bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental Figure 4 - Immunoreactivity from The Prognostic and Predictive Value of Soluble Type IV Collagen in Colorectal Cancer: A Retrospective Multicenter Study
Authors: Rolff Hans Christian , Christensen Ib Jarle , Vainer Ben , Svendsen Lars Bo , Eefsen Rikke Løvendahl , Wilhelmsen Michael , Lund Ida Katrine , Høyer-Hansen Gunilla , Nielsen Hans Jørgen , Illemann Martin
Published: April 2023

Shows the result of the immunoreactivity experiment. Figure legend in the end the "Supplementary data. Appendix 2. Assay validation" file
Supplementary Figure 5-7 from Identification of Existing Drugs That Effectively Target NTRK1 and ROS1 Rearrangements in Lung Cancer
Authors: Chong Curtis R. , Bahcall Magda , Capelletti Marzia , Kosaka Takayuki , Ercan Dalia , Sim Taebo , Sholl Lynette M. , Nishino Mizuki , Johnson Bruce E. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

Inhibition of ROS1 signaling in Ba/F3 and UMG-118 cells and the RNPC3-ROS1 fusion
Supplemental Figure 3 - Recovery from The Prognostic and Predictive Value of Soluble Type IV Collagen in Colorectal Cancer: A Retrospective Multicenter Study
Authors: Rolff Hans Christian , Christensen Ib Jarle , Vainer Ben , Svendsen Lars Bo , Eefsen Rikke Løvendahl , Wilhelmsen Michael , Lund Ida Katrine , Høyer-Hansen Gunilla , Nielsen Hans Jørgen , Illemann Martin
Published: April 2023

Shows the recovery experiment. Figure legend in the end the "Supplementary data. Appendix 2. Assay validation" file
Supplementary Figure 4 from Identification of Existing Drugs That Effectively Target NTRK1 and ROS1 Rearrangements in Lung Cancer
Authors: Chong Curtis R. , Bahcall Magda , Capelletti Marzia , Kosaka Takayuki , Ercan Dalia , Sim Taebo , Sholl Lynette M. , Nishino Mizuki , Johnson Bruce E. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

Chemical structures of lead compounds
Supplemental Figure 1 - Standard curves from The Prognostic and Predictive Value of Soluble Type IV Collagen in Colorectal Cancer: A Retrospective Multicenter Study
Authors: Rolff Hans Christian , Christensen Ib Jarle , Vainer Ben , Svendsen Lars Bo , Eefsen Rikke Løvendahl , Wilhelmsen Michael , Lund Ida Katrine , Høyer-Hansen Gunilla , Nielsen Hans Jørgen , Illemann Martin
Published: April 2023

Shows a standard curve. Figure legend in the end the "Supplementary data. Appendix 2. Assay validation" file
Supplementary Table 1 from ERRα Is a Marker of Tamoxifen Response and Survival in Triple-Negative Breast Cancer
Authors: Manna Subrata , Bostner Josefine , Sun Yang , Miller Lance D. , Alayev Anya , Schwartz Naomi S. , Lager Elin , Fornander Tommy , Nordenskjöld Bo , Yu Jane J. , Stål Olle , Holz Marina K.
Published: April 2023

ERRα protein expression and clinicopathological variables with respect to estrogen receptor (ER) and HER2 status.
Table S1-S2 from β-Cryptoxanthin Synergistically Enhances the Antitumoral Activity of Oxaliplatin through ΔNP73 Negative Regulation in Colon Cancer
Authors: San Millán Coral , Soldevilla Beatriz , Martín Paloma , Gil-Calderón Beatriz , Compte Marta , Pérez-Sacristán Belén , Donoso Encarnación , Peña Cristina , Romero Jesús , Granado-Lorencio Fernando , Bonilla Félix , Domínguez Gemma
Published: April 2023

Table S1-S2. Table S1. Top five genes deregulated in HCT116 cells after Î²-cryptoxanthin treatment using a PCR array of the p53 signaling pathway. Table S2. Top five genes deregulated in HCT116 cells after Î²-cryptoxanthin treatment using a PCR array of the DNA damage signaling pathway.
Supplementary Table 1-2, Figures S1-4 from siRNA Lipid Nanoparticle Potently Silences Clusterin and Delays Progression When Combined with Androgen Receptor Cotargeting in Enzalutamide-Resistant Prostate Cancer
Authors: Yamamoto Yoshiaki , Lin Paulo J.C. , Beraldi Eliana , Zhang Fan , Kawai Yoshihisa , Leong Jeffrey , Katsumi Hidemasa , Fazli Ladan , Fraser Robert , Cullis Pieter R. , Gleave Martin
Published: April 2023

Supplemental Table 1: Source and authentication of cell lines. Supplemental Table 2: Primers used for quantitative real-time PCR. S1: PC-3M-luc cell numbers correlated with the expression of LUC in vitro. S2: PC-3M-luc tumor volume correlated with the expression of LUC in vivo. S3: DMAP-BLP LNP LUC-siRNA decreases LUC expression in a dose dependent manner in PC-3M-luc xenograft model in vivo. S4: LNP CLU-siRNA enhances AR-ASO-induced inhibition of LNCaP cell growth.
Figure S5 from β-Cryptoxanthin Synergistically Enhances the Antitumoral Activity of Oxaliplatin through ΔNP73 Negative Regulation in Colon Cancer
Authors: San Millán Coral , Soldevilla Beatriz , Martín Paloma , Gil-Calderón Beatriz , Compte Marta , Pérez-Sacristán Belén , Donoso Encarnación , Peña Cristina , Romero Jesús , Granado-Lorencio Fernando , Bonilla Félix , Domínguez Gemma
Published: April 2023

Figure S5. Quantification of TAp73 and Î”Np73 mRNA levels in (A) kidney and (B) liver from mice after vehicle or Î²-cryptoxanthin treatment. * p<0.05. Mean {plus minus} standard deviation of seven samples per group is represented.
Supplemental Figure 4 from Epithelial–Mesenchymal Transition Predicts Polo-Like Kinase 1 Inhibitor–Mediated Apoptosis in Non–Small Cell Lung Cancer
Authors: Ferrarotto Renata , Goonatilake Ruchitha , Young Yoo Suk , Tong Pan , Giri Uma , Peng Shaohua , Minna John , Girard Luc , Wang Yuehong , Wang Liguang , Li Lerong , Diao Lixia , Peng David H. , Gibbons Don L. , Glisson Bonnie S. , Heymach John V. , Wang Jing , Byers Lauren A. , Johnson Faye M.
Published: April 2023

