , Erhard Florian , Farriol-Duran Roc , Martín-Liberal Juan , Ochoa-de-Olza Maria , Matos Ignacio , Gartner Jared J. , Ghosh Michael , Canals Francesc , Vidal August , Piulats Josep Maria , Matías-Guiu Xavier , Brana Irene , Muñoz-Couselo Eva , Garralda Elena , Schlosser Andreas , Gros Alena
Published: April 2023

Tumor cell line HLA-I typing and tumor type
Supplementary Data 2 from Crizotinib Has Preclinical Efficacy in Philadelphia-Negative Myeloproliferative Neoplasms
Authors: Gurska Lindsay M. , Okabe Rachel , Schurer Alexandra , Tong Meng Maxine , Soto Mark , Choi Daniel , Ames Kristina , Glushakow-Smith Shira , Montoya Allison , Tein Ellen , Miles Linde A. , Cheng Haiying , Hankey-Giblin Pamela , Levine Ross L. , Goel Swati , Halmos Balazs , Gritsman Kira
Published: April 2023

Table S2
Supplementary Figure S1 from Intratumoral CD16+ Macrophages Are Associated with Clinical Outcomes of Patients with Metastatic Melanoma Treated with Combination Anti-PD-1 and Anti-CTLA-4 Therapy
Authors: Lee Hansol , Ferguson Angela L. , Quek Camelia , Vergara Ismael A. , Pires daSilva Ines , Allen Ruth , Gide Tuba Nur , Conway Jordan W. , Koufariotis Lambros T. , Hayward Nicholas K. , Waddell Nicola , Carlino Matteo S. , Menzies Alexander M. , Saw Robyn P.M. , Shklovskaya Elena , Rizos Helen , Lo Serigne , Scolyer Richard A. , Long Georgina V. , Palendira Umaimainthan , Wilmott James S.
Published: April 2023

Cohort and dataset overview
Supplementary Data1 from A Phase I/II Open-Label Study of Molibresib for the Treatment of Relapsed/Refractory Hematologic Malignancies
Authors: Dawson Mark A. , Borthakur Gautam , Huntly Brian J.P. , Karadimitris Anastasios , Alegre Adrian , Chaidos Aristeidis , Vogl Dan T. , Pollyea Daniel A. , Davies Faith E. , Morgan Gareth J. , Glass Jacob L. , Kamdar Manali , Mateos Maria-Victoria , Tovar Natalia , Yeh Paul , Delgado Regina García , Basheer Faisal , Marando Ludovica , Gallipoli Paolo , Wyce Anastasia , Krishnatry Anu Shilpa , Barbash Olena , Bakirtzi Evi , Ferron-Brady Geraldine , Karpinich Natalie O. , McCabe Michael T. , Foley Shawn W. , Horner Thierry , Dhar Arindam , Kremer Brandon E. , Dickinson Michael
Published: April 2023

Supplementary Methods
Supplementary Table S1 from Longer versus Shorter Schedules of Vincristine, Irinotecan, and Temozolomide (VIT) for Relapsed or Refractory Ewing Sarcoma: A Randomized Controlled Phase 2 Trial
Authors: Xu Jie , Xie Lu , Sun Xin , Liu Kuisheng , Liang Xin , Cai Zhenyu , Tang Xiaodong , Guo Wei
Published: April 2023

Synopsis of Protocol
Supplementary Movie S8 from Anticoagulants Enhance Molecular and Cellular Immunotherapy of Cancer by Improving Tumor Microcirculation Structure and Function and Redistributing Tumor Infiltrates
Authors: Wei Fang , Su Yuling , Quan Yibo , Li Xiaojia , Zou Qi , Zhang Liuxi , Li Shu , Jiang Mengmeng , Lin Guohuan , Liang Ping , He Jie , Xie Keping
Published: April 2023

Supplementary Movie S8. IVIM in vivo imaging was used to observe that heparin promoted the infiltration of transferred CD8+ T cells into Panc02 orthotopic tumors. The video corresponded to the experiment shown in Figure 6B. Representative images at 48h of heparin combined with CD8+ T adoptive transfer group were shown in Figure 6B (Blue, angiography Evans Blue; Green, CFSE-CD8+ T cells).
Supplementary Movie S5 from Anticoagulants Enhance Molecular and Cellular Immunotherapy of Cancer by Improving Tumor Microcirculation Structure and Function and Redistributing Tumor Infiltrates
Authors: Wei Fang , Su Yuling , Quan Yibo , Li Xiaojia , Zou Qi , Zhang Liuxi , Li Shu , Jiang Mengmeng , Lin Guohuan , Liang Ping , He Jie , Xie Keping
Published: April 2023

