bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental Methods from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations
Authors: Huang Franklin W. , Mosquera Juan Miguel , Garofalo Andrea , Oh Coyin , Baco Maria , Amin-Mansour Ali , Rabasha Bokang , Bahl Samira , Mullane Stephanie A. , Robinson Brian D. , Aldubayan Saud , Khani Francesca , Karir Beerinder , Kim Eejung , Chimene-Weiss Jeremy , Hofree Matan , Romanel Alessandro , Osborne Joseph R. , Kim Jong Wook , Azabdaftari Gissou , Woloszynska-Read Anna , Sfanos Karen , De Marzo Angelo M. , Demichelis Francesca , Gabriel Stacey , Van Allen Eliezer M. , Mesirov Jill , Tamayo Pablo , Rubin Mark A. , Powell Isaac J. , Garraway Levi A.
Published: April 2023

Supplemental Methods
Supplemental Figures from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations
Authors: Huang Franklin W. , Mosquera Juan Miguel , Garofalo Andrea , Oh Coyin , Baco Maria , Amin-Mansour Ali , Rabasha Bokang , Bahl Samira , Mullane Stephanie A. , Robinson Brian D. , Aldubayan Saud , Khani Francesca , Karir Beerinder , Kim Eejung , Chimene-Weiss Jeremy , Hofree Matan , Romanel Alessandro , Osborne Joseph R. , Kim Jong Wook , Azabdaftari Gissou , Woloszynska-Read Anna , Sfanos Karen , De Marzo Angelo M. , Demichelis Francesca , Gabriel Stacey , Van Allen Eliezer M. , Mesirov Jill , Tamayo Pablo , Rubin Mark A. , Powell Isaac J. , Garraway Levi A.
Published: April 2023

Supplemental Figure 1. Copy number alterations of AAPC exome set. Supplemental Figure 2. Copy number analysis grouped by Gleason scores. Supplemental Figure 3. Recurrent somatic copy number alterations in the AAPC cohort. Supplemental Figure 4. Analysis of fraction of copy number altered genome in the AAPC exome and TCGA cohorts. Supplemental Figure 5. Prostatic adenocarcinomas with unique ERF mutations demonstrate decreased RNA expression by RNA ISH. Supplemental Figure 6. IGV screenshots of validated ERF mutations. Supplemental Figure 7. Frequencies of mutations in ERF across several published prostate cancer sequencing cohorts. Supplemental Figure 8. Visualization of deletions at chr19q13.2 in the TCGA cohort and analysis of SU2C/CRPC dataset for ERF mutations. Supplemental Figure 9. Association ERF deletion status with pathologic features. Supplemental Figure 10. Knockdown of ERF mRNA in prostate cancer cell lines and an immortalized prostate epithelial cell line. Supplemental Figure 11. Knockdown of ERF in PCâ€�3 cell line augments invasion and tumor xenograft growth. Supplemental Figure 12. Overexpression of ERF in PCâ€�3 cell line is associated with a growth inhibitory effect. Supplemental Figure 13. Knockdown of ERF in RWPEâ€�1 and LNCaP cell lines contributes to growth proliferation. Supplemental Figure 14. Overexpression of ERF in DUâ€�145 cell line. Supplemental Figure 15. Association of LHSâ€�AR ERF KD signature in the CCLE and CRPC datasets. Supplemental Figure 16. ERF mutation and deletions are mutually exclusive from ERG rearrangement events in the published TCGA cohort (n=333) (cbioportal.org). Supplemental Figure 17. ERF KD signature in setting of ERF overexpression and correlation with Gleason score. Supplemental Figure 18. Association of LHSâ€�AR ERF KD signature projected across the CCLE. Supplemental Figure 19. Mutation plot of combined AAPC (n=102) + TCGA (n=457) analysis. Supplemental Figure 20. ERF nucleotide sequence map.
Supplemental Figure Legends from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations
Authors: Huang Franklin W. , Mosquera Juan Miguel , Garofalo Andrea , Oh Coyin , Baco Maria , Amin-Mansour Ali , Rabasha Bokang , Bahl Samira , Mullane Stephanie A. , Robinson Brian D. , Aldubayan Saud , Khani Francesca , Karir Beerinder , Kim Eejung , Chimene-Weiss Jeremy , Hofree Matan , Romanel Alessandro , Osborne Joseph R. , Kim Jong Wook , Azabdaftari Gissou , Woloszynska-Read Anna , Sfanos Karen , De Marzo Angelo M. , Demichelis Francesca , Gabriel Stacey , Van Allen Eliezer M. , Mesirov Jill , Tamayo Pablo , Rubin Mark A. , Powell Isaac J. , Garraway Levi A.
Published: April 2023

Supplemental Figure Legends
Supplementary Tables S1-S15 from Biomarker Accessible and Chemically Addressable Mechanistic Subtypes of BRAF Melanoma
Authors: Eskiocak Banu , McMillan Elizabeth A. , Mendiratta Saurabh , Kollipara Rahul K. , Zhang Hailei , Humphries Caroline G. , Wang Changguang , Garcia-Rodriguez Jose , Ding Ming , Zaman Aubhishek , Rosales Tracy I. , Eskiocak Ugur , Smith Michael P. , Sudderth Jessica , Komurov Kakajan , Deberardinis Ralph J. , Wellbrock Claudia , Davies Michael A. , Wargo Jennifer A. , Yu Yonghao , De Brabander Jef K. , Williams Noelle S. , Chin Lynda , Rizos Helen , Long Georgina V. , Kittler Ralf , White Michael A.
Published: April 2023