E-cadherin knockdown does not affect NSCLC cell lines' sensitivity to PLK1 inhibition. Two epithelial NSCLC cell lines were transfected with siRNA against E-cadherin and then incubated with volasertib 48 hours later. Knockdown of E-cadherin expression did not affect cell-cycle progression (left panels), cell number as measured using an MTT assay (right panels), or apoptosis as measured using a terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay (bottom panel).
Supplemental Table 2 from Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression
Authors: Brooks Samira A. , Khandani Amir H. , Fielding Julia R. , Lin Weili , Sills Tiffany , Lee Yueh , Arreola Alexandra , Milowsky Mathew I. , Wallen Eric M. , Woods Michael E. , Smith Angie B. , Nielsen Mathew E. , Parker Joel S. , Lalush David S. , Rathmell W. Kimryn
Published: April 2023

Standard uptake values (SUV) and ccRCC subtype classifications for PET/MR samples
Supplementary Legends and Tables 1-3 from ERG/AKR1C3/AR Constitutes a Feed-Forward Loop for AR Signaling in Prostate Cancer Cells
Authors: Powell Katelyn , Semaan Louie , Conley-LaComb M. Katie , Asangani Irfan , Wu Yi-Mi , Ginsburg Kevin B. , Williams Julia , Squire Jeremy A. , Maddipati Krishna R. , Cher Michael L. , Chinni Sreenivasa R.
Published: April 2023

Supplementary Legends and Tables 1-3. Supplementary Table 1 Forward and reverse primer sequences genes used in mRNA expression, ChIP assay and cloning. Supplementary Table 2 Antibodies used in WB, ChIP, IHC and ICC studies. Supplementary Table 3 Androgens and androgen precursors used in the study.
Supplemental Figure S3 from Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression
Authors: Brooks Samira A. , Khandani Amir H. , Fielding Julia R. , Lin Weili , Sills Tiffany , Lee Yueh , Arreola Alexandra , Milowsky Mathew I. , Wallen Eric M. , Woods Michael E. , Smith Angie B. , Nielsen Mathew E. , Parker Joel S. , Lalush David S. , Rathmell W. Kimryn
Published: April 2023

PET dichotomizes ccRCC prognostic subtypes.
Supplemental Figure 2 from CDK4 Amplification Reduces Sensitivity to CDK4/6 Inhibition in Fusion-Positive Rhabdomyosarcoma
Authors: Olanich Mary E. , Sun Wenyue , Hewitt Stephen M. , Abdullaev Zied , Pack Svetlana D. , Barr Frederic G.
Published: April 2023

Supplemental Figure 2. Depletion of CDK4 represses the proliferative and transformative capacity of non-amplified fusion-positive RMS cells.
CCR Supplemental from Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression
Authors: Brooks Samira A. , Khandani Amir H. , Fielding Julia R. , Lin Weili , Sills Tiffany , Lee Yueh , Arreola Alexandra , Milowsky Mathew I. , Wallen Eric M. , Woods Michael E. , Smith Angie B. , Nielsen Mathew E. , Parker Joel S. , Lalush David S. , Rathmell W. Kimryn
Published: April 2023

Supplemental figure titles and descriptions
Supplemental Figure 1 from CDK4 Amplification Reduces Sensitivity to CDK4/6 Inhibition in Fusion-Positive Rhabdomyosarcoma
Authors: Olanich Mary E. , Sun Wenyue , Hewitt Stephen M. , Abdullaev Zied , Pack Svetlana D. , Barr Frederic G.
Published: April 2023

Supplemental Figure 1. Additional characterization of IPTG-inducible shRNA expression in Rh30 cells.
Supplementary Figures and Tables from Enhanced Antitumor Activity of an Anti-5T4 Antibody–Drug Conjugate in Combination with PI3K/mTOR inhibitors or Taxanes
Authors: Shor Boris , Kahler Jennifer , Dougher Maureen , Xu Jane , Mack Michelle , Rosfjord Ed , Wang Fang , Melamud Eugene , Sapra Puja
Published: April 2023

Supplementary Figures S1-S6. Supplementary Figure S1. 5T4 protein expression in selected preclinical models. Supplementary Figure S2. Effects of MMAF-Ome combined with PF-384. Supplementary Figure S3. Effect of PF-384 combination with auristatin-based agents on cell cycle and Aurora kinase activity. Supplementary Figure S4. Antibody array results and results of western blot for MDA-468 cells treated with 5T4-ADC/PF-384. Supplementary Figure S5. Identification and characterization of auristatin-regulated total and phospho-proteome. Supplementary Figure S6. Effect of single agent treatment of 5T4-ADC, PTX and their combinations on mitosis and microtubule disruption. Supplementary Tables S1-S3. Supplementary Table S1. List of cancer cell lines used in the study. Supplementary Table S2. Results of total- and phospho-proteomics experiment showing GO enrichment categories. Supplementary Table S3. Combination Index (CI) values for Aur101 plus WYE-132 combination.
supplemental figure legend from A Novel Anti-CD22 Anthracycline-Based Antibody–Drug Conjugate (ADC) That Overcomes Resistance to Auristatin-Based ADCs
Authors: Yu Shang-Fan , Zheng Bing , Go MaryAnn , Lau Jeff , Spencer Susan , Raab Helga , Soriano Robert , Jhunjhunwala Suchit , Cohen Robert , Caruso Michele , Polakis Paul , Flygare John , Polson Andrew G.
Published: April 2023

supplemental figure legend
Supplementary Data from A Randomized Phase II Crossover Study of Imatinib or Rituximab for Cutaneous Sclerosis after Hematopoietic Cell Transplantation
Authors: Arai Sally , Pidala Joseph , Pusic Iskra , Chai Xiaoyu , Jaglowski Samantha , Khera Nandita , Palmer Jeanne , Chen George L. , Jagasia Madan H. , Mayer Sebastian A. , Wood William A. , Green Michael , Hyun Teresa S. , Inamoto Yoshihiro , Storer Barry E. , Miklos David B. , Shulman Howard M. , Martin Paul J. , Sarantopoulos Stefanie , Lee Stephanie J. , Flowers Mary E.D.
Published: April 2023

Supplemental Table. Grade 3-5 adverse events possibly, probably or definitely attributed to imatinib or rituximab Supplemental Figure 1. Vienna Skin Score (VSS) (1) Supplemental Figure 2. Photograph Range of Motion Scale - Modified from (2) Supplemental Figure 3. Total numbers of B cells (CD19+ CD3- lymphocytes) was calculated in patients analyzed in Figure 3 who had available absolute lymphocyte counts. Supplemental Figure 4. BAFF levels at enrollment across treatment groups. Plasma soluble BAFF levels were determined in patients who later either experienced treatment success or did not respond to imatinib or rituximab.
Supplementary Table 1 from Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array
Authors: Vathipadiekal Vinod , Wang Victoria , Wei Wei , Waldron Levi , Drapkin Ronny , Gillette Michael , Skates Steven , Birrer Michael
Published: April 2023

