bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S1 from Potential Predictive Value of TP53 and KRAS Mutation Status for Response to PD-1 Blockade Immunotherapy in Lung Adenocarcinoma
Authors: Dong Zhong-Yi , Zhong Wen-Zhao , Zhang Xu-Chao , Su Jian , Xie Zhi , Liu Si-Yang , Tu Hai-Yan , Chen Hua-Jun , Sun Yue-Li , Zhou Qing , Yang Jin-Ji , Yang Xue-Ning , Lin Jia-Xin , Yan Hong-Hong , Zhai Hao-Ran , Yan Li-Xu , Liao Ri-Qiang , Wu Si-Pei , Wu Yi-Long
Published: April 2023

Demographic and clinicopathologic characteristics of lung adenocarcinoma samples in 4 independent cohorts.
Table S6 from Chemogenomic Landscape of RUNX1-mutated AML Reveals Importance of RUNX1 Allele Dosage in Genetics and Glucocorticoid Sensitivity
Authors: Simon Laura , Lavallée Vincent-Philippe , Bordeleau Marie-Eve , Krosl Jana , Baccelli Irène , Boucher Geneviève , Lehnertz Bernhard , Chagraoui Jalila , MacRae Tara , Ruel Réjean , Chantigny Yves , Lemieux Sébastien , Marinier Anne , Hébert Josée , Sauvageau Guy
Published: April 2023

Table S6
Table S2 from Chemogenomic Landscape of RUNX1-mutated AML Reveals Importance of RUNX1 Allele Dosage in Genetics and Glucocorticoid Sensitivity
Authors: Simon Laura , Lavallée Vincent-Philippe , Bordeleau Marie-Eve , Krosl Jana , Baccelli Irène , Boucher Geneviève , Lehnertz Bernhard , Chagraoui Jalila , MacRae Tara , Ruel Réjean , Chantigny Yves , Lemieux Sébastien , Marinier Anne , Hébert Josée , Sauvageau Guy
Published: April 2023

RUNX1 mutations identified in the Leucegene cohort. Position of mutations are indicated using NM_001754 and NM_001001890, coding for RUNX1 proteins of 480 and 453 AA respectively. VAF: variant allele frequency.
Supplementary Figure 2 from An miRNA–DNMT1 Axis Is Involved in Azacitidine Resistance and Predicts Survival in Higher-Risk Myelodysplastic Syndrome and Low Blast Count Acute Myeloid Leukemia
Authors: Solly Françoise , Koering Catherine , Mohamed Aminetou Mint , Maucort-Boulch Delphine , Robert Guillaume , Auberger Patrick , Flandrin-Gresta Pascale , Adès Lionel , Fenaux Pierre , Kosmider Olivier , Tavernier-Tardy Emmanuelle , Cornillon Jérôme , Guyotat Denis , Campos Lydia , Mortreux Franck , Wattel Eric
Published: April 2023

DNMT1 protein expression in SKM1 AZA-sensitive (-S) versus AZA-resistant clones (-R). The Figure corresponds to the Figure 1B with signal quantification performed with ImageJ software. The data are expressed as mean {plus minus} SD of three independent experiments, with each performed in triplicate (Mann-Whitney test, p<0.05).
Supplementary Table S1 from Analytic Validation of RNA In Situ Hybridization (RISH) for AR and AR-V7 Expression in Human Prostate Cancer
Authors: Guedes Liana B. , Morais Carlos L. , Almutairi Fawaz , Haffner Michael C. , Zheng Qizhi , Isaacs John T. , Antonarakis Emmanuel S. , Lu Changxue , Tsai Harrison , Luo Jun , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

RNA-seq reads spanning selected AR junctions in the RNA-seq data of CRPC samples from GSE50630, which was depleted of ribosomal RNA but not enriched for polyA transcripts
Supplementary Figure S6 from Analytic Validation of RNA In Situ Hybridization (RISH) for AR and AR-V7 Expression in Human Prostate Cancer
Authors: Guedes Liana B. , Morais Carlos L. , Almutairi Fawaz , Haffner Michael C. , Zheng Qizhi , Isaacs John T. , Antonarakis Emmanuel S. , Lu Changxue , Tsai Harrison , Luo Jun , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

Comparison of AR RISH in bone and soft tissue metastases from the same patient.
Figure S7 from Degalactotigonin, a Natural Compound from Solanum nigrum L., Inhibits Growth and Metastasis of Osteosarcoma through GSK3β Inactivation–Mediated Repression of the Hedgehog/Gli1 Pathway
Authors: Zhao Zhiqiang , Jia Qiang , Wu Man-Si , Xie Xianbiao , Wang Yongqian , Song Guohui , Zou Chang-Ye , Tang Qinglian , Lu Jinchang , Huang Gang , Wang Jin , Lin De-Chen , Koeffler H. Phillip , Yin Jun-Qiang , Shen Jingnan
Published: April 2023

IHC analyses of the selected proteins indicated that the DGT-treated tumor tissues from the mice in Fig. 4A
Figure S4 from Degalactotigonin, a Natural Compound from Solanum nigrum L., Inhibits Growth and Metastasis of Osteosarcoma through GSK3β Inactivation–Mediated Repression of the Hedgehog/Gli1 Pathway
Authors: Zhao Zhiqiang , Jia Qiang , Wu Man-Si , Xie Xianbiao , Wang Yongqian , Song Guohui , Zou Chang-Ye , Tang Qinglian , Lu Jinchang , Huang Gang , Wang Jin , Lin De-Chen , Koeffler H. Phillip , Yin Jun-Qiang , Shen Jingnan
Published: April 2023

The weights of lungs from mice described in Figure 5E and F.
Supplemental Methods, Supplemental Tables 1-4, Supplemental Figures 1-8 from Synergy of WEE1 and mTOR Inhibition in Mutant KRAS-Driven Lung Cancers
Authors: Hai Josephine , Liu Shengwu , Bufe Lauren , Do Khanh , Chen Ting , Wang Xiaoen , Ng Christine , Li Shuai , Tsao Ming-Sound , Shapiro Geoffrey I. , Wong Kwok-Kin
Published: April 2023

Table S1. sgRNA and PAM sequences; Table S2. The IC50 values for AZD2014 and AZD1775 in NSCLC cells; Table S3. Mutational status of human cell line models; Table S4. CalcuSyn combination indices; Figure S1. Dose response curves; Figure S2. Combined mTOR and WEE1 inhibition induces synergistic apoptotic caspase activity; Figure S3. Combination treatment suppresses human KRAS-driven tumor xenografted growth; Figure S4. Mice with active KRAS-driven lung cancer show significant tumor response upon dual AZD1775 and AZD2014 therapy; Figure S5. Rad51 foci-forming ability of NSCLC cells in response to gemcitabine and etoposide treatment; Figure S6. Ectopic expression of LKB1 is sufficient to overcome the loss of the LKB1-mediated sensitization to dual AZD2014 and AZD1775 therapy; Figure S7. Loss of LKB1 in KRAS-mutant cell lines confers partial resistance to dual WEE1 and mTOR therapy; Figure S8. Ectopic expression of LKB1 is sufficient to overcome the loss of the LKB1-mediated sensitization to dual AZD2014 and AZD1775 therapy.
Supplementary methods: from Molecular Screening for Cancer Treatment Optimization (MOSCATO-01) in Pediatric Patients: A Single-Institutional Prospective Molecular Stratification Trial
Authors: Harttrampf Anne C. , Lacroix Ludovic , Deloger Marc , Deschamps Frederic , Puget Stephanie , Auger Nathalie , Vielh Philippe , Varlet Pascale , Balogh Zsofia , Abbou Samuel , Allorant Adrien , Valteau-Couanet Dominique , Sarnacki Sabine , Gamiche-Rolland Louise , Meurice Guillaume , Minard-Colin Veronique , Grill Jacques , Brugieres Laurence , Dufour Christelle , Gaspar Nathalie , Michiels Stefan , Vassal Gilles , Soria Jean-Charles , Geoerger Birgit
Published: April 2023

