bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 1 from Targeting c-Jun is a potential therapy for luminal breast cancer bone metastasis
Authors: Han Yuxuan , Katayama Shota , Futakuchi Mitsuru , Nakamichi Kazuya , Wakabayashi Yutaro , Sakamoto Mai , Nakayama Jun , Semba Kentaro
Published: September 2024

Characterization of c-Jun overexpression in MCF7-BM cells.
Supplementary Figure Legends 1-6 from Oncostatin-M and OSM-Receptor feed-forward activation of MAPK induces separable stem-like and mesenchymal programs
Authors: Polak Kelsey L. , Tamagno Ilaria , Parameswaran Neetha , Smigiel Jacob , Chan E. Ricky , Yuan Xueer , Rios Brenda , Jackson Mark W.
Published: September 2024

Supplementary Figure Legends 1-6
Supplementary Table 4 from Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2024

Supplementary Table 4. The Chi-squared and Fisher’s Exact tests of metastases in the group of mice with orthotopic tumor.
Supplementary Figure 6 from Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2024

Figure S6. (A) Immunostaining of Gal-3 (green) and Na+/K+-ATPase (red) in control and HCQ-treated PC-3 cells; bars, 20 µm. (B) Quantification of Gal-3 integrated intensity at PM in cells from A. Mann Whitney test; *p<0.05, mean ± SD; n indicates number of cells.
Supplementary Figure 4 from Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2024

Figure S4. (A) Representative images of Golgi in DU145 cells treated with 60 µM HCQ for 72 h and stained by GM130 (green); bars, 20 µm. (B) Quantification of Golgi spots per cell in samples from A. Unpaired t test; **p<0.01, mean ± SD; n represents a number of cells counted. (C) Representative images of Golgi in DU145 cells treated with control or ATF6α siRNAs and stained by GM130 (green); bars, 20 µm. (D) Quantification of Golgi spots per cell in samples from C. Unpaired t test; ***p<0.001, mean ± SD; n represents number of cells counted. (E) ATF6 W-B of the lysates of DU145 cells transfected with control or ATF6α siRNAs; β-actin is a loading control. (F) Representative images of Golgi in PC-3 cells treated with control or ATG5 siRNAs and stained by GM130 (green); bars, 20 µm. (G) Quantification of Golgi spots per cell in samples from F. Unpaired t test; ****p<0.0001, mean ± SD; n represents number of cells counted. (H) ATG5 W-B of the lysates of PC-3 cells transfected with control or ATG5 siRNAs; γ-tubulin is a loading control. (I) Representative images of Golgi in DU145 cells treated with control or ATG5 siRNAs and stained by GM130 (green); bars, 20 µm. (J) Quantification of Golgi spots per cell in samples from I. Unpaired t test; ****p<0.0001, mean ± SD; n represents number of cells counted. (K) ATG5 W-B of the lysates of DU145 cells transfected with control or ATG5 siRNAs; γ-tubulin is a loading control. (L) Representative images of Golgi in PC-3 cells treated with Bafilomycin A1 (10 µM for 72 h) or appropriate amount of DMSO and stained by GM130 (green); bars, 20 µm. (M) Quantification of Golgi spots per cell in samples from L. Unpaired t test; ****p<0.0001, mean ± SD; n represents number of cells counted. (N-R) GRASP65 (N), GM130 (O), Giantin (P), Golgin-245 (Q), and TGN46 (R) W-Bs of the lysates of PC-3 cells treated with HCQ; β-actin is a loading control. All data presented are representative of at least three independent experiments.
Supplementary Figure 1 from Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2024

Figure S1. (A) Representative images of triple IHC staining of Integrin αvβ3 (green), Gal-3 (red), and E-cadherin (brown) in normal prostate and tumor tissues from PCa patients with different grades. Deconvoluted images of Integrin αvβ3 are shown on the right; bars, 50 µm. (B) Quantification of Integrin αvβ3 H-score at PM from samples in A. Dunn Test (1964) Kruskal-Wallis multiple comparisons, p-adjusted using Benjamini-Hochberg; ****p<0.0001 and *p<0.05, median ± SD. (C) Quantification of Integrin αvβ3 and Gal-3 colocalization at PM in normal prostate and PCa with grades 2-5. Kruskal-Wallis test; *p<0.05, mean ± SD.
Movie S1 from Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression
Authors: Macke Amanda J. , Pachikov Artem N. , Divita Taylor E. , Morris Mary E. , LaGrange Chad A. , Holzapfel Melissa S. , Kubyshkin Anatoly V. , Zyablitskaya Evgeniya Y. , Makalish Tatiana P. , Eremenko Sergey N. , Qiu Haowen , Riethoven Jean-Jack M. , Hemstreet George P. , Petrosyan Armen
Published: September 2024