Supplementary Movie S5. IVIM in vivo imaging was used to observe that heparin promoted the infiltration of transferred CD8+ T cells into Panc02 orthotopic tumors. The video corresponded to the experiment shown in Figure 6B. Representative images at 6h of heparin combined with CD8+ T adoptive transfer group were shown in Figure 6B (Blue, angiography Evans Blue; Green, CFSE-CD8+ T cells).
Data from Molecular Subtypes of Breast Cancers Detected in Mammography Screening and Outside of Screening
Authors: Sihto Harri , Lundin Johan , Lehtimäki Tiina , Sarlomo-Rikala Maarit , Bützow Ralf , Holli Kaija , Sailas Liisa , Kataja Vesa , Lundin Mikael , Turpeenniemi-Hujanen Taina , Isola Jorma , Heikkilä Päivi , Joensuu Heikki
Published: April 2023

Abstract
Purpose: The frequency and significance of gene expression profile-derived molecular subtypes of breast cancers found in mammography screening are unknown.

Experimental Design: We identified breast cancers diagnosed in women of any age living in defined geographic regions in Finland in 1991 to 1992 and collected clinical and pathologic data. Surrogates for the molecular subtypes were determined for 247 cancers found in organized mammography screening and 989 cancers detected outside of screening using immunohistochemistry or in situ hybridization. Molecular subtypes were defined as luminal A [estrogen receptor (ER) positive and/or progesterone receptor (PR) positive, HER2-], luminal B (ER+ and/or PR+, HER2+), basal-like (ER-, PR-, HER2-, cytokeratin 5+, and/or HER1+), HER2+/ER- (ER-, PR-, and HER2+), and unclassified. The median follow-up time was 9.4 years.

Results: The luminal type A was common (73.7%) and the HER2+/ER- type is rare (5.7%) in screen-detected cancer, and only 16% were HER2 positive. Women with cancer diagnosed in screening at ages 50 to 69 years had similar molecular subtype distribution as women whose cancer was found outside of screening at age >69 years. In a multivariate model, cancer detection at screening independently predicted favorable distant disease-free survival when the molecular subtype was included as a covariate in addition to age, histologic grade, and cancer size. Women with small (pT1N0M0) HER2-positive cancer had similar outcome regardless of the method of detection.

Conclusions: Molecular subtype distribution of screen-detected breast cancer differs from that of cancers found outside of screening and accounts in part for the better outcome of screen-detected cancer.
Data from Oncostatin M Induces Bone Loss and Sensitizes Rat Osteosarcoma to the Antitumor Effect of Midostaurin In vivo
Authors: Brounais Bénédicte , Chipoy Céline , Mori Kanji , Charrier Céline , Battaglia Séverine , Pilet Paul , Richards Carl D. , Heymann Dominique , Rédini Françoise , Blanchard Frédéric
Published: April 2023

Abstract
Purpose: In cultures, the cytokine oncostatin M (OSM) reduces the growth and induces differentiation of osteoblasts and osteosarcoma cells into glial/osteocytic cells. Moreover, OSM sensitizes these cells to apoptosis driven by various death inducers such as the kinase inhibitor staurosporine. Here, we asked whether OSM would have similar effects in vivo.

Experimental Design: Adenoviral gene transfer of OSM (AdOSM) was done in naive and osteosarcoma-bearing rats, alone or in combination with Midostaurin (PKC412), a derivative of staurosporine currently used in cancer clinical trials. Bone variables were analyzed by micro-computed tomography scanner, by histology, and by the levels of various serum bone markers. Osteosarcoma progression was analyzed by the development of the primary bone tumor, evolution of pulmonary metastasis, histology (necrosis and fibrosis), and animal survival.

Results: In naive rats, AdOSM reduced serum osteoblastic and osteoclastic markers in correlation with a reduced trabecular bone volume. In an osteosarcoma rat model, the combination of AdOSM with PKC412 reduced the progression of the primary bone tumor, pulmonary metastatic dissemination, and increased overall survival, whereas these agents alone had no antitumor effect. Increased tumor necrosis and tissue repair (fibrosis) were observed with this combination.

Conclusion: These in vivo experiments confirm that systemic OSM overexpression alters osteoblast/osteosarcoma activity. Because OSM sensitizes rat osteosarcoma to apoptosis/necrosis, the use of kinase inhibitors such as Midostaurin in association with OSM could represent new adjuvant treatments for this aggressive malignancy.
Data from Molecularly Targeted Radiosensitization of Human Prostate Cancer by Modulating Inhibitor of Apoptosis
Authors: Dai Yao , Liu Meilan , Tang Wenhua , DeSano Jeffrey , Burstein Ezra , Davis Mary , Pienta Kenneth , Lawrence Theodore , Xu Liang
Published: April 2023

Abstract
Purpose: The inhibitor of apoptosis proteins (IAP) are overexpressed in hormone-refractory prostate cancer, rendering the cancer cells resistant to radiation. This study aims to investigate the radiosensitizing effect of small-molecule IAP inhibitor both in vitro and in vivo in androgen-independent prostate cancer and the possible mechanism of radiosensitization.