Supplemental Table S1. Genome-wide RNAi toxicity screen z-scores, related to Supplemental Figure S1, Supplemental Table S2. Percent DNA copy number gain in melanoma tumor samples compared to normal skin, related to Supplemental Figure S1, Supplemental Table S3. Melanoma panel siRNA toxicity, related to Supplemental Figure S1, Supplemental Table S4. Whole genome transcript profiles, related to Supplemental Figure S1, Supplemental Table S5. GISTIC analysis and expression correlation of candidate melanoma hits, related to Supplemental Figure S1, Supplemental Table S6. SOX10 ChIPSeq, related to Supplemental Figure S3, Supplemental Table S7. SOX10 ChIPSeq motif targets, related to Supplemental Figure S3, Supplemental Table S8. SOX10 ChIPSeq motif targets hypergeometric distribution analysis, related to Supplemental Figure S3, Supplemental Table S9. Whole genome transcript arrays with siRNAs, related to Supplemental Figure S3, Supplemental Table S10. Candidate SOX10 targets, related to Supplemental Figure S3, Supplemental Table S11. Expression correlations in patient samples, related to Supplemental Figure S3, Supplemental Table S12. Elastic net prediction scores, related to Figures 1, 2 and 3, Supplemental Figures S4, S5 and S7, Supplemental Table S13. Elastic net prediction scores, related to Figure 2, Supplemental Table S14. S2N analysis of gene transcripts between TBK1i-sensitive and -resistant BRAF wild-type melanoma cell lines, related to Figure 3, Supplemental Table S15. TMT-phosphoproteomics peptide quantification, related to Figure S12.
Supplementary methods from A Digital RNA Signature of Circulating Tumor Cells Predicting Early Therapeutic Response in Localized and Metastatic Breast Cancer
Authors: Kwan Tanya T. , Bardia Aditya , Spring Laura M. , Giobbie-Hurder Anita , Kalinich Mark , Dubash Taronish , Sundaresan Tilak , Hong Xin , LiCausi Joseph A. , Ho Uyen , Silva Erin J. , Wittner Ben S. , Sequist Lecia V. , Kapur Ravi , Miyamoto David T. , Toner Mehmet , Haber Daniel A. , Maheswaran Shyamala
Published: April 2023

Methods describing microfluidic CTC enrichment, RNA extraction, amplification and detection, single cell and bulk RNA sequencing
Supplementary Figure S5 from Maturation Stage of T-cell Acute Lymphoblastic Leukemia Determines BCL-2 versus BCL-XL Dependence and Sensitivity to ABT-199
Authors: Chonghaile Triona Ni , Roderick Justine E. , Glenfield Cian , Ryan Jeremy , Sallan Stephen E. , Silverman Lewis B. , Loh Mignon L. , Hunger Stephen P. , Wood Brent , DeAngelo Daniel J. , Stone Richard , Harris Marian , Gutierrez Alejandro , Kelliher Michelle A. , Letai Anthony
Published: April 2023

Primary T-ALL samples were treated for six hours in short term culture with both ABT-199 and ABT-263. Apoptosis was assesed by Annexin V and Propidium Iodide staining. The calculated IC50 in μM is listed beside each of the BH3 mimetics.
Supplementary Figure S3 from Maturation Stage of T-cell Acute Lymphoblastic Leukemia Determines BCL-2 versus BCL-XL Dependence and Sensitivity to ABT-199
Authors: Chonghaile Triona Ni , Roderick Justine E. , Glenfield Cian , Ryan Jeremy , Sallan Stephen E. , Silverman Lewis B. , Loh Mignon L. , Hunger Stephen P. , Wood Brent , DeAngelo Daniel J. , Stone Richard , Harris Marian , Gutierrez Alejandro , Kelliher Michelle A. , Letai Anthony
Published: April 2023

Flow cytometry gating strategy to identify the early progenitor cells using CD44 and CD25 antibodies on the double negative CD4-/CD8- gate. BCL-2 expression and BCL-XL expression was measured on each of the gated regions listed.
Supplementary Table 6 from The Rodent Liver Undergoes Weaning-Induced Involution and Supports Breast Cancer Metastasis
Authors: Goddard Erica T. , Hill Ryan C. , Nemkov Travis , D'Alessandro Angelo , Hansen Kirk C. , Maller Ori , Mongoue-Tchokote Solange , Mori Motomi , Partridge Ann H. , Borges Virginia F. , Schedin Pepper
Published: April 2023

Patient statistical analysis summary.
Supplementary Data from Genomic Landscape of Cell-Free DNA in Patients with Colorectal Cancer
Authors: Strickler John H. , Loree Jonathan M. , Ahronian Leanne G. , Parikh Aparna R. , Niedzwiecki Donna , Pereira Allan Andresson Lima , McKinney Matthew , Korn W. Michael , Atreya Chloe E. , Banks Kimberly C. , Nagy Rebecca J. , Meric-Bernstam Funda , Lanman Richard B. , Talasaz AmirAli , Tsigelny Igor F. , Corcoran Ryan B. , Kopetz Scott
Published: April 2023

Suppementary Table S1: Gene lists and exon coverage; Supplementary Table S2: Patient Demographics; Supplementary Table S3. Mutational landscape in cfDNA; Supplementary Figure S1: Schema for identification of unique patient cases for analysis; Supplementary Figure S2. Impact of the number of mechanisms of resistance to anti-EGFR therapy on clonality and relative mutant allele frequency; Supplementary Figure S3: Clonal dynamics during anti-EGFR therapy in patient #18.
Supplementary Tables 1 and 2 and Supplementary Figures 1 and 2 from A Phase Ib Dose-Escalation Study of Encorafenib and Cetuximab with or without Alpelisib in Metastatic BRAF-Mutant Colorectal Cancer
Authors: van Geel Robin M.J.M. , Tabernero Josep , Elez Elena , Bendell Johanna C. , Spreafico Anna , Schuler Martin , Yoshino Takayuki , Delord Jean-Pierre , Yamada Yasuhide , Lolkema Martijn P. , Faris Jason E. , Eskens Ferry A.L.M. , Sharma Sunil , Yaeger Rona , Lenz Heinz-Josef , Wainberg Zev A. , Avsar Emin , Chatterjee Arkendu , Jaeger Savina , Tan Eugene , Maharry Kati , Demuth Tim , Schellens Jan H.M.
Published: April 2023

Table S1. Pharmacokinetic parameters of encorafenib and alpelisib in patients at steady state (cycle 2 day 1). Table S2. Criteria for defining dose-limited toxicities. Supplementary Figure 1. Radiological images of response for a patient treated with the dual-combination therapy of encorafenib and cetuximab. Supplementary Figure 2. Time on study by response for patients treated with the dual-combination therapy of encorafenib and cetuximab and patients treated with the triple-combination therapy of encorafenib, alpelisib, and cetuximab.
Supplementary Table 5 from Prediction of DNA Repair Inhibitor Response in Short-Term Patient-Derived Ovarian Cancer Organoids
Authors: Hill Sarah J. , Decker Brennan , Roberts Emma A. , Horowitz Neil S. , Muto Michael G. , Worley Michael J. , Feltmate Colleen M. , Nucci Marisa R. , Swisher Elizabeth M. , Nguyen Huy , Yang Chunyu , Morizane Ryuji , Kochupurakkal Bose S. , Do Khanh T. , Konstantinopoulos Panagiotis A. , Liu Joyce F. , Bonventre Joseph V. , Matulonis Ursula A. , Shapiro Geoffrey I. , Berkowitz Ross S. , Crum Christopher P. , D'Andrea Alan D.
Published: April 2023