Supplementary Table 1. Details of the secretome array, listed by each probset.
Supplementary Table 1 from Subclonal Genomic Architectures of Primary and Metastatic Colorectal Cancer Based on Intratumoral Genetic Heterogeneity
Authors: Kim Tae-Min , Jung Seung-Hyun , An Chang Hyeok , Lee Sung Hak , Baek In-Pyo , Kim Min Sung , Park Sung-Won , Rhee Je-Keun , Lee Sug-Hyung , Chung Yeun-Jun
Published: April 2023

Supplementary Table 1. Clinicopathological and sequencing information of the cases and regional biopsies
Supplementary Data from Flightless I Homolog Represses Prostate Cancer Progression through Targeting Androgen Receptor Signaling
Authors: Wang Tao , Song Wen , Chen Yuan , Chen Ruibao , Liu Zhuo , Wu Licheng , Li Mingchao , Yang Jun , Wang Liang , Liu Jihong , Ye Zhangqun , Wang Chenguang , Chen Ke
Published: April 2023

Supplementary Data from Flightless I Homolog Represses Prostate Cancer Progression through Targeting Androgen Receptor Signaling
Supplementary Table S1 from PLEKHA5 as a Biomarker and Potential Mediator of Melanoma Brain Metastasis
Authors: Jilaveanu Lucia B. , Parisi Fabio , Barr Meaghan L. , Zito Christopher R. , Cruz-Munoz William , Kerbel Robert S. , Rimm David L. , Bosenberg Marcus W. , Halaban Ruth , Kluger Yuval , Kluger Harriet M.
Published: April 2023

Supplementary Table S1: This table includes genes that were over- or under-expressed in A375Br cells compared to A375P cells. Fold differences in expression are provided for all genes in the table.
Supplementary Materials and Methods from PLEKHA5 as a Biomarker and Potential Mediator of Melanoma Brain Metastasis
Authors: Jilaveanu Lucia B. , Parisi Fabio , Barr Meaghan L. , Zito Christopher R. , Cruz-Munoz William , Kerbel Robert S. , Rimm David L. , Bosenberg Marcus W. , Halaban Ruth , Kluger Yuval , Kluger Harriet M.
Published: April 2023

This file provides additional details regarding methods for RNA extraction and quality control, gene expression profiling and analysis, immunofluorescence staining and cell lines used. It also contains information on the siRNA knock-down studies, the in vitro blood brain barrier assay, cell viability and apoptotic assays and the cell motility assay.
Supplemental Figure 4 from Chaperonin Containing TCP-1 Protein Level in Breast Cancer Cells Predicts Therapeutic Application of a Cytotoxic Peptide
Authors: Bassiouni Rania , Nemec Kathleen N. , Iketani Ashley , Flores Orielyz , Showalter Anne , Khaled Amr S. , Vishnubhotla Priya , Sprung Robert W. , Kaittanis Charalambos , Perez Jesus M. , Khaled Annette R.
Published: April 2023

Supplemental figure with pull down data
Supplementary Figures 1-6 from Autocrine Signaling by Wnt-5a Deregulates Chemotaxis of Leukemic Cells and Predicts Clinical Outcome in Chronic Lymphocytic Leukemia
Authors: Janovska Pavlina , Poppova Lucie , Plevova Karla , Plesingerova Hana , Behal Martin , Kaucka Marketa , Ovesna Petra , Hlozkova Michaela , Borsky Marek , Stehlikova Olga , Brychtova Yvona , Doubek Michael , Machalova Michaela , Baskar Sivasubramanian , Kozubik Alois , Pospisilova Sarka , Pavlova Sarka , Bryja Vitezslav
Published: April 2023

Supplementary Figures 1-6. Supplementary Fig. 1: ROR1 mRNA expression determined by qRT-PCR correlates with the amount of the surface receptor present on primary CLL cells. Supplementary Fig. 2: Expression of ROR1 in the WNT5A-negative and WNT5Apositive(A), and WNT5B-low and WNT5B-high (B) patient cohorts. Supplementary Fig. 3: A-C) Time-to-first treatment (TTFT) of patient groups stratified based on the expression of WNT5 genes was plotted using Kaplan-Meier survival curves. Supplementary Fig. 4: Expression of WNT5B mRNA levels in patients with TP53 mutations. n.s. - not significant (Mann-Whitney test). Supplementary Fig. 5: A) - C) Expression of surface receptors ROR1, CXCR4 and CCR7 was evaluated by vital staining and flow-cytometry (N=14). Supplementary Fig. 6: Freshly isolated CLL cells were treated as indicated and their migration was analysed using the Transwell assays. Supplementary Materials and Methods
Supplementary Table 3 from Phase Ia Study of FoxP3+ CD4 Treg Depletion by Infusion of a Humanized Anti-CCR4 Antibody, KW-0761, in Cancer Patients
Authors: Kurose Koji , Ohue Yoshihiro , Wada Hisashi , Iida Shinsuke , Ishida Takashi , Kojima Takashi , Doi Toshihiko , Suzuki Susumu , Isobe Midori , Funakoshi Takeru , Kakimi Kazuhiro , Nishikawa Hiroyoshi , Udono Heiichiro , Oka Mikio , Ueda Ryuzo , Nakayama Eiichi
Published: April 2023

Autoantibody response
Supplementary Table 2 from Phase Ia Study of FoxP3+ CD4 Treg Depletion by Infusion of a Humanized Anti-CCR4 Antibody, KW-0761, in Cancer Patients
Authors: Kurose Koji , Ohue Yoshihiro , Wada Hisashi , Iida Shinsuke , Ishida Takashi , Kojima Takashi , Doi Toshihiko , Suzuki Susumu , Isobe Midori , Funakoshi Takeru , Kakimi Kazuhiro , Nishikawa Hiroyoshi , Udono Heiichiro , Oka Mikio , Ueda Ryuzo , Nakayama Eiichi
Published: April 2023

Immune response
Supplementary Table 1 from Phase Ia Study of FoxP3+ CD4 Treg Depletion by Infusion of a Humanized Anti-CCR4 Antibody, KW-0761, in Cancer Patients
Authors: Kurose Koji , Ohue Yoshihiro , Wada Hisashi , Iida Shinsuke , Ishida Takashi , Kojima Takashi , Doi Toshihiko , Suzuki Susumu , Isobe Midori , Funakoshi Takeru , Kakimi Kazuhiro , Nishikawa Hiroyoshi , Udono Heiichiro , Oka Mikio , Ueda Ryuzo , Nakayama Eiichi
Published: April 2023