Experimental Design: Radiosensitization of SH-130 in human prostate cancer DU-145 cells was determined by clonogenic survival assay. Combination effect of SH-130 and ionizing radiation was evaluated by apoptosis assays. Pull-down and immunoprecipitation assays were employed to investigate the interaction between SH-130 and IAPs. DU-145 xenografts in nude mice were treated with SH-130, radiation, or combination, and tumor suppression effect was determined by caliper measurement or bioluminescence imaging. Nuclear factor-κB activation was detected by luciferase reporter assay and quantitative real-time PCR.

Results: SH-130 potently enhanced radiation-induced caspase activation and apoptosis in DU-145 cells. Both X-linked IAP and cIAP-1 can be pulled down by SH-130 but not by inactive SH-123. Moreover, SH-130 interrupted interaction between X-linked IAP/cIAP-1 and Smac. In a nude mouse xenograft model, SH-130 potently sensitized the DU-145 tumors to X-ray radiation without increasing systemic toxicity. The combination therapy suppressed tumor growth more significantly than either treatment alone, with over 80% of complete tumor regression. Furthermore, SH-130 partially blocked tumor necrosis factor-α- and radiation-induced nuclear factor-κB activation in DU-145 cells.

Conclusions: Our results show that small-molecule inhibitors of IAPs can overcome apoptosis resistance and radiosensitize human prostate cancer with high levels of IAPs. Molecular modulation of IAPs may improve the outcome of prostate cancer radiotherapy.
Data from High Skp2 Expression Characterizes High-Risk Neuroblastomas Independent of MYCN Status
Authors: Westermann Frank , Henrich Kai-Oliver , Wei Jun S. , Lutz Werner , Fischer Matthias , König Rainer , Wiedemeyer Ruprecht , Ehemann Volker , Brors Benedikt , Ernestus Karen , Leuschner Ivo , Benner Axel , Khan Javed , Schwab Manfred
Published: April 2023

Abstract
Purpose: Amplified MYCN oncogene defines a subgroup of neuroblastomas with poor outcome. However, a substantial number of MYCN single-copy neuroblastomas exhibits an aggressive phenotype similar to that of MYCN-amplified neuroblastomas even in the absence of high MYCN mRNA and/or protein levels.

Experimental Design: To identify shared molecular mechanisms that mediate the aggressive phenotype in MYCN-amplified and single-copy high-risk neuroblastomas, we defined genetic programs evoked by ectopically expressed MYCN in vitro and analyzed them in high-risk versus low-risk neuroblastoma tumors (n = 49) using cDNA microarrays. Candidate gene expression was validated in a separate cohort of 117 patients using quantitative PCR, and protein expression was analyzed in neuroblastoma tumors by immunoblotting and immunohistochemistry.

Results: We identified a genetic signature characterized by a subset of MYCN/MYC and E2F targets, including Skp2, encoding the F-box protein of the SCFSkp2 E3-ligase, to be highly expressed in high-risk neuroblastomas independent of amplified MYCN. We validated the findings for Skp2 and analyzed its expression in relation to MYCN and E2F-1 expression in a separate cohort (n = 117) using quantitative PCR. High Skp2 expression proved to be a highly significant marker of dire prognosis independent of both MYCN status and disease stage, on the basis of multivariate analysis of event-free survival (hazard ratio, 3.54; 95% confidence interval, 1.56-8.00; P = 0.002). Skp2 protein expression was inversely correlated with expression of p27, the primary target of the SCFSkp2 E3-ligase, in neuroblastoma tumors.

Conclusion: Skp2 may have a key role in the progression of neuroblastomas and should make an attractive target for therapeutic approaches.
Data from Loss of SNF5 Expression Correlates with Poor Patient Survival in Melanoma
Authors: Lin Hanyang , Wong Ronald P.C. , Martinka Magdalena , Li Gang
Published: April 2023

Abstract
Purpose: Aberrant expression of SWI/SNF chromatin remodeling complex is involved in cancer development. The tumor suppressor SNF5, the core subunit of SWI/SNF complex, has been shown to regulate cell differentiation, cell cycle control, and apoptosis. To investigate the role of SNF5 in the development of melanoma, we examined the expression of SNF5 in melanocytic lesions at different stages and analyzed the correlation between SNF5 expression and clinicopathologic variables and patient survival.

Experimental Design: Using tissue microarry and immunohistochemistry, we evaluated SNF5 staining in 51 dysplastic nevi, 88 primary melanomas, and 48 metastatic melanomas. We studied chemosensitivity of melanoma cells with reduced SNF5 expression by siRNA using cell survival and apoptosis assays.

Results: SNF5 expression was reduced in metastatic melanoma compared with dysplastic nevi (P = 0.005), in advanced primary melanoma (Clark's level V) compared with low risk Clark's level II melanoma (P = 0.019), and in melanoma at sun-exposed sites compared with sun-protected sites (P = 0.044). Furthermore, we showed a strong correlation between negative SNF5 expression and a worse 5-year survival in melanoma patients (P = 0.016). Multivariate Cox regression analysis revealed that negative SNF5 expression is an independent prognostic factor to predict patient outcome in primary melanomas (P = 0.031). Finally, we showed that knockdown of SNF5 in melanoma cell lines resulted in significant chemoresistance.