PC-3 cell treated with water, stained for Golgi (GRASP65, green) and MGAT3 (red). Surfaces were reconstructed by Imaris.
Supplementary Figure 4 from Simultaneous targeting of DNA polymerase theta and PARP1 or RAD52 triggers dual synthetic lethality in homologous recombination-deficient leukemia cells
Authors: Sullivan-Reed Katherine , Toma Monika M. , Drzewiecka Malgorzata , Nieborowska-Skorska Margaret , Nejati Reza , Karami Adam , Wasik Mariusz A. , Sliwinski Tomasz , Skorski Tomasz
Published: September 2024

S4. Targeting Polθ + PARP and Polθ + RAD52 induced dual synthetic lethality against HR -deficient MPN cells.
Supplementary Figure 2 from Simultaneous targeting of DNA polymerase theta and PARP1 or RAD52 triggers dual synthetic lethality in homologous recombination-deficient leukemia cells
Authors: Sullivan-Reed Katherine , Toma Monika M. , Drzewiecka Malgorzata , Nieborowska-Skorska Margaret , Nejati Reza , Karami Adam , Wasik Mariusz A. , Sliwinski Tomasz , Skorski Tomasz
Published: September 2024

S2. Phenotype of Polq-/-;Parp1-/- and Polq-/-;Rad52-/- mice.
Supplemental Figure 4 from Mitochondrial uncoupling inhibits reductive carboxylation in cancer cells
Authors: Jiang Haowen , He Clifford Jiajun , Li Albert M. , He Bo , Li Yang , Zhou Meng-Ning , Ye Jiangbin
Published: September 2024

S4. Mitochondrial uncoupler NEN inhibits reductive carboxylation under hypoxia.
Supplemental Figure 1 from Mitochondrial uncoupling inhibits reductive carboxylation in cancer cells
Authors: Jiang Haowen , He Clifford Jiajun , Li Albert M. , He Bo , Li Yang , Zhou Meng-Ning , Ye Jiangbin
Published: September 2024

S1. Mitochondrial uncoupler NEN increases cellular NAD+/NADH ratio and inhibits reductive carboxylation.
Supplementary Materials and Methods from Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: September 2024

Supplementary Materials and Methods
Supplemental Table 5 from Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: September 2024

Enrichment values for ER associating proteins in endometrial and breast cancer cell lines
Supplemental Table 4 from Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: September 2024

Mutant ESR1 generation: gBlock used for template amplification
Supplemental Figure 6 from Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: September 2024

Identification of novel therapeutic targets in ER active and mutant endometrial cancer
Supplementary Table 7 from LncRNA-encoded Micropeptide ACLY‍-‍BP drives lipid deposition and cell proliferation in Clear Cell Renal Cell Carcinoma via maintenance of ACLY acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: September 2024

Homer Known Motif Enrichment Results (GATA_peaks_on_LINC00887_Promoter_motif)
Supplementary Table 3 from LncRNA-encoded Micropeptide ACLY‍-‍BP drives lipid deposition and cell proliferation in Clear Cell Renal Cell Carcinoma via maintenance of ACLY acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: September 2024

Antibodies used in this study
Supplementary Table 2 from LncRNA-encoded Micropeptide ACLY‍-‍BP drives lipid deposition and cell proliferation in Clear Cell Renal Cell Carcinoma via maintenance of ACLY acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: September 2024

Primers used in this study
Figure S7 from TRIM50 inhibits gastric cancer progression by regulating the ubiquitination and nuclear translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: September 2024

Figure S7: TOPFLASH analysis of JUP in TRIM50 overexpressing versus control empty vector 293T cells.
Supplementary Figure 10 from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

Canine mucosal melanomas with PDPN high expression demonstrate enrichment of gene signatures associated with amoeboid invasion.
Supplementary Figure 1 from Telomerase upregulation induces progression of mouse BrafV600E-driven thyroid cancers and triggers non-telomeric effects
Authors: Landa Inigo , Thornton Caitlin EM , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A. , Herbert Zachary T. , Martínez Paula , Blasco Maria A. , Ghossein Ronald , Fagin James A.
Published: September 2024