Patient characteristics
Supplementary Figure 4 from MicroRNA-374b Suppresses Proliferation and Promotes Apoptosis in T-cell Lymphoblastic Lymphoma by Repressing AKT1 and Wnt-16
Authors: Qian Dong , Chen Kailin , Deng Haixia , Rao Huilan , Huang Huiqiang , Liao Yiji , Sun Xiaofei , Lu Suying , Yuan Zhiyong , Xie Dan , Cai Qingqing
Published: April 2023

miR-374b and AKT inhibitor V inhibit the AKT phosphorylation and suppress cell growth as well as enhance cell apoptosis
Supplementary Figure 3 from Phase Ia Study of FoxP3+ CD4 Treg Depletion by Infusion of a Humanized Anti-CCR4 Antibody, KW-0761, in Cancer Patients
Authors: Kurose Koji , Ohue Yoshihiro , Wada Hisashi , Iida Shinsuke , Ishida Takashi , Kojima Takashi , Doi Toshihiko , Suzuki Susumu , Isobe Midori , Funakoshi Takeru , Kakimi Kazuhiro , Nishikawa Hiroyoshi , Udono Heiichiro , Oka Mikio , Ueda Ryuzo , Nakayama Eiichi
Published: April 2023

The changes in the specific populations in PBMCs, lymphocytes and CD4 T-cells.
Table S7: from SRC3 Phosphorylation at Serine 543 Is a Positive Independent Prognostic Factor in ER-Positive Breast Cancer
Authors: Zwart Wilbert , Flach Koen D. , Rudraraju Bharath , Abdel-Fatah Tarek M.A. , Gojis Ondrej , Canisius Sander , Moore David , Nevedomskaya Ekaterina , Opdam Mark , Droog Marjolein , Hofland Ingrid , Chan Steve , Shaw Jacqui , Ellis Ian O. , Coombes R. Charles , Carroll Jason S. , Ali Simak , Palmieri Carlo
Published: April 2023

Tumour biomarkers and correlation with SRC3 and SRC3-pS543
Figure S3. Graphical overview of the experimental setup in the TC-1 tumor model. from Combination of Photodynamic Therapy and Specific Immunotherapy Efficiently Eradicates Established Tumors
Authors: Kleinovink Jan Willem , van Driel Pieter B. , Snoeks Thomas J. , Prokopi Natasa , Fransen Marieke F. , Cruz Luis J. , Mezzanotte Laura , Chan Alan , Löwik Clemens W. , Ossendorp Ferry
Published: April 2023

The setup of the experiments using the TC-1 tumor model (single-tumor setting) is shown on a timescale starting with tumor inoculation at day 0.
Figure S2. Bremachlorin photosensitizer accumulates in tumors. from Combination of Photodynamic Therapy and Specific Immunotherapy Efficiently Eradicates Established Tumors
Authors: Kleinovink Jan Willem , van Driel Pieter B. , Snoeks Thomas J. , Prokopi Natasa , Fransen Marieke F. , Cruz Luis J. , Mezzanotte Laura , Chan Alan , Löwik Clemens W. , Ossendorp Ferry
Published: April 2023

In vivo imaging of Bremachlorin fluorescence 6 hours after injection of 20 mg/kg Bremachlorin in Albino B6 mice bearing subcutaneous TC-1 or RMA tumors. Bremachlorin fluorescence in the 700 nm emission filter is represented by the red color, the tumor is indicated by a white 'T'. Representative pictures from 4 mice per tumor model.
Figure S1. Efficient photosensitizer uptake enables specific killing following laser irradiation. from Combination of Photodynamic Therapy and Specific Immunotherapy Efficiently Eradicates Established Tumors
Authors: Kleinovink Jan Willem , van Driel Pieter B. , Snoeks Thomas J. , Prokopi Natasa , Fransen Marieke F. , Cruz Luis J. , Mezzanotte Laura , Chan Alan , Löwik Clemens W. , Ossendorp Ferry
Published: April 2023

(A) Flow cytometry of Bremachlorin fluorescence on TC-1 tumor cells incubated with different concentrations of Bremachlorin for 3 hours at 37&#deg;C. (B) Flow cytometry plots showing Annexin V and 7-AAD staining of TC-1 tumor cells 16 hours after in vitro PDT treatment. Cells were incubated with 1 μg/mL Bremachlorin for 3 hours, which had shown to give high cellular uptake, and irradiated for 2 minutes. Control samples were untreated cells, photosensitizer-only or irradiation-only cells. Representative plots of 3 experiments.
Supplementary Data from A Phase I First-in-Human Study of Nesvacumab (REGN910), a Fully Human Anti–Angiopoietin-2 (Ang2) Monoclonal Antibody, in Patients with Advanced Solid Tumors
Authors: Papadopoulos Kyriakos P. , Kelley Robin Kate , Tolcher Anthony W. , Razak Albiruni R. Abdul , Van Loon Katherine , Patnaik Amita , Bedard Philippe L. , Alfaro Ariceli A. , Beeram Muralidhar , Adriaens Lieve , Brownstein Carrie M. , Lowy Israel , Kostic Ana , Trail Pamela A. , Gao Bo , DiCioccio A. Thomas , Siu Lillian L.
Published: April 2023

Supplementary Data. Study entry criteria specific to patients with HCC
Supplementary Figure 1 from Phase I Clinical Trial of Ipilimumab in Pediatric Patients with Advanced Solid Tumors
Authors: Merchant Melinda S. , Wright Matthew , Baird Kristin , Wexler Leonard H. , Rodriguez-Galindo Carlos , Bernstein Donna , Delbrook Cindy , Lodish Maya , Bishop Rachel , Wolchok Jedd D. , Streicher Howard , Mackall Crystal L.
Published: April 2023

Absolute numbers of CD3+ and CD4+ HLA-DR+ activated T cells increase at day 21 and day 42 following ipilimumab infusion.
Supplementary Table 5 from Integrated Genomic Profiling, Therapy Response, and Survival in Adult Acute Myelogenous Leukemia
Authors: Parkin Brian , Ouillette Peter , Yildiz Mehmet , Saiya-Cork Kamlai , Shedden Kerby , Malek Sami N.
Published: April 2023

Supplementary Table 5. Results of multivariate survival analyses in TCGA-dnAML group.
Supplementary Table 4 from Integrated Genomic Profiling, Therapy Response, and Survival in Adult Acute Myelogenous Leukemia
Authors: Parkin Brian , Ouillette Peter , Yildiz Mehmet , Saiya-Cork Kamlai , Shedden Kerby , Malek Sami N.
Published: April 2023

Supplementary Table 4. Catalog of somatic mutations and minimally amplified and deleted regions in the MI-AML cohort.
Supplementary Figures 1-8, Supplementary Tables 1-6 from The Initial Detection and Partial Characterization of Circulating Tumor Cells in Neuroendocrine Prostate Cancer
Authors: Beltran Himisha , Jendrisak Adam , Landers Mark , Mosquera Juan Miguel , Kossai Myriam , Louw Jessica , Krupa Rachel , Graf Ryon P. , Schreiber Nicole A. , Nanus David M. , Tagawa Scott T. , Marrinucci Dena , Dittamore Ryan , Scher Howard I.
Published: April 2023