Conclusions: Our data indicate that SNF5 may be an important marker for human melanoma progression and prognosis as well as a potential therapeutic target. (Clin Cancer Res 2009;15(20):6404–11)
Data from HER3 Is a Determinant for Poor Prognosis in Melanoma
Authors: Reschke Markus , Mihic-Probst Daniela , van der Horst Edward Htun , Knyazev Pjotr , Wild Peter J. , Hutterer Markus , Meyer Stefanie , Dummer Reinhard , Moch Holger , Ullrich Axel
Published: April 2023

Abstract
Purpose: The epidermal growth factor receptor family member HER3 is overexpressed in diverse human cancers and has been associated with poor prognosis in breast, lung, and ovarian cancer. However, the relevance of HER3 with regard to its prognostic significance and function in primary melanoma and metastases remains largely elusive.

Experimental Design: HER3 protein expression was analyzed immunohistochemically using tissue microarrays of 130 primary melanoma and 87 metastases relative to established clinical variables. The possibility of an influence of HER3 on melanoma cell proliferation, migration, invasion, and chemotherapy-induced apoptosis was studied in human melanoma cell lines.

Results: We show that HER3 is frequently expressed in malignant melanoma and metastases at elevated levels. High HER3 expression may serve as a prognostic marker because it correlates with cell proliferation, tumor progression, and reduced patient survival. Suppression of HER3 expression by RNA interference reduces melanoma cell proliferation, migration, and invasion in vitro. In addition, down-regulation of HER3 synergistically enhances dacarbazine-induced apoptosis. Moreover, monoclonal antibodies specific for the extracellular portion of HER3 efficiently block heregulin-induced proliferation, migration, and invasion of melanoma cell lines.

Conclusion: Our results provide novel insights into the role of HER3 in melanoma and point out new possibilities for therapeutic intervention.
Data from Targeting the Phosphoinositide 3-Kinase Isoform p110δ Impairs Growth and Survival in Neuroblastoma Cells
Authors: Boller Danielle , Schramm Alexander , Doepfner Kathrin T. , Shalaby Tarek , von Bueren André O. , Eggert Angelika , Grotzer Michael A. , Arcaro Alexandre
Published: April 2023

Abstract
Purpose: The phosphoinositide 3-kinase (PI3K)/Akt pathway is frequently activated in human cancer and plays a crucial role in neuroblastoma biology. We were interested in gaining further insight into the potential of targeting PI3K/Akt signaling as a novel antiproliferative approach in neuroblastoma.

Experimental Design: The expression pattern and functions of class IA PI3K isoforms were investigated in tumor samples and cell lines. Effects on cell survival and downstream signaling were analyzed following down-regulation of p110α or p110δ in SH-SY5Y and LA-N-1 cells by means of RNA interference.

Results: Overexpression of the catalytic p110δ and regulatory p85α isoforms was detected in a panel of primary neuroblastoma samples and cell lines, compared with normal adrenal gland tissue. Although down-regulation of either p110α or p110δ led to impaired cell growth, reduced expression of p110δ also had a selective effect on the survival of SH-SY5Y cells. Decreased levels of p110δ were found to induce apoptosis and lead to lower expression levels of antiapoptotic Bcl-2 family proteins. SH-SY5Y cells with decreased p110δ levels also displayed reduced activation of ribosomal protein S6 kinase in response to stimulation with epidermal growth factor and insulin-like growth factor-I.

Conclusions: Together, our data reveal a novel function of p110δ in neuroblastoma growth and survival.
Data from Novel Jet-Injection Technology for Nonviral Intratumoral Gene Transfer in Patients with Melanoma and Breast Cancer
Authors: Walther Wolfgang , Siegel Robert , Kobelt Dennis , Knösel Thomas , Dietel Manfred , Bembenek Andreas , Aumann Jutta , Schleef Martin , Baier Ruth , Stein Ulrike , Schlag Peter M.
Published: April 2023

Abstract
Purpose: This phase I clinical trial evaluated safety, feasibility, and efficiency of nonviral intratumoral jet-injection gene transfer in patients with skin metastases from melanoma and breast cancer.

Experimental Design: Seventeen patients were enrolled. The patients received five jet injections with a total dose of 0.05 mg β-galactosidase (LacZ)-expressing plasmid DNA (pCMVβ) into a single cutaneous lesion. Clinical and laboratory safety monitoring were done. Systemic plasmid clearance was monitored by quantitative real-time PCR of blood samples throughout the study. All lesions were resected after 2 to 6 days. Intratumoral plasmid DNA load, DNA distribution, and LacZ expression was analyzed by quantitative real-time PCR, quantitative reverse transcription-PCR, Western blot, immunohistochemistry, and 5-bromo-4-chloro-3-indolyl-β-d-galactoside staining.