Pairwise alignment of human:mouse telomerase reverse transcriptase (TERT) gene sequences.
Figure S4 from USP1 expression driven by EWS::FLI1 transcription factor stabilizes Survivin and mitigates replication stress in Ewing sarcoma
Authors: Mallard Halle J. , Wan Shibiao , Nidhi Prakriti , Hanscom-Trofy Yvan D. , Mohapatra Bhopal , Woods Nicholas T. , Lopez-Guerrero Jose Antonio , Llombart-Bosch Antonio , Machado Isidro , Scotlandi Katia , Kreiling Natasha F. , Perry Megan C. , Mirza Sameer , Coulter Donald W. , Band Vimla , Band Hamid , Ghosal Gargi
Published: September 2024

Figure S4 shows Identification of novel potential USP1 substrates.
Table S4 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Z-transformed difference scores for each cell line as calculated from beta scores
Table S3 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Beta scores generated for DMSO and BYL719 treated populations using MAGeCK analysis pipeline
Figure S3 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Figure S3 shows that Dasatinib renders cells hyper-sensitive to BYL719
Supplementary Methods from Stromal DDR2 promotes ovarian cancer metastasis through regulation of metabolism and secretion of extracellular matrix proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: September 2024

Additional info regarding Methods
Figure S6 from Stromal DDR2 promotes ovarian cancer metastasis through regulation of metabolism and secretion of extracellular matrix proteins
Authors: Schab Angela M. , Greenwade Molly M. , Stock Elizabeth , Lomonosova Elena , Cho Kevin , Grither Whitney R. , Noia Hollie , Wilke Daniel , Mullen Mary M. , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Khabele Dineo , Powell Matthew A. , Mutch David G. , Zhao Peinan , Shriver Leah P. , Patti Gary J. , Longmore Gregory D. , Fuh Katherine C.
Published: September 2024

Tumor LOXL2 and DDR2 expression correlates with survival
Table S1 from FBXO24 suppresses breast cancer tumorigenesis by targeting LSD1 for Ubiquitination
Authors: Dong Bo , Song Xiang , Wang Xinzhao , Dai Tao , Wang Jianlin , Yu Zhiyong , Deng Jiong , Evers B. Mark , Wu Yadi
Published: September 2024

The used antibodies including company, catalog number and dilution.
Supplemental Figure 4 from FBXO24 suppresses breast cancer tumorigenesis by targeting LSD1 for Ubiquitination
Authors: Dong Bo , Song Xiang , Wang Xinzhao , Dai Tao , Wang Jianlin , Yu Zhiyong , Deng Jiong , Evers B. Mark , Wu Yadi
Published: September 2024

The expression of FBXO24 is inversely associated with the expression of LSD1.
Supplementary Figure 1 from Competing engagement of β-arrestin isoforms balances IGF1R/p53 signaling and controls melanoma cell chemotherapeutic responsiveness
Authors: Cismas Sonia , Pasca Sylvya , Crudden Caitrin , Troccoli Drakensjo Iara , Suleymanova Naida , Zhang Simin , Gebhard Benjamin , Song Dawei , Neo Shiyong , Shibano Takashi , Smith Terry J. , Calin George A. , Girnita Ada , Girnita Leonard
Published: September 2024

Effect of β-arrestin isoform imbalance on melanoma cell viability
Supplementary Table S4 from Simple Prediction Model for Colorectal Serrated Polyps: Development and External Validation Study in US Prospective Cohorts
Authors: Lyu Zhangyan , Hang Dong , He Xiaosheng , Wu Kana , Cao Yin , Rosner Bernard , Chan Andrew T. , Ogino Shuji , Li Ni , Dai Min , Giovannucci Edward L. , Song Mingyang
Published: September 2024

Supplementary Table S4: NRI and IDI of the risk prediction models for high-risk SPs.
Supplementary Figure S3 from Precision cut lung slices as a preclinical model for non-small cell lung cancer chemoprevention
Authors: Sompel Kayla , Smith Alex J. , Hauer Caroline , Elango Alamelu P. , Clambey Eric T. , Keith Robert L. , Tennis Meredith A.
Published: September 2024

Supplementary Figure S3 shows a representative immunofluorescence image for Figure 5.
Supplemental Table S1 from Cost-Effectiveness of p16/Ki-67 Dual-Stained Cytology Reflex Following Co-Testing with hrHPV Genotyping for Cervical Cancer Screening
Authors: Harper Diane M. , Anderson Rye J. , Baker Ed , Yu Tiffany M.
Published: September 2024