Supplementary Table 5
Supplementary Table 4 from Prediction of DNA Repair Inhibitor Response in Short-Term Patient-Derived Ovarian Cancer Organoids
Authors: Hill Sarah J. , Decker Brennan , Roberts Emma A. , Horowitz Neil S. , Muto Michael G. , Worley Michael J. , Feltmate Colleen M. , Nucci Marisa R. , Swisher Elizabeth M. , Nguyen Huy , Yang Chunyu , Morizane Ryuji , Kochupurakkal Bose S. , Do Khanh T. , Konstantinopoulos Panagiotis A. , Liu Joyce F. , Bonventre Joseph V. , Matulonis Ursula A. , Shapiro Geoffrey I. , Berkowitz Ross S. , Crum Christopher P. , D'Andrea Alan D.
Published: April 2023

Supplementary Table 4
Supplementary Figures S1 - S10, Tables S1 - S2 from Cellular Senescence Promotes Adverse Effects of Chemotherapy and Cancer Relapse
Authors: Demaria Marco , O'Leary Monique N. , Chang Jianhui , Shao Lijian , Liu Su , Alimirah Fatouma , Koenig Kristin , Le Catherine , Mitin Natalia , Deal Allison M. , Alston Shani , Academia Emmeline C. , Kilmarx Sumner , Valdovinos Alexis , Wang Boshi , de Bruin Alain , Kennedy Brian K. , Melov Simon , Zhou Daohong , Sharpless Norman E. , Muss Hyman , Campisi Judith
Published: April 2023

Supplementary Figures S1 - S10, Tables S1 - S2
Supplementary Figure S4 from PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition
Authors: Mathur Deepti , Stratikopoulos Elias , Ozturk Sait , Steinbach Nicole , Pegno Sarah , Schoenfeld Sarah , Yong Raymund , Murty Vundavalli V. , Asara John M. , Cantley Lewis C. , Parsons Ramon
Published: April 2023

Supplementary Figure S4. DHODH is a target of sensitivity in PTEN deficient cells.
Supplementary Figure S3 from PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition
Authors: Mathur Deepti , Stratikopoulos Elias , Ozturk Sait , Steinbach Nicole , Pegno Sarah , Schoenfeld Sarah , Yong Raymund , Murty Vundavalli V. , Asara John M. , Cantley Lewis C. , Parsons Ramon
Published: April 2023

Supplementary Figure S3. PTEN loss confers sensitivity to de novo pyrimidine synthesis inhibition.
Table S2 from First-in-Class ERK1/2 Inhibitor Ulixertinib (BVD-523) in Patients with MAPK Mutant Advanced Solid Tumors: Results of a Phase I Dose-Escalation and Expansion Study
Authors: Sullivan Ryan J. , Infante Jeffrey R. , Janku Filip , Wong Deborah Jean Lee , Sosman Jeffrey A. , Keedy Vicki , Patel Manish R. , Shapiro Geoffrey I. , Mier James W. , Tolcher Anthony W. , Wang-Gillam Andrea , Sznol Mario , Flaherty Keith , Buchbinder Elizabeth , Carvajal Richard D. , Varghese Anna M. , Lacouture Mario E. , Ribas Antoni , Patel Sapna P. , DeCrescenzo Gary A. , Emery Caroline M. , Groover Anna L. , Saha Saurabh , Varterasian Mary , Welsch Dean J. , Hyman David M. , Li Bob T.
Published: April 2023

Dose levels enrolled in dose escalation with number and description of dose limiting toxicities at each dose level.
Table S1 from First-in-Class ERK1/2 Inhibitor Ulixertinib (BVD-523) in Patients with MAPK Mutant Advanced Solid Tumors: Results of a Phase I Dose-Escalation and Expansion Study
Authors: Sullivan Ryan J. , Infante Jeffrey R. , Janku Filip , Wong Deborah Jean Lee , Sosman Jeffrey A. , Keedy Vicki , Patel Manish R. , Shapiro Geoffrey I. , Mier James W. , Tolcher Anthony W. , Wang-Gillam Andrea , Sznol Mario , Flaherty Keith , Buchbinder Elizabeth , Carvajal Richard D. , Varghese Anna M. , Lacouture Mario E. , Ribas Antoni , Patel Sapna P. , DeCrescenzo Gary A. , Emery Caroline M. , Groover Anna L. , Saha Saurabh , Varterasian Mary , Welsch Dean J. , Hyman David M. , Li Bob T.
Published: April 2023

Tumor types and molecular alterations of enrolled patients
Supplementary Methods, Supplementary Tables 1 through 7, and Supplementary Figures 1 through 7 from Ibrutinib Unmasks Critical Role of Bruton Tyrosine Kinase in Primary CNS Lymphoma
Authors: Grommes Christian , Pastore Alessandro , Palaskas Nicolaos , Tang Sarah S. , Campos Carl , Schartz Derrek , Codega Paolo , Nichol Donna , Clark Owen , Hsieh Wan-Ying , Rohle Dan , Rosenblum Marc , Viale Agnes , Tabar Viviane S. , Brennan Cameron W. , Gavrilovic Igor T. , Kaley Thomas J. , Nolan Craig P. , Omuro Antonio , Pentsova Elena , Thomas Alissa A. , Tsyvkin Elina , Noy Ariela , Palomba M. Lia , Hamlin Paul , Sauter Craig S. , Moskowitz Craig H. , Wolfe Julia , Dogan Ahmet , Won Minhee , Glass Jon , Peak Scott , Lallana Enrico C. , Hatzoglou Vaios , Reiner Anne S. , Gutin Philip H. , Huse Jason T. , Panageas Katherine S. , Graeber Thomas G. , Schultz Nikolaus , DeAngelis Lisa M. , Mellinghoff Ingo K.
Published: April 2023