Supplementary methods genomics
Supplementary Material from Inactivation of Receptor Tyrosine Kinases Reverts Aberrant DNA Methylation in Acute Myeloid Leukemia
Authors: Shen Na , Yan Fei , Pang Jiuxia , Zhao Na , Gangat Naseema , Wu Laichu , Bode Ann M. , Al-Kali Aref , Litzow Mark R. , Liu Shujun
Published: April 2023

Supplementary Methods, Figures and References Supplementary Figure 1. Tyrosine kinases are positive regulators of DNMT-dependent DNA methylation in leukemia cells. Supplementary Figure 2. Nilotinib treatment inhibits KIT and FLT3 kinase signaling. Supplementary Figure 3. Treatment with RTK inhibitors decreases DNMT1 expression in vitro and in vivo. Supplementary Figure 4. The potential biochemical link between an RTK and DNMT1. Supplementary Figure 5. Nilotinib treatment induces global and gene specific DNA methylation through the Sp1-DNMT1 axis. Supplementary Figure 6. RTK dysfunction reactivates cyclin-dependent kinase inhibitors Supplementary Figure 7. DNMT1-dependent DNA methylation is increased in cells resistant to nilotinib. Supplementary Figure 8. Sp1 overexpression reduces the antileukemia activity of nilotinib. Supplementary Figure 9. Exposure to nilotinib leads to changes in pro- and anti-apoptotic proteins. Supplementary Figure 10. Nilotinib treatment displays no obvious changes in cell cycle. Supplementary Figure 11. Velcade or decitabine sensitizes AML cells to nilotinib treatment. Supplementary Figure 12. Nilotinib exposure induces cell apoptosis through modulation of DNA methylation in the C1498 mouse AML cell line. Supplementary Figure 13. Exposure of AML patient primary cells to nilotinib suppresses oncogene expression and promotes cell apoptosis. Supplementary Figure 14. The anti-leukemia activities of imatinib involve DNA methylation-associated pathways. Supplementary Table. Primer/probe sequences used in the experiments
Table S5. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures
Authors: Zhang Yanxiao , Koneva Lada A. , Virani Shama , Arthur Anna E. , Virani Alisha , Hall Pelle B. , Warden Charles D. , Carey Thomas E. , Chepeha Douglas B. , Prince Mark E. , McHugh Jonathan B. , Wolf Gregory T. , Rozek Laura S. , Sartor Maureen A.
Published: April 2023

The list of genes displayed in Figure 1D.
Supplementary methods and figures. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures
Authors: Zhang Yanxiao , Koneva Lada A. , Virani Shama , Arthur Anna E. , Virani Alisha , Hall Pelle B. , Warden Charles D. , Carey Thomas E. , Chepeha Douglas B. , Prince Mark E. , McHugh Jonathan B. , Wolf Gregory T. , Rozek Laura S. , Sartor Maureen A.
Published: April 2023

Supplementary methods and figures. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures
Supplemental Patient Information from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma
Authors: Chicard Mathieu , Boyault Sandrine , Colmet Daage Leo , Richer Wilfrid , Gentien David , Pierron Gaelle , Lapouble Eve , Bellini Angela , Clement Nathalie , Iacono Isabelle , Bréjon Stéphanie , Carrere Marjorie , Reyes Cécile , Hocking Toby , Bernard Virginie , Peuchmaur Michel , Corradini Nadège , Faure-Conter Cécile , Coze Carole , Plantaz Dominique , Defachelles Anne Sophie , Thebaud Estelle , Gambart Marion , Millot Frédéric , Valteau-Couanet Dominique , Michon Jean , Puisieux Alain , Delattre Olivier , Combaret Valérie , Schleiermacher Gudrun
Published: April 2023

Information on treatment protocols
Supplemental Figure 5 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma
Authors: Chicard Mathieu , Boyault Sandrine , Colmet Daage Leo , Richer Wilfrid , Gentien David , Pierron Gaelle , Lapouble Eve , Bellini Angela , Clement Nathalie , Iacono Isabelle , Bréjon Stéphanie , Carrere Marjorie , Reyes Cécile , Hocking Toby , Bernard Virginie , Peuchmaur Michel , Corradini Nadège , Faure-Conter Cécile , Coze Carole , Plantaz Dominique , Defachelles Anne Sophie , Thebaud Estelle , Gambart Marion , Millot Frédéric , Valteau-Couanet Dominique , Michon Jean , Puisieux Alain , Delattre Olivier , Combaret Valérie , Schleiermacher Gudrun
Published: April 2023

A TERT targeting breakpoint seen in the cfDNA is not seen in the primary NB DNA (case 58)
Figure S2 from In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The ϕ-Index
Authors: Bakas Spyridon , Akbari Hamed , Pisapia Jared , Martinez-Lage Maria , Rozycki Martin , Rathore Saima , Dahmane Nadia , O'Rourke Donald M. , Davatzikos Christos
Published: April 2023

Distributions of the median Euclidean distance between the near and far ROIs for each patient according to their EGFRvIII status. We note no significant difference between the two groups (p-value=0.6728).
Supplementary Table 2 from Interleukin-17–Producing Neutrophils Link Inflammatory Stimuli to Disease Progression by Promoting Angiogenesis in Gastric Cancer
Authors: Li Tuan-Jie , Jiang Yu-Ming , Hu Yan-Feng , Huang Lei , Yu Jiang , Zhao Li-Ying , Deng Hai-Jun , Mou Ting-Yu , Liu Hao , Yang Yang , Zhang Qi , Li Guo-Xin
Published: April 2023

Primers for real-time PCR
Supplementary Figure 3 from Direct Metabolic Interrogation of Dihydrotestosterone Biosynthesis from Adrenal Precursors in Primary Prostatectomy Tissues
Authors: Dai Charles , Chung Yoon-Mi , Kovac Evan , Zhu Ziqi , Li Jianneng , Magi-Galluzzi Cristina , Stephenson Andrew J. , Klein Eric A. , Sharifi Nima
Published: April 2023