Results: Jet injection of plasmid DNA was safely done in all patients. No serious side effects were observed. Thirty minutes after jet injection, peak plasmid DNA levels were detected in the blood followed by rapid decline and clearance. Plasmid DNA and LacZ mRNA and protein expression were detected in all treated lesions. Quantitative analysis revealed a correlation of plasmid DNA load and LacZ-mRNA expression confirmed by Western blot. Immunohistochemistry and 5-bromo-4-chloro-3-indolyl-β-d-galactoside staining showed LacZ-protein throughout the tumor. Transfected tumor areas were found close and distant to the jet-injection site with varying levels of DNA load and transgene expression.

Conclusion: Intratumoral jet injection of plasmid DNA led to efficient LacZ reporter gene expression in all patients. No side effects were experienced, supporting safety and applicability of this novel nonviral approach. A next step with a therapeutic gene product should determine antitumor efficacy of jet-injection gene transfer.
Data from Activation of Notch Signaling in a Xenograft Model of Brain Metastasis
Authors: Nam Do-Hyun , Jeon Hye-Min , Kim Shiyeon , Kim Mi Hyun , Lee Young-Ju , Lee Min Su , Kim Hyunggee , Joo Kyeung Min , Lee Dong-Sup , Price Janet E. , Bang Sa Ik , Park Woong-Yang
Published: April 2023

Abstract
Purpose: The potential of metastasis can be predicted from clinical features like tumor size, histologic grade, and gene expression patterns. We examined the whole-genome transcriptomic profile of a xenograft model of breast cancer to understand the characteristics of brain metastasis.

Experimental Design: Variants of the MDA-MB-435 cell were established from experimental brain metastases. The LvBr2 variant was isolated from lesions in a mouse injected in the left ventricle of the heart, and these cells were used for two cycles of injection into the internal carotid artery and selection of brain lesions, resulting in the Br4 variant. To characterize the different metastatic variants, we examined the gene expression profile of MDA-MB-435, LvBr2, and Br4 cells using microarrays.

Results: We could identify 2,016 differentially expressed genes in Br4 by using the F test. Various metastasis-related genes and a number of genes related to angiogenesis, migration, tumorigenesis, and cell cycle were differentially expressed by the Br4 cells. Notably, the Notch signaling pathway was activated in Br4, with increased Jag2 mRNA, activated Notch intracellular domain, and Notch intracellular domain/CLS promoter-luciferase activity. Br4 cells were more migratory and invasive than MDA-MB-435 cells in collagen and Matrigel Transwell assays, and the migration and invasion of Br4 cells were significantly inhibited by inactivation of Notch signaling using DAPT, a γ-secretase inhibitor, and RNA interference–mediated knockdown of Jagged 2 and Notch1.

Conclusions: Taken together, these results suggest that we have isolated variants of a human cancer cell line with enhanced brain metastatic properties, and the activation of Notch signaling might play a crucial role in brain metastasis.
Data from Stromal Matrix Protein Expression Following Preoperative Systemic Therapy in Breast Cancer
Authors: Tokes Anna-Maria , Szasz Attila Marcell , Farkas Andrea , Toth Adrienn Ildiko , Dank Magdolna , Harsanyi Laszlo , Molnar Bela Akos , Molnar Istvan Arthur , Laszlo Zsolt , Rusz Zoltan , Kulka Janina
Published: April 2023

Abstract
Purpose: Stromal alterations are observed following preoperative systemic therapy in breast cancer. The aim of the present study was to analyze the qualitative and quantitative changes of representative tumor stroma proteins in the context of neoadjuvant therapy and the response of patients undergoing preoperative systemic therapy.

Experimental Design: Fifty women receiving preoperative systemic therapy were evaluated for clinical and pathologic parameters. Clinical response was defined according to International Union against Cancer (UICC) criteria, whereas pathologic responses to preoperative systemic therapy were defined according to the Chevallier and Sataloff classifications. The expression of tenascin-C, syndecan-1, collagen IV, and smooth muscle actin proteins was investigated using morphometric analysis of immunohistochemical reactions. Quantitative reverse transcription-PCR was done to evaluate the mRNA expression level of syndecan-1 and tenascin-C. The data were compared with 20 breast cancer samples of patients not treated with preoperative systemic therapy.

Results: According to UICC criteria, the expression levels of collagen IV were up-regulated in all preoperative systemic therapy–treated patients (P = 0.002). Collagen IV was up-regulated in the preoperative systemic therapy group in both Chevallier and Sataloff classifications compared with the control cases (P = 0.025 and P = 001, respectively). There were no significant differences in the expression of smooth muscle actin between the treated and nontreated groups. The syndecan-1 proteoglycan level was significantly down-regulated in the preoperative systemic therapy group (Chevallier classes P = 0.015, Sataloff classes P = 0.015). Tenascin-C was up-regulated in women with progressive disease (P = 0.005).