Supplemental Table S1 shows the unpublished data from the IMPACT clinical trial referenced in for the model inputs
Supplementary Table 18 from Associations between physical activity and incidence of cancer among overweight adults in Korea: Results from the Health Examinees-G study
Authors: Choi Jaesung , Park JooYong , Kim Ji-Eun , Lee Miyoung , Kang Daehee , Shin Aesun , Choi Ji-Yeob
Published: September 2024

Supplementary Table 18 shows comparison of the basic characteristics between the included and excluded population
Supplementary Table 10 from Associations between physical activity and incidence of cancer among overweight adults in Korea: Results from the Health Examinees-G study
Authors: Choi Jaesung , Park JooYong , Kim Ji-Eun , Lee Miyoung , Kang Daehee , Shin Aesun , Choi Ji-Yeob
Published: September 2024

Supplementary Table 10 shows the association of physical activity with gastric cancer incidence stratified by obesity status
Data from Polymorphisms in the non-homologous end-joining DNA repair pathway are associated with HPV integration in cervical dysplasia
Authors: Geris Jennifer M. , Amirian E. Susan. , Marquez-Do Deborah A. , Guillaud Martial , Dillon Laura M. , Follen Michele , Scheurer Michael E.
Published: September 2024

Abstract
Previous evidence indicates that HPV integration status may be associated with cervical cancer development and progression. However, host genetic variation within genes that may play important roles in the viral integration process is understudied. The aim of this study was to examine the association between HPV16 and HPV18 viral integration status and single nucleotide polymorphisms (SNPs) in non-homologous end-joining (NHEJ) DNA repair pathway genes on cervical dysplasia. Women enrolled in two large trials of optical technologies for cervical cancer detection and positive for HPV16 or HPV18 were selected for HPV integration analysis and genotyping. Associations between SNPs and cytology (normal, low-grade, or high-grade lesions) were evaluated. Among women with cervical dysplasia, polytomous logistic regression models were used to evaluate the effect of each SNP on viral integration status. Of the 710 women evaluated (149 HSIL, 251 LSIL, 310 Normal), 395 (55.6%) were positive for HPV16 and 192 (27%) were positive for HPV18. Tag-SNPs in 13 DNA repair genes, including RAD50, WRN, and XRCC4, were significantly associated with cervical dysplasia. HPV16 integration status was differential across cervical cytology, but overall, most participants had a mix of both episomal and integrated HPV16. Four tag-SNPs in the XRCC4 gene were found to be significantly associated with HPV16 integration status. Our findings indicate that host genetic variation in NHEJ DNA repair pathway genes, specifically XRCC4, are significantly associated with HPV integration, and that these genes may play an important role in determining cervical cancer development and progression.
Data from Association and prediction utilizing craniocaudal and mediolateral oblique view digital mammography and long-term breast cancer risk
Authors: Chen Simin , Tamimi Rulla M. , Colditz Graham A. , Jiang Shu
Published: September 2024

Abstract
Mammographic percent volumetric density is an important risk factor for breast cancer. Epidemiology studies historically used film images often limited to craniocaudal (CC) views to estimate area-based breast density. More recent studies using digital mammography images typically utilize the averaged density between craniocaudal (CC) and mediolateral oblique (MLO) view mammography for 5- and 10-year risk prediction. The performance in using either and both mammogram views has not been well-investigated. We use 3,804 full-field digital mammograms from the Joanne Knight Breast Health Cohort (294 incident cases and 657 controls), to quantity the association between volumetric percent density extracted from either and both mammography views and to assess the 5 and 10-year breast cancer risk prediction performance. Our results show that the association between percent volumetric density from CC, MLO, and the average between the two, retain essentially the same association with breast cancer risk. The 5- and 10-year risk prediction also show similar prediction accuracy. Thus, one view is sufficient to assess association and predict future risk of breast cancer over a 5 or 10-year interval.
Supplemental Figure S3 from Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy
Authors: Linde Miles H. , Fan Amy C. , Kohnke Thomas , Trotman-Grant Aaron C. , Gurev Sarah F. , Phan Paul , Zhao Feifei , Haddock Naomi L. , Nuno Kevin A. , Gars Eric J. , Stafford Melissa , Marshall Payton L. , Dove Christopher G. , Linde Ian L. , Landberg Niklas , Miller Lindsay P. , Majzner Robbie G. , Zhang Tian Yi. , Majeti Ravindra
Published: September 2024