Figure S3. T serves as a co-substrate of 5α-reductase but does not considerably alter the kinetics of AD metabolism in primary prostate tissues under mixed substrate conditions.
Table S10. Clinical characteristics of patients with CNS relapse. from Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P–Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases
Authors: Dubois Sydney , Viailly Pierre-Julien , Bohers Elodie , Bertrand Philippe , Ruminy Philippe , Marchand Vinciane , Maingonnat Catherine , Mareschal Sylvain , Picquenot Jean-Michel , Penther Dominique , Jais Jean-Philippe , Tesson Bruno , Peyrouze Pauline , Figeac Martin , Desmots Fabienne , Fest Thierry , Haioun Corinne , Lamy Thierry , Copie-Bergman Christiane , Fabiani Bettina , Delarue Richard , Peyrade Frédéric , André Marc , Ketterer Nicolas , Leroy Karen , Salles Gilles , Molina Thierry J. , Tilly Hervé , Jardin Fabrice
Published: April 2023

Clinical characteristics of the 17 patients with CNS relapse are provided, included time to CNS relapse, first-line treatment and response after first-line treatment. CR, Complete Response; PR, Partial Response; PD, Progressive Disease.
Multiplex genome editing to generate universal CAR T cells resistant to PD1 inhibition sup from Multiplex Genome Editing to Generate Universal CAR T Cells Resistant to PD1 Inhibition
Authors: Ren Jiangtao , Liu Xiaojun , Fang Chongyun , Jiang Shuguang , June Carl H. , Zhao Yangbing
Published: April 2023

Treating cancers using allogeneic universal CAR T cells resistant to PD1 inhibition generated by multiplex genome editing via CRISPR/Cas9 Supplementary Figure 1. Strategy of introducing CRISPR/Cas9 into T cells. Supplementary Figure 2. Multiple deliveries of gRNAs disrupts genes in human primary T cells with high efficiency without impairing effector function. Supplementary Figure 3. Proliferation test of CD3neg T cells. Supplementary Figure 4. Reduced alloreactivity of TCR and B2M double-disrupted T cells. Supplementary Figure 5. GVHD effect of gene-modified CAR T cells Supplementary Figure 5. Generation of universal CART cells deficient of PD1. Supplementary table 1
Supplementary table S1 from Molecular Markers Increase Precision of the European Association of Urology Non–Muscle-Invasive Bladder Cancer Progression Risk Groups
Authors: van Kessel Kim E.M. , van der Keur Kirstin A. , Dyrskjøt Lars , Algaba Ferran , Welvaart Naeromy Y.C. , Beukers Willemien , Segersten Ulrika , Keck Bastian , Maurer Tobias , Simic Tatjana , Horstmann Marcus , Grimm Marc-Oliver , Hermann Gregers G. , Mogensen Karin , Hartmann Arndt , Harving Niels , Petersen Astrid C. , Jensen Jørgen B. , Junker Kerstin , Boormans Joost L. , Real Francisco X. , Malats Núria , Malmström Per-Uno , Ørntoft Torben F. , Zwarthoff Ellen C.
Published: April 2023

Supplementary Table S1. Sequences of the primers and probes used in the methylation analyses for the different CpGs in the GATA2, TBX2, TBX3 and ZIC4 genes. All sequences are noted from 5'' to 3''.
Supplementary figure S7 from Molecular Markers Increase Precision of the European Association of Urology Non–Muscle-Invasive Bladder Cancer Progression Risk Groups
Authors: van Kessel Kim E.M. , van der Keur Kirstin A. , Dyrskjøt Lars , Algaba Ferran , Welvaart Naeromy Y.C. , Beukers Willemien , Segersten Ulrika , Keck Bastian , Maurer Tobias , Simic Tatjana , Horstmann Marcus , Grimm Marc-Oliver , Hermann Gregers G. , Mogensen Karin , Hartmann Arndt , Harving Niels , Petersen Astrid C. , Jensen Jørgen B. , Junker Kerstin , Boormans Joost L. , Real Francisco X. , Malats Núria , Malmström Per-Uno , Ørntoft Torben F. , Zwarthoff Ellen C.
Published: April 2023

Supplementary figure S7. Progression-free survival curve in patients with all EAU low risk tumors and EAU high risk patients with a good class tumor (good class: hypomethylated GATA2 and mutated FGFR3). Progressive disease is defined as progression to stage T2 or higher stage disease.
Table S7 from High-Risk TP53 Mutations Are Associated with Extranodal Extension in Oral Cavity Squamous Cell Carcinoma
Authors: Sandulache Vlad C. , Michikawa Chieko , Kataria Pranav , Gleber-Netto Frederico O. , Bell Diana , Trivedi Sanchit , Rao Xiayu , Wang Jing , Zhao Mei , Jasser Samar , Myers Jeffrey N. , Pickering Curtis R.
Published: April 2023

Table S7 from High-Risk TP53 Mutations Are Associated with Extranodal Extension in Oral Cavity Squamous Cell Carcinoma
Figure S2 from High-Risk TP53 Mutations Are Associated with Extranodal Extension in Oral Cavity Squamous Cell Carcinoma
Authors: Sandulache Vlad C. , Michikawa Chieko , Kataria Pranav , Gleber-Netto Frederico O. , Bell Diana , Trivedi Sanchit , Rao Xiayu , Wang Jing , Zhao Mei , Jasser Samar , Myers Jeffrey N. , Pickering Curtis R.
Published: April 2023

Figure S2 from High-Risk TP53 Mutations Are Associated with Extranodal Extension in Oral Cavity Squamous Cell Carcinoma
Figure S7 from The Transcriptional Coactivator TAZ Is a Potent Mediator of Alveolar Rhabdomyosarcoma Tumorigenesis
Authors: Deel Michael D. , Slemmons Katherine K. , Hinson Ashley R. , Genadry Katia C. , Burgess Breanne A. , Crose Lisa E.S. , Kuprasertkul Nina , Oristian Kristianne M. , Bentley Rex C. , Linardic Corinne M.
Published: April 2023

Additional analysis of xenograft tumors and drug studies.
Figure S6 from The Transcriptional Coactivator TAZ Is a Potent Mediator of Alveolar Rhabdomyosarcoma Tumorigenesis
Authors: Deel Michael D. , Slemmons Katherine K. , Hinson Ashley R. , Genadry Katia C. , Burgess Breanne A. , Crose Lisa E.S. , Kuprasertkul Nina , Oristian Kristianne M. , Bentley Rex C. , Linardic Corinne M.
Published: April 2023

Validation of Dox-inducible TAZ shRNA constructs in Rh30 cells.
Supplementary Figure 4 from T-Cell Exhaustion Signatures Vary with Tumor Type and Are Severe in Glioblastoma
Authors: Woroniecka Karolina , Chongsathidkiet Pakawat , Rhodin Kristen , Kemeny Hanna , Dechant Cosette , Farber S. Harrison , Elsamadicy Aladine A. , Cui Xiuyu , Koyama Shohei , Jackson Christina , Hansen Landon J. , Johanns Tanner M. , Sanchez-Perez Luis , Chandramohan Vidyalakshmi , Yu Yen-Rei Andrea , Bigner Darell D. , Giles Amber , Healy Patrick , Dranoff Glenn , Weinhold Kent J. , Dunn Gavin P. , Fecci Peter E.
Published: April 2023