Supplementary Methods. Supplementary Table S1: Baseline characteristics of PCNSL Patients. Supplementary Table S2: Baseline characteristics of SCNSL patients. Supplementary Table S3: Corticosteroid use. Supplementary Table S4: Genes with Recurrent Mutations in PCNSL (non-aSHM). Supplementary Table S5: Genes that are targeted by aSHM in PCNSL. Supplementary Table S6: Comparison of mutation prevalence in current PCNSL genomic landscape analysis (red) with prior studies in PCNSL and DLBCL. Supplementary Table S7: Gene set enrichment analysis of CD79B-mutant PCNSLs compared to CD79B-wildtype PCNSLs. Supplementary Figure S1: Ibrutinib concentrations in Cerebrospinal Fluid (CSF). Supplementary Figure S2: Comparison of mutation frequencies in PCNSL and DLBCL outside the CNS. Supplementary Figure S3: Cell-of-origin (COO) Markers in PCNSL. Supplementary Figure S4: CD79B-mutant PCNSL xenograft models. Supplementary Figure S5: Comparison of PCNSL cells with non-CNS DLBCL cell lines. Supplementary Figure S6: Inhibition of individual PI3K isoforms does not induce cell death in CD79B-mutant PCNSL cells. Supplementary Figure S7: In-vitro effects of ibrutinib on CD79B-mutant PCNSL cells.
Supplementary Figure S8 from Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko
Published: April 2023

Supplementary Figure S8. The analysis of cells in the liver of DMBA-treated, HFD-fed mice.
Supplementary Figure S7 from Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko
Published: April 2023

Supplementary Figure S7. Lipidomics analysis revealed that PGs accumulate in the liver tumor areas.
Supplementary Figure S3 from Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko
Published: April 2023

Supplementary Figure S3. TLR2 specific response by LTA.
Supplementary Figure S2 from Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko
Published: April 2023

Supplementary Figure S2. Detection of cellular senescence in hepatic stellate cells.
Supplementary Figures 1 through 7, Supplementary Tables 1 through 7, and Supplementary Materials and Methods from Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer
Authors: Zou Min , Toivanen Roxanne , Mitrofanova Antonina , Floch Nicolas , Hayati Sheida , Sun Yanping , Le Magnen Clémentine , Chester Daniel , Mostaghel Elahe A. , Califano Andrea , Rubin Mark A. , Shen Michael M. , Abate-Shen Cory
Published: April 2023

Figure S1: Additional analyses of NP and NPp53 GEM models Figure S2: Tolerance and efficacy of abiraterone in mouse prostate Figure S3: Additional analyses of tumor volumes in GEM models before and after treatment Figure S4: Analyses of abiraterone treatment of cell lines from NP and NPp53 tumors Figure S5: Examples of alternative histopathologies of NPp53 CRPC Figure S6: Additional cross-species computational analyses Figure S7: Additional analyses of expression of SOX11 and other NE genes Table S1: Description of human datasets used in this study Table S2: Summary of preclinical phenotypic analyses Table S3: Summary of histopathology of individual mouse tumors Table S4: List of master regulators Table S5: Quantitation of synaptophysin-positive cells in mouse CRPC Table S6: List of antibodies used in this study Table S7: List of primers and shRNA used in this study Detailed experimental procedures
Supplementary Tables S1 - S10 from The Genetic Basis of Hepatosplenic T-cell Lymphoma
Authors: McKinney Matthew , Moffitt Andrea B. , Gaulard Philippe , Travert Marion , De Leval Laurence , Nicolae Alina , Raffeld Mark , Jaffe Elaine S. , Pittaluga Stefania , Xi Liqiang , Heavican Tayla , Iqbal Javeed , Belhadj Karim , Delfau-Larue Marie Helene , Fataccioli Virginie , Czader Magdalena B. , Lossos Izidore S. , Chapman-Fredricks Jennifer R. , Richards Kristy L. , Fedoriw Yuri , Ondrejka Sarah L. , Hsi Eric D. , Low Lawrence , Weisenburger Dennis , Chan Wing C. , Mehta-Shah Neha , Horwitz Steven , Bernal-Mizrachi Leon , Flowers Christopher R. , Beaven Anne W. , Parihar Mayur , Baseggio Lucile , Parrens Marie , Moreau Anne , Sujobert Pierre , Pilichowska Monika , Evens Andrew M. , Chadburn Amy , Au-Yeung Rex K.H. , Srivastava Gopesh , Choi William W. L. , Goodlad John R. , Aurer Igor , Basic-Kinda Sandra , Gascoyne Randy D. , Davis Nicholas S. , Li Guojie , Zhang Jenny , Rajagopalan Deepthi , Reddy Anupama , Love Cassandra , Levy Shawn , Zhuang Yuan , Datta Jyotishka , Dunson David B. , Davé Sandeep S.
Published: April 2023

Supplementary Table S1. Sanger validated variants. Supplementary Table S2. Mutations in HSTL driver genes. Supplementary Table S3. Other mutations identified by exome sequencing. Supplementary Table S4. Copy number of HSTL patients and cell lines. Supplementary Table S5. Clinical and pathological characteristics of HSTL patients. Supplementary Tables S6, S7. Comparison to HSTL clinical data in the literature. Supplementary Table S8. Mutational frequencies in other lymphomas. Supplementary Table S9. HSTL mutations in other lymphoma driver genes. Supplementary Table S10. Gene set enrichment analysis of DERL2 SETD2 shRNA.
Supplementary_table_S2 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Authors: Yang Dian , Denny Sarah K. , Greenside Peyton G. , Chaikovsky Andrea C. , Brady Jennifer J. , Ouadah Youcef , Granja Jeffrey M. , Jahchan Nadine S. , Lim Jing Shan , Kwok Shirley , Kong Christina S. , Berghoff Anna S. , Schmitt Anna , Reinhardt H. Christian , Park Kwon-Sik , Preusser Matthias , Kundaje Anshul , Greenleaf William J. , Sage Julien , Winslow Monte M.
Published: April 2023

table_S2_housekeeping_genes
Supplementary Figure 7 from AZD9291, an Irreversible EGFR TKI, Overcomes T790M-Mediated Resistance to EGFR Inhibitors in Lung Cancer
Authors: Cross Darren A.E. , Ashton Susan E. , Ghiorghiu Serban , Eberlein Cath , Nebhan Caroline A. , Spitzler Paula J. , Orme Jonathon P. , Finlay M. Raymond V. , Ward Richard A. , Mellor Martine J. , Hughes Gareth , Rahi Amar , Jacobs Vivien N. , Brewer Monica Red , Ichihara Eiki , Sun Jing , Jin Hailing , Ballard Peter , Al-Kadhimi Katherine , Rowlinson Rachel , Klinowska Teresa , Richmond Graham H.P. , Cantarini Mireille , Kim Dong-Wan , Ranson Malcolm R. , Pao William
Published: April 2023