In vivo TR-APC induction results in expansion of activated and memory T cells, and decreased frequency of Tregs
Supplementary Methods from Abatacept/Ruxolitinib and Screening for Concomitant Respiratory Muscle Failure to Mitigate Fatality of Immune-Checkpoint Inhibitor Myocarditis
Authors: Salem Joe-Elie , Bretagne Marie , Abbar Baptiste , LEONARD-LOUIS Sarah , Ederhy Stephane , REDHEUIL Alban , BOUSSOUAR Samia , NGUYEN Lee S. , PROCUREUR Adrien , STEIN Frederic , FENIOUX Charlotte , DEVOS Perrine , GOUGIS Paul , DRES Martin , DEMOULE Alexandre , Psimaras Dimitri , LENGLET Timothee , MAISONOBE Thierry , PINETON DE CHAMBRUN Marc , HEKIMIAN Guillaume , STRAUS Christian , GONZALEZ-BERMEJO Jesus , Klatzmann David , RIGOLET Aude , GUILLAUME-JUGNOT Perrine , CHAMPTIAUX Nicolas , BENVENISTE Olivier , WEISS Nicolas , SAHEB Samir , ROUVIER Philippe , PLU Isabelle , GANDJBAKHCH Estelle , KERNEIS Mathieu , HAMMOUDI Nadjib , ZAHR Noel , LLONTOP Claudia , MORELOT-PANZINI Capucine , Lehmann Lorenz , Qin Juan , Moslehi Javid J. , ROSENZWAJG Michelle , SIMILOWSKI Thomas , Allenbach Yves
Published: September 2024

Methods concerning Immune-checkpoint proteins profiling on peripheral blood mononuclear cells and Circulating immune checkpoint agents drug monitoring
Figure S2 from Abatacept/Ruxolitinib and Screening for Concomitant Respiratory Muscle Failure to Mitigate Fatality of Immune-Checkpoint Inhibitor Myocarditis
Authors: Salem Joe-Elie , Bretagne Marie , Abbar Baptiste , LEONARD-LOUIS Sarah , Ederhy Stephane , REDHEUIL Alban , BOUSSOUAR Samia , NGUYEN Lee S. , PROCUREUR Adrien , STEIN Frederic , FENIOUX Charlotte , DEVOS Perrine , GOUGIS Paul , DRES Martin , DEMOULE Alexandre , Psimaras Dimitri , LENGLET Timothee , MAISONOBE Thierry , PINETON DE CHAMBRUN Marc , HEKIMIAN Guillaume , STRAUS Christian , GONZALEZ-BERMEJO Jesus , Klatzmann David , RIGOLET Aude , GUILLAUME-JUGNOT Perrine , CHAMPTIAUX Nicolas , BENVENISTE Olivier , WEISS Nicolas , SAHEB Samir , ROUVIER Philippe , PLU Isabelle , GANDJBAKHCH Estelle , KERNEIS Mathieu , HAMMOUDI Nadjib , ZAHR Noel , LLONTOP Claudia , MORELOT-PANZINI Capucine , Lehmann Lorenz , Qin Juan , Moslehi Javid J. , ROSENZWAJG Michelle , SIMILOWSKI Thomas , Allenbach Yves
Published: September 2024

Delay between presentation for ICI myocarditis, appearance of life-threatening myotoxicity criteria (severity grade 4, Supplementary Table 5 for details concerning grading) and start of the immunosuppressive treatments (with dose) in severe ICI-myocarditis patients requiring abatacept.
Table S3 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines
Authors: Ito Yoshinaga , Pan Deng , Zhang Wubing , Zhang Xixi , Juan Tiffany Y. , Pyrdol Jason W. , Kyrysyuk Oleksandr , Doench John G. , Liu X. Shirley , Wucherpfennig Kai W.
Published: September 2024

Supplementary Table S3: ## Raw count matrix of the RNA-seq data. ## Atg5-KO vs Ctrl-KO (Veh).
Supplementary Fig. S7 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines
Authors: Ito Yoshinaga , Pan Deng , Zhang Wubing , Zhang Xixi , Juan Tiffany Y. , Pyrdol Jason W. , Kyrysyuk Oleksandr , Doench John G. , Liu X. Shirley , Wucherpfennig Kai W.
Published: September 2024