Cytokine production across immunologic compartments
Supplementary data from Dual Inhibition of PIK3C3 and FGFR as a New Therapeutic Approach to Treat Bladder Cancer
Authors: Chen Chun-Han , Changou Chun A. , Hsieh Tsung-Han , Lee Yu-Ching , Chu Cheng-Ying , Hsu Kai-Cheng , Wang Hao-Ching , Lin Yu-Chen , Lo Yan-Ni , Liu Yun-Ru , Liou Jing-Ping , Yen Yun
Published: April 2023

Supplementary Fig. S1, Time-dependent effects of BGJ398 on autophagy in bladder cancer cells. Supplementary Figure. S2. In vitro inhibitory effects of MPT0L145 and SAR405 on PIK3C3 (VPS34). Supplementary Figure. S3. A and B, The potentiation of MPT0L145-increased cytotoxicity by PIK3C3 knockdown in Panc1 and A2780 cells. C and D, ROS inhibitors partially reversed MPT0L145-decreased cell viability. Supplementary Figure S4. Validation of ATG5-knockout (K.O.) RT-112 cells. Supplementary Fig. S5. A, Effect of specific CSF1R inhibitor, BLZ945, on the viability in RT-112 and RT-4 cells. B, Dual inhibition of FGFR3 signaling and autophagy by MPT0L145. C, Effect of MPT0L145 on necrosis in bladder cancer cells.
Supplemental Methods and Materials from The RARS–MAD1L1 Fusion Gene Induces Cancer Stem Cell–like Properties and Therapeutic Resistance in Nasopharyngeal Carcinoma
Authors: Zhong Qian , Liu Zhi-Hua , Lin Zhi-Rui , Hu Ze-Dong , Yuan Li , Liu Yan-min , Zhou Ai-Jun , Xu Li-Hua , Hu Li-Juan , Wang Zi-Feng , Guan Xin-Yuan , Hao Jia-Jie , Lui Vivian W.Y. , Guo Ling , Mai Hai-Qiang , Chen Ming-Yuan , Han Fei , Xia Yun-Fei , Grandis Jennifer R. , Zhang Xing , Zeng Mu-Sheng
Published: April 2023

Supplemental Methods and Materials
Supplementary Data from Autologous Dendritic Cells Pulsed with Allogeneic Tumor Cell Lysate in Mesothelioma: From Mouse to Human
Authors: Aerts Joachim G.J.V. , de Goeje Pauline L. , Cornelissen Robin , Kaijen-Lambers Margaretha E.H. , Bezemer Koen , van der Leest Cor H. , Mahaweni Niken M. , Kunert André , Eskens Ferry A.L.M. , Waasdorp Cynthia , Braakman Eric , van der Holt Bronno , Vulto Arnold G. , Hendriks Rudi W. , Hegmans Joost P.J.J. , Hoogsteden Henk C.
Published: April 2023

Supplementary Material and Methods: Preparation of allogeneic tumor lysate Figure S1: CD8 T-cells from DC immunotherapy treated mice show tumor cell killing capacity Figure S2: Progression free survival of patients in the first-in-human clinical study. Figure S3: Pre- and post-vaccination CT scans of patient 5 at two different heights. Table S1: Specification of all observed grade 1 and 2 respiratory, gastrointestinal and lab abnormalities Table S2: Additional treatment after progression
Supplementary Table S5 from FAM198B Is Associated with Prolonged Survival and Inhibits Metastasis in Lung Adenocarcinoma via Blockage of ERK-Mediated MMP-1 Expression
Authors: Hsu Chia-Ying , Chang Gee-Chen , Chen Yi-Ju , Hsu Yi-Chiung , Hsiao Yi-Jing , Su Kang-Yi , Chen Hsuan-Yu , Lin Chien-Yu , Chen Jin-Shing , Chen Yu-Ju , Hong Qi-Sheng , Ku Wen-Hui , Wu Chih-Ying , Ho Bing-Ching , Chiang Ching-Cheng , Yang Pan-Chyr , Yu Sung-Liang
Published: April 2023

Supplementary Table S5. is a List of Intact glycopeptides of purified FAM198B identified by Orbitrap Velos MS analysis and Byonic processing.
Figure S4 from The Glucocorticoid Receptor Is a Key Player for Prostate Cancer Cell Survival and a Target for Improved Antiandrogen Therapy
Authors: Puhr Martin , Hoefer Julia , Eigentler Andrea , Ploner Christian , Handle Florian , Schaefer Georg , Kroon Jan , Leo Angela , Heidegger Isabel , Eder Iris , Culig Zoran , Van der Pluijm Gabri , Klocker Helmut
Published: April 2023

(A,B) Measurement of cell proliferation by [3H]thymidine incorporation (A) or WST assay (B) after treatment with increasing concentrations of RU-486 for 6 d (data represent mean + SE from at least 3 independent experiments (***, p< 0.001).
Figure S10 from The Glucocorticoid Receptor Is a Key Player for Prostate Cancer Cell Survival and a Target for Improved Antiandrogen Therapy
Authors: Puhr Martin , Hoefer Julia , Eigentler Andrea , Ploner Christian , Handle Florian , Schaefer Georg , Kroon Jan , Leo Angela , Heidegger Isabel , Eder Iris , Culig Zoran , Van der Pluijm Gabri , Klocker Helmut
Published: April 2023

Analysis of GR mRNA and protein expression in long-term enzalutamide treated LNCaPabl, DUCaP, LAPC4, and LNCaP cells was performed by qRT-PCR and Western blot, respectively.
Supplementary Figure S1 from Lifetime Genistein Intake Increases the Response of Mammary Tumors to Tamoxifen in Rats
Authors: Zhang Xiyuan , Cook Katherine L. , Warri Anni , Cruz Idalia M. , Rosim Mariana , Riskin Jeffrey , Helferich William , Doerge Daniel , Clarke Robert , Hilakivi-Clarke Leena
Published: April 2023

Mammary tumor burden during tamoxifen (TAM) treatment in animals exposed to genistein (GEN).
Figure S2B from Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes
Authors: Xochelli Aliki , Baliakas Panagiotis , Kavakiotis Ioannis , Agathangelidis Andreas , Sutton Lesley-Ann , Minga Eva , Ntoufa Stavroula , Tausch Eugen , Yan Xiao-Jie , Shanafelt Tait , Plevova Karla , Boudjogra Myriam , Rossi Davide , Davis Zadie , Navarro Alba , Sandberg Yorick , Vojdeman Fie Juhl , Scarfo Lydia , Stavroyianni Niki , Sudarikov Andrey , Veronese Silvio , Tzenou Tatiana , Karan-Djurasevic Teodora , Catherwood Mark , Kienle Dirk , Chatzouli Maria , Facco Monica , Bahlo Jasmin , Pott Christiane , Pedersen Lone Bredo , Mansouri Larry , Smedby Karin E. , Chu Charles C. , Giudicelli Véronique , Lefranc Marie-Paule , Panagiotidis Panagiotis , Juliusson Gunnar , Anagnostopoulos Achilles , Vlahavas Ioannis , Antic Darko , Trentin Livio , Montillo Marco , Niemann Carsten , Döhner Hartmut , Langerak Anton W. , Pospisilova Sarka , Hallek Michael , Campo Elias , Chiorazzi Nicholas , Maglaveras Nikos , Oscier David , Gaidano Gianluca , Jelinek Diane F. , Stilgenbauer Stephan , Chouvarda Ioanna , Darzentas Nikos , Belessi Chrysoula , Davi Frederic , Hadzidimitriou Anastasia , Rosenquist Richard , Ghia Paolo , Stamatopoulos Kostas
Published: April 2023