PDF file - 470KB, Effect of AZD9291 and AZ5104 in transgenic models of EGFR-TKI sensitizing (C/L858R and C/ex19del) and T790M resistant (C/L+T) lung cancer.
Table S6 from TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia
Authors: Lobbardi Riadh , Pinder Jordan , Martinez-Pastor Barbara , Theodorou Marina , Blackburn Jessica S. , Abraham Brian J. , Namiki Yuka , Mansour Marc , Abdelfattah Nouran S. , Molodtsov Aleksey , Alexe Gabriela , Toiber Debra , de Waard Manon , Jain Esha , Boukhali Myriam , Lion Mattia , Bhere Deepak , Shah Khalid , Gutierrez Alejandro , Stegmaier Kimberly , Silverman Lewis B. , Sadreyev Ruslan I. , Asara John M. , Oettinger Marjorie A. , Haas Wilhelm , Look A. Thomas , Young Richard A. , Mostoslavsky Raul , Dellaire Graham , Langenau David M.
Published: April 2023

Table S6
Table S5 from TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia
Authors: Lobbardi Riadh , Pinder Jordan , Martinez-Pastor Barbara , Theodorou Marina , Blackburn Jessica S. , Abraham Brian J. , Namiki Yuka , Mansour Marc , Abdelfattah Nouran S. , Molodtsov Aleksey , Alexe Gabriela , Toiber Debra , de Waard Manon , Jain Esha , Boukhali Myriam , Lion Mattia , Bhere Deepak , Shah Khalid , Gutierrez Alejandro , Stegmaier Kimberly , Silverman Lewis B. , Sadreyev Ruslan I. , Asara John M. , Oettinger Marjorie A. , Haas Wilhelm , Look A. Thomas , Young Richard A. , Mostoslavsky Raul , Dellaire Graham , Langenau David M.
Published: April 2023

Table S5
Table S3 from TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia
Authors: Lobbardi Riadh , Pinder Jordan , Martinez-Pastor Barbara , Theodorou Marina , Blackburn Jessica S. , Abraham Brian J. , Namiki Yuka , Mansour Marc , Abdelfattah Nouran S. , Molodtsov Aleksey , Alexe Gabriela , Toiber Debra , de Waard Manon , Jain Esha , Boukhali Myriam , Lion Mattia , Bhere Deepak , Shah Khalid , Gutierrez Alejandro , Stegmaier Kimberly , Silverman Lewis B. , Sadreyev Ruslan I. , Asara John M. , Oettinger Marjorie A. , Haas Wilhelm , Look A. Thomas , Young Richard A. , Mostoslavsky Raul , Dellaire Graham , Langenau David M.
Published: April 2023

Table S3
Table S2 from TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia
Authors: Lobbardi Riadh , Pinder Jordan , Martinez-Pastor Barbara , Theodorou Marina , Blackburn Jessica S. , Abraham Brian J. , Namiki Yuka , Mansour Marc , Abdelfattah Nouran S. , Molodtsov Aleksey , Alexe Gabriela , Toiber Debra , de Waard Manon , Jain Esha , Boukhali Myriam , Lion Mattia , Bhere Deepak , Shah Khalid , Gutierrez Alejandro , Stegmaier Kimberly , Silverman Lewis B. , Sadreyev Ruslan I. , Asara John M. , Oettinger Marjorie A. , Haas Wilhelm , Look A. Thomas , Young Richard A. , Mostoslavsky Raul , Dellaire Graham , Langenau David M.
Published: April 2023

Table S2
Table S1 from TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia
Authors: Lobbardi Riadh , Pinder Jordan , Martinez-Pastor Barbara , Theodorou Marina , Blackburn Jessica S. , Abraham Brian J. , Namiki Yuka , Mansour Marc , Abdelfattah Nouran S. , Molodtsov Aleksey , Alexe Gabriela , Toiber Debra , de Waard Manon , Jain Esha , Boukhali Myriam , Lion Mattia , Bhere Deepak , Shah Khalid , Gutierrez Alejandro , Stegmaier Kimberly , Silverman Lewis B. , Sadreyev Ruslan I. , Asara John M. , Oettinger Marjorie A. , Haas Wilhelm , Look A. Thomas , Young Richard A. , Mostoslavsky Raul , Dellaire Graham , Langenau David M.
Published: April 2023

Table S1
Supplementary Methods, Tables 1 - 19, Figures 1 - 5 from Identification of Predictive Biomarkers for Cytokine Release Syndrome after Chimeric Antigen Receptor T-cell Therapy for Acute Lymphoblastic Leukemia
Authors: Teachey David T. , Lacey Simon F. , Shaw Pamela A. , Melenhorst J. Joseph , Maude Shannon L. , Frey Noelle , Pequignot Edward , Gonzalez Vanessa E. , Chen Fang , Finklestein Jeffrey , Barrett David M. , Weiss Scott L. , Fitzgerald Julie C. , Berg Robert A. , Aplenc Richard , Callahan Colleen , Rheingold Susan R. , Zheng Zhaohui , Rose-John Stefan , White Jason C. , Nazimuddin Farzana , Wertheim Gerald , Levine Bruce L. , June Carl H. , Porter David L. , Grupp Stephan A.
Published: April 2023