Conclusion: We have observed that the stromal component of breast carcinomas following preoperative systemic therapy differs from the nontreated tumors, which can be evaluated with the analysis of the above mentioned proteins.
Data from Overexpression of Class III β-Tubulin Predicts Good Response to Taxane-Based Chemotherapy in Ovarian Clear Cell Adenocarcinoma
Authors: Aoki Daisuke , Oda Yoshinao , Hattori Satoshi , Taguchi Ken-ichi , Ohishi Yoshihiro , Basaki Yuji , Oie Shinji , Suzuki Nao , Kono Suminori , Tsuneyoshi Masazumi , Ono Mayumi , Yanagawa Takashi , Kuwano Michihiko
Published: April 2023

Abstract
Purpose: Of the various microtubule-associated molecules, β-tubulin III has been reported to be closely associated with the therapeutic efficacy of taxane-based chemotherapy against ovarian cancer. Stathmin and microtubule-associated protein 4 (MAP4) have been reported to play an important role in microtubule stabilization. In this study, we investigated whether expression of these microtubule-associated factors affects the therapeutic efficacy of taxane-based chemotherapy in ovarian clear cell adenocarcinoma.

Experimental Design: Drug sensitivity of paclitaxel or cisplatin was assessed in ovarian cancer cell lines treated with small interfering RNA of tubulin isoforms, MAP4, and stathmin. We examined 94 surgically resected ovarian clear cell adenocarcinoma specimens from patients treated with taxane-containing regimens (n = 44) and with taxane-free regimens (n = 50), using immunohistochemistry to detect expression of β-tubulin III, stathmin, and MAP4.

Results: Knockdown of β-tubulin III and IV specifically conferred drug resistance to paclitaxel in one ovarian cancer cell line, but not to other molecules. Estimated overall survival revealed a significant synergistic effect between taxane and β-tubulin III in patients with ovarian clear cell adenocarcinoma. Of three microtubule-related molecules, among the taxane-based chemotherapy group, cases with higher β-tubulin III expression were associated with a significantly more favorable prognosis compared with those having lower β-tubulin III expression. By contrast, there was no statistical significance in the synergistic relationships between stathmin and taxane or between MAP4 and taxane.

Conclusions: Taxane-based chemotherapy was effective for patients with ovarian clear cell adenocarcinomas who were positive for β-tubulin III but not for those who were negative for these proteins.
Data from Clinical Pharmacokinetics of Amifostine and WR1065 in Pediatric Patients with Medulloblastoma
Authors: McKibbin Trevor , Panetta John C. , Fouladi Maryam , Gajjar Amar , Bai Feng , Okcu M. Fatih , Stewart Clinton F.
Published: April 2023

Abstract
Purpose: We evaluated the pharmacokinetics of amifostine and WR1065 in pediatric patients with newly diagnosed medulloblastoma to assess the influence of patient covariates, including demographics, clinical characteristics, and genetic polymorphisms, on amifostine and WR1065 pharmacokinetic parameters.

Experimental Design: We assessed the pharmacokinetics of amifostine and WR1065 in 33 children who received amifostine (1-minute infusion, 600 mg/m2) just before the start of and 3 hours into a 6-hour cisplatin infusion. Serial blood samples were collected after doses 1 (0 hour) and 2 (3 hours) of course 1. Amifostine and WR1065 were quantitated by high performance liquid chromatography with electrochemical detection. A pharmacokinetic model was simultaneously fit to amifostine and WR1065 plasma or whole blood concentration-versus-time data. The influence of demographic, biochemical, and pharmacogenetic covariates on amifostine and WR1065 disposition was evaluated.

Results: Body surface area was the primary size-based covariate for amifostine pharmacokinetics explaining 53% and 56% of interindividual variability in plasma and whole-blood amifostine clearance, respectively. The population-predicted values for amifostine clearance, volume, and apparent WR1065 clearance from the plasma data were 107 L/h/m2, 5.53 L/m2, and 30.6 L/h/m2. The population-predicted values for amifostine clearance, volume, and apparent WR1065 clearance from whole blood data were 136 L/h/m2, 7.23 L/m2, and 12.5 L/h/m2.

Conclusions: These results support using body surface area for calculating doses of amifostine in children. Similar to data in adults, amifostine and WR1065 are rapidly cleared from plasma and whole blood in children. Clin Cancer Res; 16(3); 1049–57
Data from Vascular Endothelial Growth Factor Receptor-1 Is Synthetic Lethal to Aberrant β-Catenin Activation in Colon Cancer
Authors: Naik Snehal , Dothager Robin S. , Marasa Jayne , Lewis Cory L. , Piwnica-Worms David
Published: April 2023

Abstract
Purpose: The Wnt/β-catenin (β-cat) signaling cascade is a key regulator of development, and dysregulation of Wnt/β-cat contributes to selected cancers, such as colorectal, breast, and hepatocellular carcinoma, through abnormal activation of Wnt target genes. To identify novel modulators of the Wnt/β-cat pathway that may emerge as therapeutic targets, we did an unbiased high-throughput RNA interference screen.