Figure S1: Examples of a decision boundary that separate class A (red) from class B (blue) in 1 dimension (figure 1A) and 2 dimensions (figure 1B); Figure S2: Schematic of the supervised learning process (A) and leave one out cross validation (B); Figure S3: Single iteration of Leave-One-Out Cross-Validation performed at the blood sample level; Figure S4: An example of concordance of AURKA amplification in tumor and CTCs; Figure S5: (A) Kernel Density Estimate (KDE) curves of the classifier output are plotted for each patient sample colored by their diagnosis: NEPC (red) and CRPC (blue); Figure S6: Cell-level NEPC classifier (A) Receiver-Operating-Characteristic (ROC) curve generated on the classifier's single-cell output after LOOCV; Figure S7: To address whether the CTC classifier is simply stochastic, a reflection of an overall higher CTC count, linearity was assessed with a Pearson's coefficient showing a weak relationship between frequency of NEPC CTCs and total cell count; Table S1: A summary of cell-level features utilized to train Random Forest cell-level classifiers in both the LOOCV and for the classification of CTCs in the test cohort; Table S2: Patient characteristics (discovery cohort) including prior systemic therapies, serum markers including PSA (ng/ml), Chromogranin (ng/ml), NSE (ng/ml) and CTC counts; Table S3: Liver metastases in NEPC vs. CRPC; Table S4: The median concentration of CK-negative and AR-negative CTCs in CRPC, atypical CRPC, and NEPC patients; Table S5: Confusion matrix for the ability of CD56 staining to discriminate patients diagnosed with Small Cell Carcinoma NEPC vs CRPC; Table S6: Example of results from a single tube of blood.
Supplementary Table 1 from Integrated Genomic Profiling, Therapy Response, and Survival in Adult Acute Myelogenous Leukemia
Authors: Parkin Brian , Ouillette Peter , Yildiz Mehmet , Saiya-Cork Kamlai , Shedden Kerby , Malek Sami N.
Published: April 2023

Supplementary Table 1. Clinical characteristics of MI-AML and TCGA patients.
Supplementary Figure 3 from Not all NOTCH Is Created Equal: The Oncogenic Role of NOTCH2 in Bladder Cancer and Its Implications for Targeted Therapy
Authors: Hayashi Tetsutaro , Gust Kilian M. , Wyatt Alexander W. , Goriki Akihiro , Jäger Wolfgang , Awrey Shannon , Li Na , Oo Htoo Zarni , Altamirano-Dimas Manuel , Buttyan Ralph , Fazli Ladan , Matsubara Akio , Black Peter C.
Published: April 2023

NOTCH2 silencing inhibited tumor progression through decreased cell proliferation and invasion.
Supplemental Figure 6 from Hepatitis B Virus X Protein (HBx) Is Responsible for Resistance to Targeted Therapies in Hepatocellular Carcinoma: Ex Vivo Culture Evidence
Authors: Huang Pinbo , Zhuang Baoxiong , Zhang Heyun , Yan Haiyan , Xiao Zhiyu , Li Wenbin , Zhang Jianlong , Tang Qibin , Hu Kaishun , Koeffler H. Phillip , Wang Jie , Yin Dong
Published: April 2023

Supplemental Figure 6. Effects of bortezomib and PD98059 on murine body weight.
Supplementary Tab S1-S9 from miR-195 Inhibits Tumor Progression by Targeting RPS6KB1 in Human Prostate Cancer
Authors: Cai Chao , Chen Qing-Biao , Han Zhao-Dong , Zhang Yan-Qiong , He Hui-Chan , Chen Jia-Hong , Chen Yan-Ru , Yang Sheng-Bang , Wu Yong-Ding , Zeng Yan-Ru , Qin Guo-Qiang , Liang Yu-Xiang , Dai Qi-Shan , Jiang Fu-Neng , Wu Shu-lin , Zeng Guo-Hua , Zhong Wei-De , Wu Chin-Lee
Published: April 2023

Supplementary Tab S1-S9. Supplementary Tab. S1. Follow-up clinicopathological information of patients from MGH cohort; Supplementary Tab. S2. ligonucleotide Sequence for all the primers used in the study; Supplementary Tab.S3. The antibodies used in this study; Supplementary Tab.S4. Associations of miR-195 and RPS6KB1 protein expression with clinicopathological features of prostate cancer (PCa) patients; Supplementary Tab.S5. Prognostic value of miR-195 expression for the biochemical recurrence-free survival in univariate and multivariate analysis by Cox Regression; Supplementary Tab. S6 Differentially expressed proteins detected by iTRAQ; Supplementary Tab. S7 Canonical pathways analysis by IPA; Supplementary Tab. S8 Diseases and bio functions analysis by IPA; Supplementary Tab.S9. Prognostic value of RPS6KB1 expression for the biochemical recurrence-free survival in univariate and multivariate analysis by Cox Regression.
Supplementary Figure and Table Legends from miR-195 Inhibits Tumor Progression by Targeting RPS6KB1 in Human Prostate Cancer
Authors: Cai Chao , Chen Qing-Biao , Han Zhao-Dong , Zhang Yan-Qiong , He Hui-Chan , Chen Jia-Hong , Chen Yan-Ru , Yang Sheng-Bang , Wu Yong-Ding , Zeng Yan-Ru , Qin Guo-Qiang , Liang Yu-Xiang , Dai Qi-Shan , Jiang Fu-Neng , Wu Shu-lin , Zeng Guo-Hua , Zhong Wei-De , Wu Chin-Lee
Published: April 2023

Supplementary Figure and Table Legends. List of supporting information
Supplementary Fig. S1-S9 from miR-195 Inhibits Tumor Progression by Targeting RPS6KB1 in Human Prostate Cancer
Authors: Cai Chao , Chen Qing-Biao , Han Zhao-Dong , Zhang Yan-Qiong , He Hui-Chan , Chen Jia-Hong , Chen Yan-Ru , Yang Sheng-Bang , Wu Yong-Ding , Zeng Yan-Ru , Qin Guo-Qiang , Liang Yu-Xiang , Dai Qi-Shan , Jiang Fu-Neng , Wu Shu-lin , Zeng Guo-Hua , Zhong Wei-De , Wu Chin-Lee
Published: April 2023

Supplementary Fig. S1-S9. Supplementary Fig. S1. miR-195 expression is significantly reduced in both human PCa cells and tissues; Supplementary Fig. S2. Kaplan-Meier analyses of biochemical recurrence (BCR)-free survival, non-metastatic BCR-free, survival overall survival and non-metastatic survival of prostate cancer (PCa) patients based on miR-195 expression in Taylor dataset; Supplementary Fig. S3. Knockdown of miR-195 expression enhances invasion, migration, but inhibits apoptosis of LNCaP and DU145 cells; Supplementary Fig. S4. The inhibition of miR-195 enhances tumor growth, angiogenesis and invasion in vivo; Supplementary Fig. S5. Top ten enriched KEGG pathways (A) and gene ontology (GO) biological processes (B) involved by differentially-expressed proteins induced by miR-195; Supplementary Fig. S6. The knockdown of RPS6KB1 could imitate the tumor suppressive effects of miR-195; Supplementary Fig. S7. The re-expression and knockdown of RPS6KB1 could respectively rescue and imitate the tumor suppressive effects of miR-195; Supplementary Fig. S8. Reverse correlation between miR-195 and RPS6KB1 expression in human PCa tissues; Supplementary Fig. S9. MMP-9, VEGF, BAD and E-cadherin function as downstream effectors of miR-195-RPS6KB1 axis.
Supplementary figure from Correlating Surrogate Endpoints with Overall Survival at the Individual Patient Level in BRAFV600E-Mutated Metastatic Melanoma Patients Treated with Vemurafenib
Authors: Zabor Emily C. , Heller Glenn , Schwartz Lawrence H. , Chapman Paul B.
Published: April 2023