Distinct immunogenetic profiles of CLL with mutated IGHV4-34 receptors are associated with distinct clinicobiological characterists. B. IGHV4-34 expressing M-CLL stereotyped subsets are characterized by distinct clinicobiological characteristics suggesting distinct disease models implicating both cell-intrinsic and cell-extrinsic factors in disease ontogeny and evolution.
Figure S2A from Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes
Authors: Xochelli Aliki , Baliakas Panagiotis , Kavakiotis Ioannis , Agathangelidis Andreas , Sutton Lesley-Ann , Minga Eva , Ntoufa Stavroula , Tausch Eugen , Yan Xiao-Jie , Shanafelt Tait , Plevova Karla , Boudjogra Myriam , Rossi Davide , Davis Zadie , Navarro Alba , Sandberg Yorick , Vojdeman Fie Juhl , Scarfo Lydia , Stavroyianni Niki , Sudarikov Andrey , Veronese Silvio , Tzenou Tatiana , Karan-Djurasevic Teodora , Catherwood Mark , Kienle Dirk , Chatzouli Maria , Facco Monica , Bahlo Jasmin , Pott Christiane , Pedersen Lone Bredo , Mansouri Larry , Smedby Karin E. , Chu Charles C. , Giudicelli Véronique , Lefranc Marie-Paule , Panagiotidis Panagiotis , Juliusson Gunnar , Anagnostopoulos Achilles , Vlahavas Ioannis , Antic Darko , Trentin Livio , Montillo Marco , Niemann Carsten , Döhner Hartmut , Langerak Anton W. , Pospisilova Sarka , Hallek Michael , Campo Elias , Chiorazzi Nicholas , Maglaveras Nikos , Oscier David , Gaidano Gianluca , Jelinek Diane F. , Stilgenbauer Stephan , Chouvarda Ioanna , Darzentas Nikos , Belessi Chrysoula , Davi Frederic , Hadzidimitriou Anastasia , Rosenquist Richard , Ghia Paolo , Stamatopoulos Kostas
Published: April 2023

Distinct immunogenetic profiles of CLL with mutated IGHV4-34 receptors are associated with distinct clinicobiological characterists. A. IGHV4-34 expressing M-CLL stereotyped subsets are characterized by ''public'' as well subset-biased SHM patterns that allude to both shared and distinct immunopathogenetic processes.
Figure S3E from Gene Expression Profiling in BRAF-Mutated Melanoma Reveals Patient Subgroups with Poor Outcomes to Vemurafenib That May Be Overcome by Cobimetinib Plus Vemurafenib
Authors: Wongchenko Matthew J. , McArthur Grant A. , Dréno Brigitte , Larkin James , Ascierto Paolo A. , Sosman Jeffrey , Andries Luc , Kockx Mark , Hurst Stephen D. , Caro Ivor , Rooney Isabelle , Hegde Priti S. , Molinero Luciana , Yue Huibin , Chang Ilsung , Amler Lukas , Yan Yibing , Ribas Antoni
Published: April 2023

Supplementary Figure S3. Association of the cell cycle/immune signature with E, disease stage.
Figure S3D from Gene Expression Profiling in BRAF-Mutated Melanoma Reveals Patient Subgroups with Poor Outcomes to Vemurafenib That May Be Overcome by Cobimetinib Plus Vemurafenib
Authors: Wongchenko Matthew J. , McArthur Grant A. , Dréno Brigitte , Larkin James , Ascierto Paolo A. , Sosman Jeffrey , Andries Luc , Kockx Mark , Hurst Stephen D. , Caro Ivor , Rooney Isabelle , Hegde Priti S. , Molinero Luciana , Yue Huibin , Chang Ilsung , Amler Lukas , Yan Yibing , Ribas Antoni
Published: April 2023

Supplementary Figure S3. Association of the cell cycle/immune signature with D, biopsy site.
Figure S3C from Gene Expression Profiling in BRAF-Mutated Melanoma Reveals Patient Subgroups with Poor Outcomes to Vemurafenib That May Be Overcome by Cobimetinib Plus Vemurafenib
Authors: Wongchenko Matthew J. , McArthur Grant A. , Dréno Brigitte , Larkin James , Ascierto Paolo A. , Sosman Jeffrey , Andries Luc , Kockx Mark , Hurst Stephen D. , Caro Ivor , Rooney Isabelle , Hegde Priti S. , Molinero Luciana , Yue Huibin , Chang Ilsung , Amler Lukas , Yan Yibing , Ribas Antoni
Published: April 2023

Supplementary Figure S3. Association of the cell cycle/immune signature with C, melanoma subtype.
Figure S3A from Gene Expression Profiling in BRAF-Mutated Melanoma Reveals Patient Subgroups with Poor Outcomes to Vemurafenib That May Be Overcome by Cobimetinib Plus Vemurafenib
Authors: Wongchenko Matthew J. , McArthur Grant A. , Dréno Brigitte , Larkin James , Ascierto Paolo A. , Sosman Jeffrey , Andries Luc , Kockx Mark , Hurst Stephen D. , Caro Ivor , Rooney Isabelle , Hegde Priti S. , Molinero Luciana , Yue Huibin , Chang Ilsung , Amler Lukas , Yan Yibing , Ribas Antoni
Published: April 2023

Supplementary Figure S3. Association of the cell cycle/immune signature with A, ECOG performance status.
Supplementary Table 3 from Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer
Authors: De Robertis Mariangela , Loiacono Luisa , Fusilli Caterina , Poeta Maria Luana , Mazza Tommaso , Sanchez Massimo , Marchionni Luigi , Signori Emanuela , Lamorte Giuseppe , Vescovi Angelo Luigi , Garcia-Foncillas Jesus , Fazio Vito Michele
Published: April 2023

Supplementary Table 3 - Univariate and multivariate analyses of factors affecting PFS in patients who received Cetuximab monotherapy belonging to EphA2high group (cohort 5, N=40).
Supplementary legend from Dendritic Cell/Cytokine-Induced Killer Cell Immunotherapy Combined with S-1 in Patients with Advanced Pancreatic Cancer: A Prospective Study
Authors: Jiang Ni , Qiao Guoliang , Wang Xiaoli , Morse Michael A. , Gwin William R. , Zhou Lei , Song Yuguang , Zhao Yanjie , Chen Feng , Zhou Xinna , Huang Lefu , Hobeika Amy , Yi Xin , Xia Xuefeng , Guan Yanfang , Song Jin , Ren Jun , Lyerly H. Kim
Published: April 2023