Experimental Design: A synthetic oligonucleotide small interfering RNA library targeting 691 known and predicted human kinases was screened in Wnt3a-stimulated human cells in a live cell luciferase assay for modulation of Wnt/β-cat–dependent transcription. Follow-up studies of a selected high-confidence “hit” were conducted.

Results: A robust quartile-based statistical analysis and secondary screen yielded several kinases worthy of further investigation, including Cdc2L1, Lmtk3, Pank2, ErbB3, and, of note, vascular endothelial growth factor receptor (VEGFR)1/Flt1, a receptor tyrosine kinase (TK) with putative weak kinase activity conventionally believed to be a negative regulator of angiogenesis. A series of loss-of-function, genetic null, and VEGFR TK inhibitor assays further revealed that VEGFR1 is a positive regulator of Wnt signaling that functions in a glycogen synthase kinase-3β (GSK3β)–independent manner as a potential synthetic lethal target in Wnt/β-cat–addicted colon carcinoma cells.

Conclusions: This unanticipated non-endothelial link between VEGFR1 TK activity and Wnt/β-cat signaling may refine our understanding of aberrant Wnt signaling in colon carcinoma and points to new combinatorial therapeutics targeted to the tumor cell compartment, rather than angiogenesis, in the context of colon cancer. (Clin Cancer Res 2009;15(24):7529–37)
Data from Antitumor Activity of Targeting Src Kinases in Endothelial and Myeloid Cell Compartments of the Tumor Microenvironment
Authors: Liang Wei , Kujawski Maciej , Wu Jun , Lu Jianming , Herrmann Andreas , Loera Sofia , Yen Yun , Lee Frank , Yu Hua , Wen Wei , Jove Richard
Published: April 2023

Abstract
Purpose: Several Src family kinase (SFK) inhibitors have entered clinical trials based on their direct effects against tumor cells. Here, we characterize the effects of targeting Src kinases on the tumor microenvironment and how these effects influence tumor growth.

Experimental Design: Human cancer cells grown in cell culture or in mice were treated with dasatinib, a small-molecule inhibitor of SFKs. Tumor cell, endothelial cell, and myeloid cell compartments within the tumor microenvironment were analyzed. Primary human endothelial cells and freshly isolated CD11b+/CD11c− myeloid cells from mice were treated with dasatinib in cell culture. Cellular functions and signaling pathways affected by dasatinib were evaluated.

Results: Dasatinib was not cytotoxic in cell culture against the human cancer cell lines investigated here. However, dasatinib administration in human tumor–bearing mice suppressed tumor growth associated with increased tumor cell apoptosis, decreased microvessel density, and reduced intratumoral CD11b+ myeloid cells. Dasatinib directly inhibited motility and other functions of endothelial and myeloid cells, accompanied by the inhibition of phosphorylation of SFKs and downstream signaling. Tumor-infiltrating myeloid cells were identified as the major source of matrix metalloproteinase (MMP)-9 in the tumor microenvironment. Dasatinib treatment reduced MMP-9 levels in the tumor microenvironment through the simultaneous inhibition of recruitment of MMP9+ myeloid cells and MMP-9 gene expression in tumor-infiltrating myeloid cells.

Conclusions: These findings suggest that Src kinase inhibitors such as dasatinib possess a previously unrecognized anticancer mechanism of action by targeting both host-derived endothelial and myeloid cell compartments within the tumor microenvironment. Clin Cancer Res; 16(3); 924–35
Data from Suppression of Androgen-Independent Prostate Cancer Cell Aggressiveness by FTY720: Validating Runx2 as a Potential Antimetastatic Drug Screening Platform
Authors: Chua Chee-Wai , Chiu Yung-Tuen , Yuen Hiu-Fung , Chan Kwok-Wah , Man Kwan , Wang Xianghong , Ling Ming-Tat , Wong Yong-Chuan
Published: April 2023

Abstract
Purpose: Previously, FTY720 was found to possess potent anticancer effects on various types of cancer. In the present study, we aimed to first verify the role of Runx2 in prostate cancer progression and metastasis, and, subsequently, assessed if FTY720 could modulate Runx2 expression, thus interfering downstream events regulated by this protein.

Experimental Design: First, the association between Runx2 and prostate cancer progression was assessed using localized prostate cancer specimens and mechanistic investigation of Runx2-induced cancer aggressiveness was then carried out. Subsequently, the effect of FTY720 on Runx2 expression and transcriptional activity was investigated using PC-3 cells, which highly expressed Runx2 protein. Last, the involvement of Runx2 in FTY720-induced anticancer effects was evaluated by modulating Runx2 expression in various prostate cancer cell lines.