Correlation of tumor response over the first 12 weeks with overall survival in patients on the vemurafenib arm on BRIM3.
Supplementary Table S5 from Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer
Authors: Hurley Paula J. , Sundi Debasish , Shinder Brian , Simons Brian W. , Hughes Robert M. , Miller Rebecca M. , Benzon Benjamin , Faraj Sheila F. , Netto George J. , Vergara Ismael A. , Erho Nicholas , Davicioni Elai , Karnes R. Jeffrey , Yan Guifang , Ewing Charles , Isaacs Sarah D. , Berman David M. , Rider Jennifer R. , Jordahl Kristina M. , Mucci Lorelei A. , Huang Jessie , An Steven S. , Park Ben H. , Isaacs William B. , Marchionni Luigi , Ross Ashley E. , Schaeffer Edward M.
Published: April 2023

Comparison of prostate cancer characteristics of men undergoing radical prostatectomy at JHH with the most common germline ASPN D-repeat-length genotypes and alleles.
Supplementary Figures 1-6 from CD126 and Targeted Therapy with Tocilizumab in Chronic Lymphocytic Leukemia
Authors: Liu Feng-Ting , Jia Li , Wang Ping , Farren Timothy , Li Hong , Hao Xishan , Agrawal Samir G.
Published: April 2023

Figure S1: CD126 expression on CLL cells; S2: In vitro and in vivo chemoresponsiveness in CLL patients with 11q-/17p- and with higher or lower CD126 expression; S3: Correlation between CD126 expression and the sensitivity to Fludarabine-induced cell death; S4: Autocrine of IL-6 by fresh CLL cells; S5: Cytotoxicity of Tocilizumab on CLL cells; S6: Chlorambucil-induced CLL cell death.
Supplementary Table S1 from Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer
Authors: Hurley Paula J. , Sundi Debasish , Shinder Brian , Simons Brian W. , Hughes Robert M. , Miller Rebecca M. , Benzon Benjamin , Faraj Sheila F. , Netto George J. , Vergara Ismael A. , Erho Nicholas , Davicioni Elai , Karnes R. Jeffrey , Yan Guifang , Ewing Charles , Isaacs Sarah D. , Berman David M. , Rider Jennifer R. , Jordahl Kristina M. , Mucci Lorelei A. , Huang Jessie , An Steven S. , Park Ben H. , Isaacs William B. , Marchionni Luigi , Ross Ashley E. , Schaeffer Edward M.
Published: April 2023

Frequency of germline ASPN D-repeat-length in JHH prostate cancer cases and controls.
Supplementary Figure S4. from Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer
Authors: Hurley Paula J. , Sundi Debasish , Shinder Brian , Simons Brian W. , Hughes Robert M. , Miller Rebecca M. , Benzon Benjamin , Faraj Sheila F. , Netto George J. , Vergara Ismael A. , Erho Nicholas , Davicioni Elai , Karnes R. Jeffrey , Yan Guifang , Ewing Charles , Isaacs Sarah D. , Berman David M. , Rider Jennifer R. , Jordahl Kristina M. , Mucci Lorelei A. , Huang Jessie , An Steven S. , Park Ben H. , Isaacs William B. , Marchionni Luigi , Ross Ashley E. , Schaeffer Edward M.
Published: April 2023

ASPN expression is associated with biochemical recurrence and metastatic recurrence.
Supplementary Figure S3. from Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer
Authors: Hurley Paula J. , Sundi Debasish , Shinder Brian , Simons Brian W. , Hughes Robert M. , Miller Rebecca M. , Benzon Benjamin , Faraj Sheila F. , Netto George J. , Vergara Ismael A. , Erho Nicholas , Davicioni Elai , Karnes R. Jeffrey , Yan Guifang , Ewing Charles , Isaacs Sarah D. , Berman David M. , Rider Jennifer R. , Jordahl Kristina M. , Mucci Lorelei A. , Huang Jessie , An Steven S. , Park Ben H. , Isaacs William B. , Marchionni Luigi , Ross Ashley E. , Schaeffer Edward M.
Published: April 2023

ASPN expression is elevated in PCAFs.
Supplementary Figure S1 from Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer
Authors: Hurley Paula J. , Sundi Debasish , Shinder Brian , Simons Brian W. , Hughes Robert M. , Miller Rebecca M. , Benzon Benjamin , Faraj Sheila F. , Netto George J. , Vergara Ismael A. , Erho Nicholas , Davicioni Elai , Karnes R. Jeffrey , Yan Guifang , Ewing Charles , Isaacs Sarah D. , Berman David M. , Rider Jennifer R. , Jordahl Kristina M. , Mucci Lorelei A. , Huang Jessie , An Steven S. , Park Ben H. , Isaacs William B. , Marchionni Luigi , Ross Ashley E. , Schaeffer Edward M.
Published: April 2023

ASPN antibody validation.
Supplementary figures S1-5, Tables S1-5 from XPO1/CRM1 Inhibition Causes Antitumor Effects by Mitochondrial Accumulation of eIF5A
Authors: Miyake Takahito , Pradeep Sunila , Wu Sherry Y. , Rupaimoole Rajesha , Zand Behrouz , Wen Yunfei , Gharpure Kshipra M. , Nagaraja Archana S. , Hu Wei , Cho Min Soon , Dalton Heather J. , Previs Rebecca A. , Taylor Morgan L. , Hisamatsu Takeshi , Kang Yu , Liu Tao , Shacham Sharon , McCauley Dilara , Hawke David H. , Wiktorowicz John E. , Coleman Robert L. , Sood Anil K.
Published: April 2023