Supplementary Fig. S7 shows effect of PD-1 inhibition on treatment of tumors containing a B2m-/- population.
Supplementary Fig. S3 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines
Authors: Ito Yoshinaga , Pan Deng , Zhang Wubing , Zhang Xixi , Juan Tiffany Y. , Pyrdol Jason W. , Kyrysyuk Oleksandr , Doench John G. , Liu X. Shirley , Wucherpfennig Kai W.
Published: September 2024

Supplementary Fig. S3 generation of tumor cell lines with multiple gene edits.
Supplementary Fig. S1 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines
Authors: Ito Yoshinaga , Pan Deng , Zhang Wubing , Zhang Xixi , Juan Tiffany Y. , Pyrdol Jason W. , Kyrysyuk Oleksandr , Doench John G. , Liu X. Shirley , Wucherpfennig Kai W.
Published: September 2024

Supplementary Fig. S1 shows regulators of MHC-I independent and MHC-I dependent T cell mediated killing.
Supplementary Table S3 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Supplementary Table S3 shows the rank order list of genes targeted by sgRNAs enriched in the genome-wide CRISPR/Cas9 knockout screens.
Supplementary Figure S4 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

ChIP-seq analysis of primary AML patient samples.
Supplementary Figure S2 from (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: September 2024

Inhibition of KDM5 enzymes by the (R)- and (S)-enantiomers of 2-hydroxyglutarate.
Supplementary Tables S1-S11 from Integrative pan-cancer genomic and transcriptomic analyses of refractory metastatic cancer
Authors: Pradat Yoann , Viot Julien , Yurchenko Andrey A. , Gunbin Konstantin , Cerbone Luigi , Deloger Marc , Grisay Guillaume , Verlingue Loic , Scott Veronique , Padioleau Ismael , Panunzi Leonardo , Michiels Stefan , Hollebecque Antoine , Jules-Clement Gerome , Mezquita Laura , Laine Antoine , Loriot Yohann , Besse Benjamin , Friboulet Luc , Andre Fabrice , Cournede Paul-Henry , Gautheret Daniel , Nikolaev Sergey I.
Published: September 2024

These tables present clinical data, sample data, whole-exome and transcriptome sequencing results, literature references, and external data sources that were used for the analyses presented in the main text.
Supplementary Table S6 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Table S6 lists the genes regulated by HNF4a
Supplementary Figure S3 from Early infiltration of innate immune cells to the liver depletes HNF4a and promotes extra-hepatic carcinogenesis
Authors: Goldman Omer , Adler Lital N. , Hajaj Emma , Croese Tommaso , Darzi Naama , Galai Sivan , Tishler Hila , Ariav Yarden , Lavie Dor , Fellus-Alyagor Liat , Oren Roni , Kuznetsov Yuri , David Eyal , Jaschek Rami , Stossel Chani , Singer Oded , Malitsky Sergey , Barak Renana , Seger Rony , Erez Neta , Amit Ido , Tanay Amos , Saada Ann , Golan Talia , Rubinek Tamar , Sang Lee Joo , Ben-Shachar Shay , Wolf Ido , Erez Ayelet
Published: September 2024

Supplementary Figure S3 shows that targeting the IL-6-pSTAT-HNF4a pathway preserves liver metabolism and restricts BC growth
Supplementary Figure S4 from Co-mutations and KRAS G12C inhibitor efficacy in advanced NSCLC
Authors: Negrao Marcelo V. , Araujo Haniel A. , Lamberti Giuseppe , Cooper Alissa J. , Akhave Neal S. , Zhou Teng , Delasos Lukas , Hicks J Kevin. , Aldea Mihaela , Minuti Gabriele , Hines Jacobi , Aredo Jacqueline V. , Dennis Michael J. , Chakrabarti Turja , Scott Susan C. , Bironzo Paolo , Scheffler Matthias , Christopoulos Petros , Stenzinger Albrecht , Riess Jonathan W. , Kim So Yeon , Goldberg Sarah B. , Li Mingjia , Wang Qi , Qing Yun , Ni Ying , Do Minh Truong , Lee Richard , Ricciuti Biagio , Alessi Joao Victor. , Wang Jing , Resuli Blerina , Landi Lorenza , Tseng Shu-Chi , Nishino Mizuki , Digumarthy Subba R. , Rinsurongkawong Waree , Rinsurongkawong Vadeerat , Vaporciyan Ara A , Blumenschein George R. , Zhang Jianjun , Owen Dwight H. , Blakely Collin M. , Mountzios Giannis , Shu Catherine A. , Bestvina Christine M. , Garassino Marina Chiara. , Marrone Kristen A. , Gray Jhanelle E. , Patel Sandip Pravin. , Cummings Amy L. , Wakelee Heather A. , Wolf Juergen , Scagliotti Giorgio Vittorio. , Cappuzzo Federico , Barlesi Fabrice , Patil Pradnya D. , Drusbosky Leylah , Gibbons Don L. , Meric-Bernstam Funda , Lee J. Jack , Heymach John V. , Hong David S. , Heist Rebecca S. , Awad Mark M. , Skoulidis Ferdinandos
Published: September 2024