Results: Runx2 nuclear expression was found to be up-regulated in prostate cancer and its expression could be used as a predictor of metastasis in prostate cancer. Further mechanistic studies indicated that Runx2 accelerated prostate cancer aggressiveness through promotion of cadherin switching, invasion toward collagen I, and Akt activation. Subsequently, we found that FTY720 treatment down-regulated Runx2 expression and its transcriptional activity, as well as inhibited its regulated downstream events. More importantly, silencing Runx2 in PC-3 enhanced FTY720-induced anticancer effects as well as cell viability inhibition, whereas overexpressing Runx2 in 22Rv1 that expressed very low endogenous Runx2 protein conferred resistance in the same events.

Conclusion: This study provided a novel mechanism for the anticancer effect of FTY720 on advanced prostate cancer, thus highlighting the therapeutic potential of this drug in treating this disease.
Data from Interactions between MDM2 and TP53 Genetic Alterations, and Their Impact on Response to MDM2 Inhibitors and Other Chemotherapeutic Drugs in Cancer Cells
Authors: Liu Wanqing , He Lijun , Ramírez Jacqueline , Ratain Mark J.
Published: April 2023

Abstract
Purpose: MDM2 is a key negative regulator of the p53 signaling pathway. We aimed to evaluate the inter-relationships between MDM2 SNP309, mRNA expression, amplification, and TP53 mutations, as well as their correlations with responsiveness to MDM2 inhibitors and other commonly used cytotoxic drugs tested in the NCI-60 cancer cell panel.

Experimental Design: SNP309 was genotyped in the NCI-60 cancer cell lines. MDM2 mRNA levels and gene copy number were measured using real-time PCR. We assessed the inter-relationship between MDM2 genetic alterations, TP53 mutations, and the cytotoxicity of two MDM2 inhibitors (RITA and Nutlin-3) as well as 111 other drugs with known mechanisms of action.

Results: In the overall NCI-60 cell panel, MDM2 mRNA levels were not associated with SNP309 but with increased gene copy number. However, SNP309 strongly determined the MDM2 mRNA expression in cancer cells with wild-type TP53. Cancer cells with wild-type TP53 also had significantly higher MDM2 copies. In the overall panel, MDM2 copy number was independently correlated with increased sensitivity to commonly used alkylating agents and topoisomerase I and II inhibitors. SNP309 was significantly associated with increased sensitivity to alkylating agents and topoisomerase I inhibitors in the cells with wild-type TP53. In addition, TP53 mutations were the only factor significantly associated with cellular resistance to the MDM2 inhibitor RITA.

Conclusions: Our results suggest that MDM2 copy number and SNP309 may predict for response to alkylating agents and topoisomerase inhibitors. These markers should be tested further, particularly in combination with other putative predictive biomarkers. (Clin Cancer Res 2009;15(24):7602–7)
Data from Novel Inhibitors of Fatty Acid Synthase with Anticancer Activity
Authors: Puig Teresa , Turrado Carlos , Benhamú Bellinda , Aguilar Helena , Relat Joana , Ortega-Gutiérrez Silvia , Casals Gemma , Marrero Pedro F. , Urruticoechea Ander , Haro Diego , López-Rodríguez María Luz , Colomer Ramon
Published: April 2023

Abstract
Purpose: Fatty acid synthase (FASN) is overexpressed in human breast carcinoma. The natural polyphenol (−)-epigallocatechin-3-gallate blocks in vitro FASN activity and leads to apoptosis in breast cancer cells without any effects on carnitine palmitoyltransferase-1 (CPT-1) activity, and in vivo, does not decrease body weight. We synthesized a panel of new polyphenolic compounds and tested their effects on breast cancer models.

Experimental Design: We evaluated the in vitro effects of the compounds on breast cancer cell growth (SK-Br3, MCF-7, and MDA-MB-231), apoptosis [as assessed by cleavage of poly(ADP-ribose) polymerase], cell signaling (HER2, ERK1/2, and AKT), and fatty acid metabolism enzymes (FASN and CPT-1). In vivo, we have evaluated their antitumor activity and their effect on body weight in a mice model of BT474 breast cancer cells.

Results: Two compounds potently inhibited FASN activity and showed high cytotoxicity. Moreover, the compounds induced apoptosis and caused a marked decrease in the active forms of HER2, AKT, and ERK1/2 proteins. Interestingly, the compounds did not stimulate CPT-1 activity in vitro. We show evidence that one of the FASN inhibitors blocked the growth of BT474 breast cancer xenografts and did not induce weight loss in vivo.

Conclusions: The synthesized polyphenolic compounds represent a novel class of FASN inhibitors, with in vitro and in vivo anticancer activity, that do not exhibit cross-activation of β-oxidation and do not induce weight loss in animals. One of the compounds blocked the growth of breast cancer xenografts. These FASN inhibitors may represent new agents for breast cancer treatment. (Clin Cancer Res 2009;15(24):7608–15)