Supplementary Figures S1-5, Tables S1-5. Figure S1 The Cytotoxic Effect of KPT-185 is Tumor Suppressor-independent. Figure S2 Combination Index of KPT-185 with Chemotherapeutic Agents. Figure S3 1D Gel Analysis of Cytoplasmic Protein. Figure S4 Effects of Selinexor (KPT-330) in an Ovarian Cancer Mouse Model. Figure S5 The Efficacy of Selinexor (KPT-330) on Tumor Regression and Metastasis Table S1 p53 status and IC50 concentration of KPT-185 after 72 hours of incubation in human cancer cell lines Table S2 Combination index (CI) of KPT-185 with cytotoxic agents Table S3 Proteins showing altered mitochondrial localization after treatment with KPT-185 Table S4 1D Proteomic analysis of cytoplasmic proteins immunoprecipitated with eIF5A Table S5 siRNA Sequences
Supplementary Figure 3 from Baseline Peripheral Blood Biomarkers Associated with Clinical Outcome of Advanced Melanoma Patients Treated with Ipilimumab
Authors: Martens Alexander , Wistuba-Hamprecht Kilian , Foppen Marnix Geukes , Yuan Jianda , Postow Michael A. , Wong Phillip , Romano Emanuela , Khammari Amir , Dreno Brigitte , Capone Mariaelena , Ascierto Paolo A. , Di Giacomo Anna Maria , Maio Michele , Schilling Bastian , Sucker Antje , Schadendorf Dirk , Hassel Jessica C. , Eigentler Thomas K. , Martus Peter , Wolchok Jedd D. , Blank Christian , Pawelec Graham , Garbe Claus , Weide Benjamin
Published: April 2023

Calibration of combination models. Calibration was calculated after 12 and 24 months using the calibrate function in the rms package of R for combination model 1 (A) and combination model 2 (B). Bootstrapping (1000 repeats) was performed to obtain bias-corrected estimates of predicted vs. observed values. Non-convergence reduced the number of included bootstrapping steps for combination model 2 to 981 or 990 after 12 or 24 months, respectively. "Predicted" survival probabilities at 12 or 24 months are those predicted by the Cox model, and "observed" refers to the corresponding Kaplan-Meier survival estimate at the given time-point. Mean absolute error in predictions, the mean squared error, and the 0.9 quantile of the absolute error is reported. "Error" refers to the difference between the predicted values and the corresponding bias-corrected calibrated values. Mean error was <3% for both combination models and both time-points. The calibration according to Kolmogorov Smirnov was excellent for combination model 1 and satisfactory for model 2 (p=0.657 and p=0.021, respectively).
Tables 1 and 2 from Genetic Engineering of T Cells to Target HERV-K, an Ancient Retrovirus on Melanoma
Authors: Krishnamurthy Janani , Rabinovich Brian A. , Mi Tiejuan , Switzer Kirsten C. , Olivares Simon , Maiti Sourindra N. , Plummer Joshua B. , Singh Harjeet , Kumaresan Pappanaicken R. , Huls Helen M. , Wang-Johanning Feng , Cooper Laurence J.N.
Published: April 2023

Tables 1 and 2. Table 1: List of antibodies used in this study. Table 2: List of mRNA sequences assessed by digital molecular barcoding using the nCounter
Supplementary Table 1A and Table 1B from Incorporation of Next-Generation Sequencing into Routine Clinical Care to Direct Treatment of Head and Neck Squamous Cell Carcinoma
Authors: Chau Nicole G. , Li Yvonne Y. , Jo Vickie Y. , Rabinowits Guilherme , Lorch Jochen H. , Tishler Roy B. , Margalit Danielle N. , Schoenfeld Jonathan D. , Annino Don J. , Goguen Laura A. , Thomas Tom , Becker Hailey , Haddad Tyler , Krane Jeffrey F. , Lindeman Neal I. , Shapiro Geoffrey I. , Haddad Robert I. , Hammerman Peter S.
Published: April 2023

Supplementary Table 1A. A list of all mutations presented in Figure 1A, annotated by gene, mutation, amino acid change, type and tier. Supplementary Table 1B. Examples of Patients Enrolled on Clinical Trial with Agents Matched or Unmatched to Genomic Alteration.
Supplementary Video C from Genetic Engineering of T Cells to Target HERV-K, an Ancient Retrovirus on Melanoma
Authors: Krishnamurthy Janani , Rabinovich Brian A. , Mi Tiejuan , Switzer Kirsten C. , Olivares Simon , Maiti Sourindra N. , Plummer Joshua B. , Singh Harjeet , Kumaresan Pappanaicken R. , Huls Helen M. , Wang-Johanning Feng , Cooper Laurence J.N.
Published: April 2023

Supplementary Video C. VTLM single cell killing of HEK293 cells by HERV-K env-specific CAR+ T cells
Figure S2 from Development and Validation of a Six-Gene Recurrence Risk Score Assay for Gastric Cancer
Authors: Lee Keun-Wook , Lee Sung Sook , Hwang Jun-Eul , Jang Hee-Jin , Lee Hyun-Sung , Oh Sang Cheul , Lee Sang Ho , Sohn Bo Hwa , Kim Sang Bae , Shim Jae-Jun , Jeong Woojin , Cha Minse , Cheong Jae-Ho , Cho Jae Yong , Lim Jae Yun , Park Eun Sung , Kim Sang Cheol , Kang Yoon-Koo , Noh Sung Hoon , Ajani Jaffer A. , Lee Ju-Seog
Published: April 2023

YAP1 signature and selection of candidate genes
Supplemental Information from IGF1R Protein Expression Is Not Associated with Differential Benefit to Concurrent Trastuzumab in Early-Stage HER2+ Breast Cancer from the North Central Cancer Treatment Group (Alliance) Adjuvant Trastuzumab Trial N9831
Authors: Reinholz Monica M. , Chen Beiyun , Dueck Amylou C. , Tenner Kathleen , Ballman Karla , Riehle Darren , Jenkins Robert B. , Geiger Xochiquetzal J. , McCullough Ann E. , Perez Edith A.
Published: April 2023

Supplemental Table 1. Heterogeneity of Cores in Patients with Multiple Cores (N=961) Supplemental Table 2. Clinicopathological Characteristics of Cohort and Non-Cohort Patients. Supplemental Table 3. Patient/Disease Characteristics by {greater than or equal to}2+ IGF1R protein staining >0% (N=1734). Supplemental Table 4. DFS for Patients with Hormone Receptor Positive Patients Breast Tumors by IGF1R Membrane Staining (0,1+ vs 2,3+ ) N=909 (Stratified by nodal status) Supplemental Table 5. DFS for Patients with Hormone Receptor-Negative Breast Tumors by IGF1R Membrane Staining (0,1+ vs 2,3+ ) N=825 (Stratified by nodal status) Supplemental Figure 1. NCCTG N9831 Trial Incorporating Trastuzumab in Adjuvant Therapy Supplemental Figure 2. Patient Flow Diagram. Supplemental Figure 3. Disease-Free Survival by IGF1R Protein Expression in Patients with Hormone Receptor-Positive Breast Tumors. Supplemental Figure 4. Disease-Free Survival by IGF1R Protein Expression in Patients with Hormone Receptor-Negative Breast Tumors.
Supplementary Figures 1-3 from Sonic Hedgehog and Gli1 Expression Predict Outcome in Resected Pancreatic Adenocarcinoma
Authors: Maréchal Raphaël , Bachet Jean-Baptiste , Calomme Annabelle , Demetter Pieter , Delpero Jean Robert , Svrcek Magali , Cros Jérôme , Bardier-Dupas Armelle , Puleo Francesco , Monges Geneviève , Hammel Pascal , Louvet Christophe , Paye François , Bachelier Philippe , Le Treut Yves Patrice , Vaillant Jean-Christophe , Sauvanet Alain , André Thierry , Salmon Isabelle , Devière Jacques , Emile Jean-François , Van Laethem Jean-Luc
Published: April 2023