Supplementary methods, statistical methods, results, tables, and figures. Supplementary Table 1. CRS grading system. Supplementary Table 2. Samples collected and time points on the trials. Supplementary Table 3. HLH diagnostic criteria. Supplementary Table 4. Timing of severe CRS relative to CRS onset and time from infusion. Supplementary Table 5. Patient demographics and baseline characteristics. Supplementary Table 6. Co-morbid infections. Supplementary Table 7. Median (range) for baseline cytokine values comparing normal subjects and total study population, children on the trials, and adults on the trials. Supplementary Table 8. Median (range) baseline cytokine values comparing baseline disease burden. Supplementary Table 9. Median (range) one-month peak cytokine values in children and adults comparing CRS grades (0-3 vs 4-5). Supplementary Table 10. Time points of target cytokine assessment listed as day since CTL019 infusion, with the acceptable windows provided by the study protocols. Supplementary Table 11. Median (range) day 1-3 peak cytokine values for those with severe (grade 4-5) and without severe (grade 0-3) CRS for total study population, and split into adults and children. Supplementary Table 12. Summary of all predictive models generated by discovery cohort and validated. Supplementary Table 13. Clinical details on the validation cohort. Supplementary Table 14. Therapies used for CRS. Supplementary Table 15. Tocilizumab use by grade and age, as well as, clinical effects of tocilizumab on CRS. Supplementary Table 16. Lee CRS grading scale. Supplementary Table 17. Davila CRS grading scale. Supplementary Table 18. Reclassification of CRS severity by dividing grade 3 into 3a and 3b. Supplementary Table 19. Summary of top predictive models with alternate determination of CRS severity. Supplementary Figure 1. CRP and ferritin are poor early predictors of severe CRS. Supplementary Figure 2. Early increases in IFNγ and sgp130 after CTL019 infusion are associated with development of severe CRS. Supplementary Figure 3. Severity of CRS correlates moderately with CAR T cell expansion but early expansion of CAR T cells does not predict CRS severity. Supplementary Figure 4. Cytokine profiles predict CRS. Supplementary Figure 5. Alternate CRS prediction models.
Supplementary Tables from Longitudinal Liquid Biopsy and Mathematical Modeling of Clonal Evolution Forecast Time to Treatment Failure in the PROSPECT-C Phase II Colorectal Cancer Clinical Trial
Authors: Khan Khurum H. , Cunningham David , Werner Benjamin , Vlachogiannis Georgios , Spiteri Inmaculada , Heide Timon , Mateos Javier Fernandez , Vatsiou Alexandra , Lampis Andrea , Damavandi Mahnaz Darvish , Lote Hazel , Huntingford Ian Said , Hedayat Somaieh , Chau Ian , Tunariu Nina , Mentrasti Giulia , Trevisani Francesco , Rao Sheela , Anandappa Gayathri , Watkins David , Starling Naureen , Thomas Janet , Peckitt Clare , Khan Nasir , Rugge Massimo , Begum Ruwaida , Hezelova Blanka , Bryant Annette , Jones Thomas , Proszek Paula , Fassan Matteo , Hahne Jens C. , Hubank Michael , Braconi Chiara , Sottoriva Andrea , Valeri Nicola
Published: April 2023

Supplementary Tables
Supplementary Figure S2 from Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade
Authors: Gu Yi-Feng , Cohn Shannon , Christie Alana , McKenzie Tiffani , Wolff Nicholas , Do Quyen N. , Madhuranthakam Ananth J. , Pedrosa Ivan , Wang Tao , Dey Anwesha , Busslinger Meinrad , Xie Xian-Jin , Hammer Robert E. , McKay Renée M. , Kapur Payal , Brugarolas James
Published: April 2023

Validation of Pax8-Cre;Vhl;Pbrm1 mice
Supplementary Figure 1 from Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research
Authors: Hidalgo Manuel , Amant Frederic , Biankin Andrew V. , Budinská Eva , Byrne Annette T. , Caldas Carlos , Clarke Robert B. , de Jong Steven , Jonkers Jos , Mælandsmo Gunhild Mari , Roman-Roman Sergio , Seoane Joan , Trusolino Livio , Villanueva Alberto
Published: April 2023

Genomics Mimicry for Personalized Cancer Treatment.
Supplementary Methods, References, Figures 1-4, Tables 1-3 from A Next-Generation TRK Kinase Inhibitor Overcomes Acquired Resistance to Prior TRK Kinase Inhibition in Patients with TRK Fusion–Positive Solid Tumors
Authors: Drilon Alexander , Nagasubramanian Ramamoorthy , Blake James F. , Ku Nora , Tuch Brian B. , Ebata Kevin , Smith Steve , Lauriault Veronique , Kolakowski Gabrielle R. , Brandhuber Barbara J. , Larsen Paul D. , Bouhana Karyn S. , Winski Shannon L. , Hamor Robyn , Wu Wen-I , Parker Andrew , Morales Tony H. , Sullivan Francis X. , DeWolf Walter E. , Wollenberg Lance A. , Gordon Paul R. , Douglas-Lindsay Dorothea N. , Scaltriti Maurizio , Benayed Ryma , Raj Sandeep , Hanusch Bethany , Schram Alison M. , Jonsson Philip , Berger Michael F. , Hechtman Jaclyn F. , Taylor Barry S. , Andrews Steve , Rothenberg S. Michael , Hyman David M.
Published: April 2023

Supplementary Methods Supplementary References Supplementary Figure 1. Effect of acquired resistance mutations on TRK inhibitor activity. Supplementary Figure 2. Further characterization of LOXO-195 inhibitory activity against acquired resistance mutations. Supplementary Figure 3. LOXO-195 is selectively cytotoxic to TRK-fusion cell lines. Supplementary Figure 4. Identification of a clonal NTRK1 (TRKA)-G595R mutation after larotrectinib treatment. Supplementary Table 1. LOXO-195 ADME properties. Supplementary Table 2. Selectivity of LOXO-195 for 228 kinases. Supplementary Table 3. Summary of LOXO-195 PK parameters for each patient during intra-patient dose escalation.
Supplementary Tables S1 - S5 from In Vivo Genetic Screens of Patient-Derived Tumors Revealed Unexpected Frailty of the Transformed Phenotype
Authors: Bossi Daniela , Cicalese Angelo , Dellino Gaetano I. , Luzi Lucilla , Riva Laura , D'Alesio Carolina , Diaferia Giuseppe R. , Carugo Alessandro , Cavallaro Elena , Piccioni Rossana , Barberis Massimo , Mazzarol Giovanni , Testori Alessandro , Punzi Simona , Pallavicini Isabella , Tosti Giulio , Giacó Luciano , Melloni Giorgio , Heffernan Timothy P. , Natoli Gioacchino , Draetta Giulio F. , Minucci Saverio , Pelicci PierGiuseppe , Lanfrancone Luisa
Published: April 2023

Supplementary Table S1. Patient Demographics, and Clinical Characteristics of the Metastatic Cutaneous Melanomas and the Patient-derived xenografts (PDXs). Supplementary Table S2. A, Analysis of the epigenetic screening performed in MM13, MM16 and MM27 PDXs. B, Summary of the epigenetic screening results. Supplementary Table S3. List of shRNAs composing the 80sh-library (shRNA ID), sequenced hairpins and associated barcodes, and Log2(ratio) values derived from the screening analysis of MM13, MM16 and MM27 PDXs. Supplementary Table S4. List of the 103 genes specifically de-regulated in the two NRAS-mutated patients. Supplementary Table S5. Values of RNA expression of 52 candidate genes in metastatic melanoma PDXs.
Table S8 from A Phase Ib Dose-Escalation and Expansion Study of the BCL2 Inhibitor Venetoclax Combined with Tamoxifen in ER and BCL2–Positive Metastatic Breast Cancer
Authors: Lok Sheau W. , Whittle James R. , Vaillant François , Teh Charis E. , Lo Louisa L. , Policheni Antonia N. , Bergin Alice R.T. , Desai Jayesh , Ftouni Sarah , Gandolfo Luke C. , Liew Danny , Liu He K. , Mann G. Bruce , Moodie Kate , Murugasu Anand , Pal Bhupinder , Roberts Andrew W. , Rosenthal Mark A. , Shackleton Kylie , Silva Maria João , Siow Zhen R. , Smyth Gordon K. , Taylor Leanne , Travers Avraham , Yeo Belinda , Yeung Miriam M. , Bujak Andjelija Zivanovic , Dawson Sarah-Jane , Gray Daniel H.D. , Visvader Jane E. , Lindeman Geoffrey J.
Published: April 2023