Clinical outcomes with KRAS G12Ci therapy according to co-mutation status for A) KEAP1, B) SMARCA4, and C) CDKN2A in patients previously treated with immune checkpoint inhibitors.
Supplementary Figure S10 from Co-mutations and KRAS G12C inhibitor efficacy in advanced NSCLC
Authors: Negrao Marcelo V. , Araujo Haniel A. , Lamberti Giuseppe , Cooper Alissa J. , Akhave Neal S. , Zhou Teng , Delasos Lukas , Hicks J Kevin. , Aldea Mihaela , Minuti Gabriele , Hines Jacobi , Aredo Jacqueline V. , Dennis Michael J. , Chakrabarti Turja , Scott Susan C. , Bironzo Paolo , Scheffler Matthias , Christopoulos Petros , Stenzinger Albrecht , Riess Jonathan W. , Kim So Yeon , Goldberg Sarah B. , Li Mingjia , Wang Qi , Qing Yun , Ni Ying , Do Minh Truong , Lee Richard , Ricciuti Biagio , Alessi Joao Victor. , Wang Jing , Resuli Blerina , Landi Lorenza , Tseng Shu-Chi , Nishino Mizuki , Digumarthy Subba R. , Rinsurongkawong Waree , Rinsurongkawong Vadeerat , Vaporciyan Ara A , Blumenschein George R. , Zhang Jianjun , Owen Dwight H. , Blakely Collin M. , Mountzios Giannis , Shu Catherine A. , Bestvina Christine M. , Garassino Marina Chiara. , Marrone Kristen A. , Gray Jhanelle E. , Patel Sandip Pravin. , Cummings Amy L. , Wakelee Heather A. , Wolf Juergen , Scagliotti Giorgio Vittorio. , Cappuzzo Federico , Barlesi Fabrice , Patil Pradnya D. , Drusbosky Leylah , Gibbons Don L. , Meric-Bernstam Funda , Lee J. Jack , Heymach John V. , Hong David S. , Heist Rebecca S. , Awad Mark M. , Skoulidis Ferdinandos
Published: September 2024

Integrated model for patient stratification and clinical outcome prediction with KRAS G12Ci monotherapy in KRASG12C-mutant NSCLC.
Supplementary Table S6 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S6: Proteomic analysis of FLT3-ITD AML cell lines treated with vehicle or QUIZ
Table S8 from A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: September 2024

List of available interactomes (gene regulatory networks) that have been generated from RNASeq datasets of patient tumor samples using the ARACNe algorithm.
Table S3 from A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: September 2024

Detailed summary of drugs prioritized for testing in PDX models, based on rank of OncoTarget and OncoTreat predictions by –log10(Bonferroni p).
Table S2 from A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: September 2024

Prioritized drugs, prediction basis, and dosing schedule for PDX therapeutic study.
Supplementary Figures S1-S6 from A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: September 2024

Supplementary Figures S1-S6 and figure legends.
Key Resources Table from A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: September 2024

Key Resources Table
Supplementary Tables from Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early neoplastic lesions.
Authors: Carpenter Eileen S. , Elhossiny Ahmed M. , Kadiyala Padma , Li Jay , McGue Jake , Griffith Brian D. , Zhang Yaqing , Edwards Jacob , Nelson Sarah , Lima Fatima , Donahue Katelyn L. , Du Wenting , Bischoff Allison C. , Alomari Danyah , Watkoske Hannah R. , Mattea Michael , The Stephanie , Espinoza Carlos E. , Barrett Meredith , Sonnenday Christopher J. , Olden Nicholas , Chen Chin-Tung , Peterson Nicole , Gunchick Valerie , Sahai Vaibhav , Rao Arvind , Bednar Filip , Shi Jiaqi , Frankel Timothy L. , Pasca di Magliano Marina
Published: September 2024

Supplemental Table 1: Demographics and clinical data for donor Gife of Life Samples
Supplemental Table 2: Putative Ligand-Receptor pairs comparing all cell types from single cell sequencing of tumor samples compared to healthy samples.
Supplemental Table 3: Differential gene expression using linear mixed model analysis of cell types from spatial transcriptomic ROIs.
Supplemental Table 4: Kras mutational profiling on select donor samples

Supplemental Table 5: Antibodies used for multiplex immunofluoresence.