Supplementary legend
Figure S7 from Comparative Transcriptome Profiling Reveals Coding and Noncoding RNA Differences in NSCLC from African Americans and European Americans
Authors: Mitchell Khadijah A. , Zingone Adriana , Toulabi Leila , Boeckelman Jacob , Ryan Bríd M.
Published: April 2023

Hypergeometric testing for overlap between coding and noncoding expression signatures in AAs and EAs.
Figure S2 from Comparative Transcriptome Profiling Reveals Coding and Noncoding RNA Differences in NSCLC from African Americans and European Americans
Authors: Mitchell Khadijah A. , Zingone Adriana , Toulabi Leila , Boeckelman Jacob , Ryan Bríd M.
Published: April 2023

Unsupervised PCA of total gene expression from lung cancers in both AAs and EAs.
Table S6 from In-depth Genetic Analysis of Sclerosing Epithelioid Fibrosarcoma Reveals Recurrent Genomic Alterations and Potential Treatment Targets
Authors: Arbajian Elsa , Puls Florian , Antonescu Cristina R. , Amary Fernanda , Sciot Raf , Debiec-Rychter Maria , Sumathi Vaiyapuri P. , Järås Marcus , Magnusson Linda , Nilsson Jenny , Hofvander Jakob , Mertens Fredrik
Published: April 2023

Expression of the SEF vs controls 100-top up-regulated genes in Tet-On 3G cells expressing the EWSR1-CREB3L1 fusion
Figure S2 from Targeting Androgen Receptor Activation Function-1 with EPI to Overcome Resistance Mechanisms in Castration-Resistant Prostate Cancer
Authors: Yang Yu Chi , Banuelos Carmen Adriana , Mawji Nasrin R. , Wang Jun , Kato Minoru , Haile Simon , McEwan Iain J. , Plymate Stephen , Sadar Marianne D.
Published: April 2023

Immunohistochemistry of representative sections of LNCaP95 xenografts stained for AR-V7 and full-length (FL) AR. AR-V7 was stained by anti-AR-V7 antibody (Abcam) and FL AR was stained by anti-AR C19 antibody (Santa Cruz). Scale bars (red) indicate 20 µm.
Supplementary figure 5 from Synergistic Drug Combinations with a CDK4/6 Inhibitor in T-cell Acute Lymphoblastic Leukemia
Authors: Pikman Yana , Alexe Gabriela , Roti Giovanni , Conway Amy Saur , Furman Andrew , Lee Emily S. , Place Andrew E. , Kim Sunkyu , Saran Chitra , Modiste Rebecca , Weinstock David M. , Harris Marian , Kung Andrew L. , Silverman Lewis B. , Stegmaier Kimberly
Published: April 2023

LEE011 is synergistic with dexamethasone and everolimus.
Supplemental Figure 2 from Phase I Study of GDC-0425, a Checkpoint Kinase 1 Inhibitor, in Combination with Gemcitabine in Patients with Refractory Solid Tumors
Authors: Infante Jeffrey R. , Hollebecque Antoine , Postel-Vinay Sophie , Bauer Todd M. , Blackwood Elizabeth M. , Evangelista Marie , Mahrus Sami , Peale Franklin V. , Lu Xuyang , Sahasranaman Srikumar , Zhu Rui , Chen Yuan , Ding Xiao , Murray Elaine R. , Schutzman Jennifer L. , Lauchle Jennifer O. , Soria Jean-Charles , LoRusso Patricia M.
Published: April 2023

Supplemental Figure 2. Preclinical xenograft immunohistochemistry. HT-29 xenografts were analyzed for pCDK1/2 and Ki-67 expression. Representative images from 2 unique animals in each treatment group (n=5 animals per group) are shown. Ki-67 expression in surviving tumor cells is relatively consistent among treatment groups. pCDK1/2 expression increases from baseline (A, B) after gemcitabine treatment (I, J), whereas GDC-0425 alone (E, F) had little effect. In contrast, GDC-0425 given 16 hours after gemcitabine caused marked inhibition of the gemcitabine-induced expression of pCDK1/2. Scale bar=90 Âµm.
Supplementary Figure 2 from Synergistic Drug Combinations with a CDK4/6 Inhibitor in T-cell Acute Lymphoblastic Leukemia
Authors: Pikman Yana , Alexe Gabriela , Roti Giovanni , Conway Amy Saur , Furman Andrew , Lee Emily S. , Place Andrew E. , Kim Sunkyu , Saran Chitra , Modiste Rebecca , Weinstock David M. , Harris Marian , Kung Andrew L. , Silverman Lewis B. , Stegmaier Kimberly
Published: April 2023

LEE011 remains antagonistic with methotrexate, mercaptopurine, L-asparaginase and doxorubicin when cells are treated sequentially with each drug combination.
Supplemental Table 1 from Alterations in the Immune Cell Composition in Premalignant Breast Tissue that Precede Breast Cancer Development
Authors: Degnim Amy C. , Hoskin Tanya L. , Arshad Muhammad , Frost Marlene H. , Winham Stacey J. , Brahmbhatt Rushin A. , Pena Alvaro , Carter Jodi M. , Stallings-Mann Melody L. , Murphy Linda M. , Miller Erin E. , Denison Lori A. , Vachon Celine M. , Knutson Keith L. , Radisky Derek C. , Visscher Daniel W.
Published: April 2023

Distribution of immune cell densities per sample presented as a five-number summary including the minimum (Min), 25th percentile (Q25), median (Q50), 75th percentile (Q75), and maximum (Max).
Supplemental Table 3 from Phase 1 Study of Tabalumab, a Human Anti-B-Cell Activating Factor Antibody, and Bortezomib in Patients with Relapsed/Refractory Multiple Myeloma
Authors: Raje Noopur S. , Faber Edward A. , Richardson Paul G. , Schiller Gary , Hohl Raymond J. , Cohen Adam D. , Forero Andres , Carpenter Susan , Nguyen Tuan S. , Conti Ilaria , Kaiser Christopher J. , Cronier Damien M. , Wooldridge James E. , Anderson Kenneth C.
Published: April 2023

Bortezomib pharmacokinetic parameters following a single intravenous 1.3 mg/m2 bolus dose in the presence or absence of tabalumab and dexamethasone
Supplementary Table 4 from High Intratumoral Stromal Content Defines Reactive Breast Cancer as a Low-risk Breast Cancer Subtype
Authors: Dennison Jennifer B. , Shahmoradgoli Maria , Liu Wenbin , Ju Zhenlin , Meric-Bernstam Funda , Perou Charles M. , Sahin Aysegul A. , Welm Alana , Oesterreich Steffi , Sikora Matthew J. , Brown Robert E. , Mills Gordon B.
Published: April 2023

Classification of RPPA platform antibodies as "stromal" or ER-pos "cancer" enriched (Excel sheet)
Supplementary information from Inhibition of ID1–BMPR2 Intrinsic Signaling Sensitizes Glioma Stem Cells to Differentiation Therapy
Authors: Jin Xiong , Jin Xun , Kim Leo J.Y. , Dixit Deobrat , Jeon Hee-Young , Kim Eun-Jung , Kim Jun-Kyum , Lee Seon Yong , Yin Jinlong , Rich Jeremy N. , Kim Hyunggee
Published: April 2023