Supplementary Table S8
Table S6 from A Phase Ib Dose-Escalation and Expansion Study of the BCL2 Inhibitor Venetoclax Combined with Tamoxifen in ER and BCL2–Positive Metastatic Breast Cancer
Authors: Lok Sheau W. , Whittle James R. , Vaillant François , Teh Charis E. , Lo Louisa L. , Policheni Antonia N. , Bergin Alice R.T. , Desai Jayesh , Ftouni Sarah , Gandolfo Luke C. , Liew Danny , Liu He K. , Mann G. Bruce , Moodie Kate , Murugasu Anand , Pal Bhupinder , Roberts Andrew W. , Rosenthal Mark A. , Shackleton Kylie , Silva Maria João , Siow Zhen R. , Smyth Gordon K. , Taylor Leanne , Travers Avraham , Yeo Belinda , Yeung Miriam M. , Bujak Andjelija Zivanovic , Dawson Sarah-Jane , Gray Daniel H.D. , Visvader Jane E. , Lindeman Geoffrey J.
Published: April 2023

Supplementary Table S6
Figures S1-8 from A Phase Ib Dose-Escalation and Expansion Study of the BCL2 Inhibitor Venetoclax Combined with Tamoxifen in ER and BCL2–Positive Metastatic Breast Cancer
Authors: Lok Sheau W. , Whittle James R. , Vaillant François , Teh Charis E. , Lo Louisa L. , Policheni Antonia N. , Bergin Alice R.T. , Desai Jayesh , Ftouni Sarah , Gandolfo Luke C. , Liew Danny , Liu He K. , Mann G. Bruce , Moodie Kate , Murugasu Anand , Pal Bhupinder , Roberts Andrew W. , Rosenthal Mark A. , Shackleton Kylie , Silva Maria João , Siow Zhen R. , Smyth Gordon K. , Taylor Leanne , Travers Avraham , Yeo Belinda , Yeung Miriam M. , Bujak Andjelija Zivanovic , Dawson Sarah-Jane , Gray Daniel H.D. , Visvader Jane E. , Lindeman Geoffrey J.
Published: April 2023

Supplementary Figures
supplementary table S2 from HOXA9 Cooperates with Activated JAK/STAT Signaling to Drive Leukemia Development
Authors: de Bock Charles E. , Demeyer Sofie , Degryse Sandrine , Verbeke Delphine , Sweron Bram , Gielen Olga , Vandepoel Roel , Vicente Carmen , Vanden Bempt Marlies , Dagklis Antonis , Geerdens Ellen , Bornschein Simon , Gijsbers Rik , Soulier Jean , Meijerink Jules P. , Heinäniemi Merja , Teppo Susanna , Bouvy-Liivrand Maria , Lohi Olli , Radaelli Enrico , Cools Jan
Published: April 2023

supplementary table (excel)
Supplemental tables and figures from HOXA9 Cooperates with Activated JAK/STAT Signaling to Drive Leukemia Development
Authors: de Bock Charles E. , Demeyer Sofie , Degryse Sandrine , Verbeke Delphine , Sweron Bram , Gielen Olga , Vandepoel Roel , Vicente Carmen , Vanden Bempt Marlies , Dagklis Antonis , Geerdens Ellen , Bornschein Simon , Gijsbers Rik , Soulier Jean , Meijerink Jules P. , Heinäniemi Merja , Teppo Susanna , Bouvy-Liivrand Maria , Lohi Olli , Radaelli Enrico , Cools Jan
Published: April 2023

Supplemental tables and figures
Supplementary Table 2 from A Stromal Lysolipid–Autotaxin Signaling Axis Promotes Pancreatic Tumor Progression
Authors: Auciello Francesca R. , Bulusu Vinay , Oon Chet , Tait-Mulder Jacqueline , Berry Mark , Bhattacharyya Sohinee , Tumanov Sergey , Allen-Petersen Brittany L. , Link Jason , Kendsersky Nicholas D. , Vringer Esmee , Schug Michelle , Novo David , Hwang Rosa F. , Evans Ronald M. , Nixon Colin , Dorrell Craig , Morton Jennifer P. , Norman Jim C. , Sears Rosalie C. , Kamphorst Jurre J. , Sherman Mara H.
Published: April 2023

Table S2
Supplementary Figures from A Stromal Lysolipid–Autotaxin Signaling Axis Promotes Pancreatic Tumor Progression
Authors: Auciello Francesca R. , Bulusu Vinay , Oon Chet , Tait-Mulder Jacqueline , Berry Mark , Bhattacharyya Sohinee , Tumanov Sergey , Allen-Petersen Brittany L. , Link Jason , Kendsersky Nicholas D. , Vringer Esmee , Schug Michelle , Novo David , Hwang Rosa F. , Evans Ronald M. , Nixon Colin , Dorrell Craig , Morton Jennifer P. , Norman Jim C. , Sears Rosalie C. , Kamphorst Jurre J. , Sherman Mara H.
Published: April 2023

Figure S1-S5 with legends
Table S3 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

Antibodies and reagents used in Materials and Methods.
Supplementary Table 3 from Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress
Authors: Port Jennifer , Muthalagu Nathiya , Raja Meera , Ceteci Fatih , Monteverde Tiziana , Kruspig Björn , Hedley Ann , Kalna Gabriela , Lilla Sergio , Neilson Lisa , Brucoli Martina , Gyuraszova Katarina , Tait-Mulder Jacqueline , Mezna Mokdad , Svambaryte Silvija , Bryson Amy , Sumpton David , McVie Allan , Nixon Colin , Drysdale Martin , Esumi Hiroyasu , Murray Graeme I. , Sansom Owen J. , Zanivan Sara R. , Murphy Daniel J.
Published: April 2023

Excel spreadsheet of NUAK1 inhibitor induced phospho-peptide alterations
Table S2 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