Supplementary Figures 1-3. Figure 1: Flow chart of patients thought the study for the 3 cohorts of patients. Figure 2: Caption : Photomicrographs showing examples of PDAC. Figure 3: Cumulative overall survival according to the combined expression of Shh and Gli1
Supplementary Data from Structural Alterations of MET Trigger Response to MET Kinase Inhibition in Lung Adenocarcinoma Patients
Authors: Plenker Dennis , Bertrand Miriam , de Langen Adrianus J. , Riedel Richard , Lorenz Carina , Scheel Andreas H. , Müller Judith , Brägelmann Johannes , Daßler-Plenker Juliane , Kobe Carsten , Persigehl Thorsten , Kluge Alexander , Wurdinger Thomas , Schellen Pepijn , Hartmann Gunther , Zacherle Tobias , Menon Roopika , Thunnissen Erik , Büttner Reinhard , Griesinger Frank , Wolf Jürgen , Heukamp Lukas , Sos Martin L. , Heuckmann Johannes M.
Published: April 2023

Supplementary Methods Supplementary Figure S1. Characterization of KIF5B- and STARD3NL-MET rearrangements. A) IGV screenshots of next-generation sequencing reads from breakpoint regions of KIF5B- and STARD3NL-MET positive patient tissue. Due to homology in both regions the breakpoint region is marked with a red bar. The spanning read indicates the genomic sequence of the rearrangement. B) Dideoxy sequencing of exonic breakpoint regions of patient cDNA extracted from FFPE cuts for KIF5B- and STARD3NL-MET. C) PET/CT scans of KIF5B-MET patient. Numbers below indicate reduction of SUVmax under crizotinib therapy. D) Immunoblots of NIH-3T3 cells transduced with KIF5B-MET (upper panel) and STARD3NL-MET (lower panel) treated with 1 µM crizotinib or tepotinib over time. HSP90 serves as loading control. A representative blot from n=3 independent experiments is shown. E) Dose-response curves (72 h) of Ba/F3 cells stably transduced with KIF5B-MET or STARD3NL-MET supplemented with IL-3 (10% conditioned Wehi-3b media) and treated with crizotinib, tepotinib and erlotinib (as control compound). (n=3) Supplementary Figure S1. Characterization of KIF5B- and STARD3NL-MET rearrangements. A) IGV screenshots of next-generation sequencing reads from breakpoint regions of KIF5B- and STARD3NL-MET positive patient tissue. Due to homology in both regions the breakpoint region is marked with a red bar. The spanning read indicates the genomic sequence of the rearrangement. B) Dideoxy sequencing of exonic breakpoint regions of patient cDNA extracted from FFPE cuts for KIF5B- and STARD3NL-MET. C) PET/CT scans of KIF5B-MET patient. Numbers below indicate reduction of SUVmax under crizotinib therapy. D) Immunoblots of NIH-3T3 cells transduced with KIF5B-MET (upper panel) and STARD3NL-MET (lower panel) treated with 1 µM crizotinib or tepotinib over time. HSP90 serves as loading control. A representative blot from n=3 independent experiments is shown. E) Dose-response curves (72 h) of Ba/F3 cells stably transduced with KIF5B-MET or STARD3NL-MET supplemented with IL-3 (10% conditioned Wehi-3b media) and treated with crizotinib, tepotinib and erlotinib (as control compound). (n=3)
Supplementary Table 1 from A Pilot Trial Using Lymphocytes Genetically Engineered with an NY-ESO-1–Reactive T-cell Receptor: Long-term Follow-up and Correlates with Response
Authors: Robbins Paul F. , Kassim Sadik H. , Tran Thai L.N. , Crystal Jessica S. , Morgan Richard A. , Feldman Steven A. , Yang James C. , Dudley Mark E. , Wunderlich John R. , Sherry Richard M. , Kammula Udai S. , Hughes Marybeth S. , Restifo Nicholas P. , Raffeld Mark , Lee Chyi-Chia R. , Li Yong F. , El-Gamil Mona , Rosenberg Steven A.
Published: April 2023

Supplementary Table 1. Melanoma patients: Prior treatments
Supplemental Figure 2 from SMO Gene Amplification and Activation of the Hedgehog Pathway as Novel Mechanisms of Resistance to Anti-Epidermal Growth Factor Receptor Drugs in Human Lung Cancer
Authors: Della Corte Carminia Maria , Bellevicine Claudio , Vicidomini Giovanni , Vitagliano Donata , Malapelle Umberto , Accardo Marina , Fabozzi Alessio , Fiorelli Alfonso , Fasano Morena , Papaccio Federica , Martinelli Erika , Troiani Teresa , Troncone Giancarlo , Santini Mario , Bianco Roberto , Ciardiello Fortunato , Morgillo Floriana
Published: April 2023

A) GLI1 promoter activity in EGFR-WT NSCLC cell lines. Effects of Hh and EGFR inhibition in EGFR-WT NSCLC cell lines on their abilities to B) growth, C) invade , D)migrate and E) colony forming. F)In vivo efficacy of erlotinib and LDE225 on EGFR-WT NSCLC xenografts in nude mice.
Supplementary material and methods, Tables 1-3 from A Phase I/II Study of the mTOR Inhibitor Everolimus in Combination with HyperCVAD Chemotherapy in Patients with Relapsed/Refractory Acute Lymphoblastic Leukemia
Authors: Daver Naval , Boumber Yanis , Kantarjian Hagop , Ravandi Farhad , Cortes Jorge , Rytting Michael E. , Kawedia Jitesh D. , Basnett Jordan , Culotta Kirk S. , Zeng Zhihong , Lu Hongbo , Richie Mary Ann , Garris Rebecca , Xiao Lianchun , Liu Wenbin , Baggerly Keith A. , Jabbour Elias , O'Brien Susan , Burger Jan , Bendall Linda J. , Thomas Deborah , Konopleva Marina
Published: April 2023

Supplementary material and methods, Tables 1-3. Supplementary table 1. Changes in the expression of proteins and their phosphorylated forms with everolimus treatment analyzed by RPPA; Supplementary table 2. Results of binomial analysis showing direction of changes in the expression of proteins and their phosphorylated forms, analyzed by RPPA, for individual patients; Supplementary Table 3. Major everolimus pharmacokinetic parameters in cycles 1 and 2a.