Supplementary figures 1-7, supplementary tables 1-4.
Table S2 from In Vivo Hemin Conditioning Targets the Vascular and Immunologic Compartments and Restrains Prostate Tumor Development
Authors: Jaworski Felipe M. , Gentilini Lucas D. , Gueron Geraldine , Meiss Roberto P. , Ortiz Emiliano G. , Berguer Paula M. , Ahmed Asif , Navone Nora , Rabinovich Gabriel A. , Compagno Daniel , Laderach Diego J. , Vazquez Elba S.
Published: April 2023

Expression microarray studies available in the Oncomine database that met our eligibility criteria.
Supplementary Figure 4 from Increases in Absolute Lymphocytes and Circulating CD4+ and CD8+ T Cells Are Associated with Positive Clinical Outcome of Melanoma Patients Treated with Ipilimumab
Authors: Martens Alexander , Wistuba-Hamprecht Kilian , Yuan Jianda , Postow Michael A. , Wong Phillip , Capone Mariaelena , Madonna Gabriele , Khammari Amir , Schilling Bastian , Sucker Antje , Schadendorf Dirk , Martus Peter , Dreno Brigitte , Ascierto Paolo A. , Wolchok Jedd D. , Pawelec Graham , Garbe Claus , Weide Benjamin
Published: April 2023

Impact of delayed increases in % of CD8+ T cells on overall survival. Kaplan-Meier analysis of overall survival according to delayed changes (increase vs. decrease) of % of CD8+ T cells observed during ipilimumab treatment within patients showing early increases in ALC and delayed increase in % of CD4+ T cells. Censoring is indicated by vertical lines; p-values were calculated by log rank statistics.
Supplementary Figure 1 from Increases in Absolute Lymphocytes and Circulating CD4+ and CD8+ T Cells Are Associated with Positive Clinical Outcome of Melanoma Patients Treated with Ipilimumab
Authors: Martens Alexander , Wistuba-Hamprecht Kilian , Yuan Jianda , Postow Michael A. , Wong Phillip , Capone Mariaelena , Madonna Gabriele , Khammari Amir , Schilling Bastian , Sucker Antje , Schadendorf Dirk , Martus Peter , Dreno Brigitte , Ascierto Paolo A. , Wolchok Jedd D. , Pawelec Graham , Garbe Claus , Weide Benjamin
Published: April 2023

Gating strategy for quantification of subsets of T cells and regulatory T cells (Tregs), monocytes and myeloid-derived suppressor cells (MDSCs). Total cells were selected by gating on Time vs. SSC-A. Duplicates were removed via progressive gating on FSC-H vs. FSC-A and SSC-H vs. SSC-A. Dead cells were excluded by considering only EMA-negative cells. (A) A morphological gate was used to identify the population of lymphocytes. Next, CD3+ cells were selected and further separated into CD4+ and CD8+ cells. Ki67 expression was investigated on CD4+ and CD8+ cells. CD8+ T cells with suppressive potential were defined as CD103+. Previously described phenotypes of Tregs were defined as CD4+CD25+FoxP3+ and CD4+CD127lowCD25+FoxP3+. These were further subdivided into proliferating (Ki67+CD45RA-) and non-proliferating Tregs (Ki67-CD45RA+). (B) A lineage cocktail (CD3, CD19, CD56) was used to avoid cross-contamination. Previously described MDSC populations were identified as Lin-CD14+HLA-DRlow and Lin-CD14-CD15+CD11b+ within the all-cell gate. Overall monocytes were defined as CD14+, while subsets were separated into classical monocytes (Lin-CD14+CD16-HLA-DR+), non-classical monocytes (Lin-CD14-CD16+HLA-DR+) and Lin- CD14-CD16dimHLA-DR+ monocytes within the all-cell gate.
Supplemental Tables from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay
Authors: Wang Lisha , Harms Paul W. , Palanisamy Nallasivam , Carskadon Shannon , Cao Xuhong , Siddiqui Javed , Patel Rajiv M. , Zelenka-Wang Sylvia , Durham Alison B. , Fullen Douglas R. , Harms Kelly L. , Su Fengyun , Shukla Sudhanshu , Mehra Rohit , Chinnaiyan Arul M.
Published: April 2023

ISH product scores.
Figure S4 from Genetic and Methylation-Induced Loss of miR-181a2/181b2 within chr9q33.3 Facilitates Tumor Growth of Cervical Cancer through the PIK3R3/Akt/FoxO Signaling Pathway
Authors: Mei Qian , Li Xiang , Zhang Kang , Wu Zhiqiang , Li Xiaolei , Meng Yuanguang , Guo Mingzhou , Luo Guangbin , Fu Xiaobing , Han Weidong
Published: April 2023

Figure S4. miR-181a2/b2 regulates PI3K/Akt/FoxO signal transduction in cervical cancer cells
Tables S1 and S3 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer
Authors: Beglyarova Natalya , Banina Eugenia , Zhou Yan , Mukhamadeeva Ramilia , Andrianov Grigorii , Bobrov Egor , Lysenko Elena , Skobeleva Natalya , Gabitova Linara , Restifo Diana , Pressman Max , Serebriiskii Ilya G. , Hoffman John P. , Paz Keren , Behrens Diana , Khazak Vladimir , Jablonski Sandra A. , Golemis Erica A. , Weiner Louis M. , Astsaturov Igor
Published: April 2023

Table S1. Genetic characterization of patient-derived xenografts using the Illumina Trusight panel capturing frequent mutations in 94 genes and 284 SNPs associated with cancer Table S3. Triptolide-induced effects on the mRNA abundance was determined by Illumina HighSeq RNA sequencing of 001 cells treated with 100 nM triptolide in vitro for 6 hours.
Figure S2 from Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects
Authors: Meijer Titia G. , Verkaik Nicole S. , Sieuwerts Anieta M. , van Riet Job , Naipal Kishan A.T. , van Deurzen Carolien H.M. , den Bakker Michael A. , Sleddens Hein F.B.M. , Dubbink Hendrikus-Jan , den Toom T. Dorine , Dinjens Winand N.M. , Lips Esther , Nederlof Petra M. , Smid Marcel , van de Werken Harmen J.G. , Kanaar Roland , Martens John W.M. , Jager Agnes , van Gent Dik C.
Published: April 2023

BRCA1 promoter hypermethylation and RNA in situ hybridization by RNAscope. M248, M253, M112 and M232 clearly showed presence of BRCA1 RNA, whereas in M94 (BRCA1 deletion) no BRCA1 RNA was present. M131 and M277 showed heterogeneous presence of BRCA1 RNA. PPIB probe = positive control
Supplemental Table 1 from Characterization of an Immunogenic Mutation in a Patient with Metastatic Triple-Negative Breast Cancer
Authors: Assadipour Yasmine , Zacharakis Nikolaos , Crystal Jessica S. , Prickett Todd D. , Gartner Jared J. , Somerville Robert P.T. , Xu Hui , Black Mary A. , Jia Li , Chinnasamy Harshini , Kriley Isaac , Lu Lily , Wunderlich John R. , Zheng Zhili , Lu Yong-Chen , Robbins Paul F. , Rosenberg Steven A. , Goff Stephanie L. , Feldman Steven A.
Published: April 2023