Grading system for neurotoxicity.
Supplementary Methods from Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress
Authors: Port Jennifer , Muthalagu Nathiya , Raja Meera , Ceteci Fatih , Monteverde Tiziana , Kruspig Björn , Hedley Ann , Kalna Gabriela , Lilla Sergio , Neilson Lisa , Brucoli Martina , Gyuraszova Katarina , Tait-Mulder Jacqueline , Mezna Mokdad , Svambaryte Silvija , Bryson Amy , Sumpton David , McVie Allan , Nixon Colin , Drysdale Martin , Esumi Hiroyasu , Murray Graeme I. , Sansom Owen J. , Zanivan Sara R. , Murphy Daniel J.
Published: April 2023

Supplementary Methods
Table S1 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

CD20 CAR T cell ex vivo expansion characteristics.
Figure S5 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

CSF and serum levels of 21 cytokines and chemokines measured before and at indicated days after adoptive CD20 CAR T cell transfer.
Figure S2 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

Absolute numbers of RM EGFRt- (non-CAR) T cells before and at indicated days after adoptive CD20 CAR T cell transfer in the blood.
Supplemetary Material and Tables from Identification of Pik3ca Mutation as a Genetic Driver of Prostate Cancer That Cooperates with Pten Loss to Accelerate Progression and Castration-Resistant Growth
Authors: Pearson Helen B. , Li Jason , Meniel Valerie S. , Fennell Christina M. , Waring Paul , Montgomery Karen G. , Rebello Richard J. , Macpherson Arthi A. , Koushyar Sarah , Furic Luc , Cullinane Carleen , Clarkson Richard W. , Smalley Matthew J. , Simpson Kaylene J. , Phesse Toby J. , Shepherd Peter R. , Humbert Patrick O. , Sansom Owen J. , Phillips Wayne A.
Published: April 2023

Supplemetary Material and Tables S1 - S7
Figure S5 from Identification of Pik3ca Mutation as a Genetic Driver of Prostate Cancer That Cooperates with Pten Loss to Accelerate Progression and Castration-Resistant Growth
Authors: Pearson Helen B. , Li Jason , Meniel Valerie S. , Fennell Christina M. , Waring Paul , Montgomery Karen G. , Rebello Richard J. , Macpherson Arthi A. , Koushyar Sarah , Furic Luc , Cullinane Carleen , Clarkson Richard W. , Smalley Matthew J. , Simpson Kaylene J. , Phesse Toby J. , Shepherd Peter R. , Humbert Patrick O. , Sansom Owen J. , Phillips Wayne A.
Published: April 2023

Supplementary Figure 5: Pik3caH1047R mutation and Pten-deletion synergize to promote prostate cancer by increasing mTORC1/2 signaling. Histograms displaying phenotype incidence for anterior (A) and ventral (B) prostate lobes at 56 and 100 days of age. (C) Representative IHC images of Pik3ca+/HR;Ptenfl/fl prostate tumors at 100 d stained to detect CK8, CK5 and SMA (n = 3, scale bar: 50 um). (D) Bar chart displaying total prostate weight normalised to body weight for Wt (n = 7), Pik3ca+/HR (n = 8), Ptenfl/fl (n = 8) and Pik3ca+/HR;Ptenfl/fl (n = 7) 100 d old mice. Error bars: SEM, *P <0.05 compared to Wt or as indicated, one-way ANOVA with Tukey's multiple comparison test. (E) Quantitation of the apoptotic marker Cleaved-Caspase-3 (CC3) positive nuclei and (F) representative IHC images of CC3 staining in Pik3ca+/HR, Ptenfl/fl and Pik3ca+/HR;Ptenfl/fl stage-matched invasive prostate carcinoma (scale bar: 50 um, n = 3, one-way ANOVA with Tukey's multiple comparison test. Error bars: SEM). (G) Representative IHC images of Pik3ca+/HR, Ptenfl/fl and Pik3ca+/HR;Ptenfl/fl stage-matched invasive prostate carcinoma stained to detect p-AKT Thr308, p-RPS6 Ser235/236, p-4E-BP1 Thr37/46, p-AKT Ser473 and p-NDRG1 Thr346 (scale bar: 50 um). (H) Representative images of RNA in situ hybridisation (ISH) to detect positive (housekeeping gene PPIB, peptidylprolyl isomerase B) and negative (bacterial gene dapB) control probes to confirm RNA quality and the absence of background signal respectively (scale bar: 50 um, insert scale bar: 5 um).
Figure S4 from Identification of Pik3ca Mutation as a Genetic Driver of Prostate Cancer That Cooperates with Pten Loss to Accelerate Progression and Castration-Resistant Growth
Authors: Pearson Helen B. , Li Jason , Meniel Valerie S. , Fennell Christina M. , Waring Paul , Montgomery Karen G. , Rebello Richard J. , Macpherson Arthi A. , Koushyar Sarah , Furic Luc , Cullinane Carleen , Clarkson Richard W. , Smalley Matthew J. , Simpson Kaylene J. , Phesse Toby J. , Shepherd Peter R. , Humbert Patrick O. , Sansom Owen J. , Phillips Wayne A.
Published: April 2023

Supplementary Figure 4: Pik3caH1047R heterozygous oncogenic mutation causes p110alpha-dependent prostate cancer. Representative H&E images (scale bar: 100 um) for Pik3ca+/HR and Ptenfl/fl dorsolateral prostate and histograms displaying phenotype incidence for anterior (B) and ventral (C) prostate lobes from Pik3ca+/HR and Ptenfl/fl mice treated with vehicle, p110alphaï�¡inhibitor (A66), p110beta inhibitor (TGX-221), pan-PI3K inhibitor (BKM120) or A66 + TGX-221 for 4 weeks. ND = not done. A66 and TGX-221 were generated in house by P.R.S. (University of Auckland, New Zealand) (14) and BKM120 was obtained from SYNkinase (Australia).
Supplementary Material from Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in BRAFV600E Colorectal Cancer
Authors: Hazar-Rethinam Mehlika , Kleyman Marianna , Han G. Celine , Liu David , Ahronian Leanne G. , Shahzade Heather A. , Chen Lifeng , Parikh Aparna R. , Allen Jill N. , Clark Jeffrey W. , Kwak Eunice L. , Faris Jason E. , Murphy Janet E. , Hong Theodore S. , Van Seventer Emily E. , Nadres Brandon , Hong Catriona B. , Gurski Joseph M. , Jessop Nicholas A. , Dias-Santagata Dora , Iafrate A. John , Van Allen Eliezer M. , Corcoran Ryan B.
Published: April 2023

Supplementary Figures, Tables, Methods