Tumor mutation profile.
Table S4 from Phase III Trial of Adjuvant Sunitinib in Patients with High-Risk Renal Cell Carcinoma: Exploratory Pharmacogenomic Analysis
Authors: George Daniel J. , Martini Jean-Francois , Staehler Michael , Motzer Robert J. , Magheli Ahmed , Donskov Frede , Escudier Bernard , Li Sherry , Casey Michelle , Valota Olga , Laguerre Brigitte , Pantuck Allan J. , Pandha Hardev S. , Patel Anup , Lechuga Maria , Ravaud Alain
Published: April 2023

Comparison of OS stratified by genotype and treatment group
Supplementary Figure S1 from Immune Microenvironment in Microsatellite-Instable Endometrial Cancers: Hereditary or Sporadic Origin Matters
Authors: Pakish Janelle B. , Zhang Qian , Chen Zhongyuan , Liang Han , Chisholm Gary B. , Yuan Ying , Mok Samuel C. , Broaddus Russell R. , Lu Karen H. , Yates Melinda S.
Published: April 2023

Supplementary Figure S1 shows example images of the fluorescent IHC multiplexing panels
Table S2 from Integrative Kinome Profiling Identifies mTORC1/2 Inhibition as Treatment Strategy in Ovarian Clear Cell Carcinoma
Authors: Caumanns Joseph J. , Berns Katrien , Wisman G. Bea A. , Fehrmann Rudolf S.N. , Tomar Tushar , Klip Harry , Meersma Gert J. , Hijmans E. Marielle , Gennissen Annemiek M.C. , Duiker Evelien W. , Weening Desiree , Itamochi Hiroaki , Kluin Roelof J.C. , Reyners Anna K.L. , Birrer Michael J. , Salvesen Helga B. , Vergote Ignace , van Nieuwenhuysen Els , Brenton James , Braicu E. Ioana , Kupryjanczyk Jolanta , Spiewankiewicz Beata , Mittempergher Lorenza , Bernards René , van der Zee Ate G.J. , de Jong Steven
Published: April 2023

Supplementary Table 2 | Gene set for Haloplex sequencing.
Supplementary Figure S2 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Authors: Vantaku Venkatrao , Dong Jianrong , Ambati Chandrashekar R. , Perera Dimuthu , Donepudi Sri Ramya , Amara Chandra Sekhar , Putluri Vasanta , Ravi Shiva Shankar , Robertson Matthew J. , Piyarathna Danthasinghe Waduge Badrajee , Villanueva Mariana , von Rundstedt Friedrich-Carl , Karanam Balasubramanyam , Ballester Leomar Y. , Terris Martha K. , Bollag Roni J. , Lerner Seth P. , Apolo Andrea B. , Villanueva Hugo , Lee MinJae , Sikora Andrew G. , Lotan Yair , Sreekumar Arun , Coarfa Cristian , Putluri Nagireddy
Published: April 2023

Supplementary Figure S2. Chromatographic reproducibility of metabolomics of liver samples over three technical replicates identified by LC-MS using HILIC positive, HILIC negative, and reverse phase positive ionization modes. B) Chromatographic reproducibility of lipidomics of liver samples over three technical replicates identified on the LC-MS using positive and, negative ionization modes.
Supplemental legend from Targeted Assessment of G0S2 Methylation Identifies a Rapidly Recurrent, Routinely Fatal Molecular Subtype of Adrenocortical Carcinoma
Authors: Mohan Dipika R. , Lerario Antonio Marcondes , Else Tobias , Mukherjee Bhramar , Almeida Madson Q. , Vinco Michelle , Rege Juilee , Mariani Beatriz M. P. , Zerbini Maria Claudia N. , Mendonca Berenice B. , Latronico Ana Claudia , Marie Suely K. N. , Rainey William E. , Giordano Thomas J. , Fragoso Maria Candida B. V. , Hammer Gary D.
Published: April 2023

Supplemental legend
Suupl. Figure 3 from Integrated Genomic and Immunophenotypic Classification of Pancreatic Cancer Reveals Three Distinct Subtypes with Prognostic/Predictive Significance
Authors: Wartenberg Martin , Cibin Silvia , Zlobec Inti , Vassella Erik , Eppenberger-Castori Serenella , Terracciano Luigi , Eichmann Micha David , Worni Mathias , Gloor Beat , Perren Aurel , Karamitopoulou Eva
Published: April 2023

CD8/Foxp3 and tumor budding
Suppl. Figure 5 from Integrated Genomic and Immunophenotypic Classification of Pancreatic Cancer Reveals Three Distinct Subtypes with Prognostic/Predictive Significance
Authors: Wartenberg Martin , Cibin Silvia , Zlobec Inti , Vassella Erik , Eppenberger-Castori Serenella , Terracciano Luigi , Eichmann Micha David , Worni Mathias , Gloor Beat , Perren Aurel , Karamitopoulou Eva
Published: April 2023

Density of Immune Infiltrates
Supplementary Table S4 from Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma
Authors: Wei Jun S. , Kuznetsov Igor B. , Zhang Shile , Song Young K. , Asgharzadeh Shahab , Sindiri Sivasish , Wen Xinyu , Patidar Rajesh , Najaraj Sushma , Walton Ashley , Auvil Jaime M. Guidry , Gerhard Daniela S. , Yuksel Aysen , Catchpoole Daniel , Hewitt Stephen M. , Sondel Paul M. , Seeger Robert , Maris John M. , Khan Javed
Published: April 2023

Supplementary Table S4
Supplementary Table S3 from Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma
Authors: Wei Jun S. , Kuznetsov Igor B. , Zhang Shile , Song Young K. , Asgharzadeh Shahab , Sindiri Sivasish , Wen Xinyu , Patidar Rajesh , Najaraj Sushma , Walton Ashley , Guidry Auvil Jaime M. , Gerhard Daniela S. , Yuksel Aysen , Catchpoole Daniel , Hewitt Stephen M. , Sondel Paul M. , Seeger Robert , Maris John M. , Khan Javed
Published: April 2023

Supplementary Table S3
Supplemental Table 3 from Prospective Genotyping of Hepatocellular Carcinoma: Clinical Implications of Next-Generation Sequencing for Matching Patients to Targeted and Immune Therapies
Authors: Harding James J. , Nandakumar Subhiksha , Armenia Joshua , Khalil Danny N. , Albano Melanie , Ly Michele , Shia Jinru , Hechtman Jaclyn F. , Kundra Ritika , El Dika Imane , Do Richard K. , Sun Yichao , Kingham T. Peter , D'Angelica Michael I. , Berger Michael F. , Hyman David M. , Jarnagin William , Klimstra David S. , Janjigian Yelena Y. , Solit David B. , Schultz Nikolaus , Abou-Alfa Ghassan K.
Published: April 2023

Outcomes to treatment based on genomic mutation