Supplemental Table 6: Antibodies and RNAScope probe used for co-IF/ISH.
Supplementary Tables S1-S24 from Integrative analysis of a large real-world cohort of small cell lung cancer identifies distinct genetic subtypes and insights into histological transformation
Authors: Sivakumar Smruthy , Moore Jay A. , Montesion Meagan , Sharaf Radwa , Lin Douglas I. , Colon Caterina I. , Fleischmann Zoe , Ebot Ericka M. , Newberg Justin Y. , Mills Jennifer M. , Hegde Priti S. , Pan Quintin , Dowlati Afshin , Frampton Garrett M. , Sage Julien , Lovly Christine M.
Published: September 2024

Supplementary Table S1: First-, second-, and third-line systemic therapy in the SCLC clinical cohort.
Supplementary Table S2: Genes analyzed as part of this study.
Supplementary Table S3: Prevalence of alterations in the genes analyzed.
Supplementary Table S4: Prevalence of gene alterations in 81 cases with liquid biopsies.
Supplementary Table S5: Chromosomal losses and gains in SCLC.
Supplementary Table S6: TET2 loss of function alterations detected in SCLCs.
Supplementary Table S7: Manual review of specific mutation subgroups in SCLCs.
Supplementary Table S8: Patterns of gene alterations in SMARCA4 altered and wild-type tumors.
Supplementary Table S9: Prevalence of gene alterations in rearrangement-positive SCLCs.
Supplementary Table S10: Univariate analysis of association between gene alterations and overall surival in the clinical cohort of stage III/IV SCLC tumors.
Supplementary Table S11: Patterns of tumor mutational burden based on site of biopsy.
Supplementary Table 12: Summary of tumor purity and tumor mutational burden by biopsy site.
Supplementary Table S13: Aneuploidy patterns based on site of biopsy.
Supplementary Table S14: Comparison of gene alterations in each biopsy site against lung biopsies.
Supplementary Table S15: Comparison of gene alterations in liver and brain metastases.
Supplementary Table S16: Summary of PTEN alterations in brain and other biopsy sites.
Supplementary Table S17: Patterns of co-occurrence and mutual exclusivity between gene alterations in the overall SCLC cohort.
Supplementary Table S18: Patterns of gene alterations in TP53 and/or RB1 mutant and wild-type cohorts.
Supplementary Table S19: Patterns of gene alterations in young and older patients with SCLC.
Supplementary Table S20: Patterns of gene alterations in HPV positive and HPV negative tumors.
Supplementary Table S21: Manual review of specific HPV+ SCLCs.
Supplementary Table S22: Patterns of gene alterations in STK11 mutant and wild-type cohorts.
Supplementary Table S23: Patterns of gene alterations in EGFR mutant and wild-type cohorts.
Supplementary Table S24: EGFR kinase domain alterations identified in the overall SCLC cohort.
Table S6 from An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression
Authors: Indeglia Alexandra , Leung Jessica C. , Miller Sven A. , Leu Julia I-Ju , Dougherty James F. , Clarke Nicole L. , Kirven Nicole A. , Shao Chunlei , Ke Lei , Lovell Scott , Barnoud Thibaut , Lu David Y. , Lin Cindy , Kannan Toshitha , Battaile Kevin P. , Yang Tyler Hong Loong. , Batista Oliva Isabela , Claiborne Daniel T. , Vogel Peter , Liu Lijun , Liu Qin , Nefedova Yulia , Cassel Joel , Auslander Noam , Kossenkov Andrew V. , Karanicolas John , Murphy Maureen E.
Published: September 2024

Key Reagents List for this study.
Table S2 from An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression
Authors: Indeglia Alexandra , Leung Jessica C. , Miller Sven A. , Leu Julia I-Ju , Dougherty James F. , Clarke Nicole L. , Kirven Nicole A. , Shao Chunlei , Ke Lei , Lovell Scott , Barnoud Thibaut , Lu David Y. , Lin Cindy , Kannan Toshitha , Battaile Kevin P. , Yang Tyler Hong Loong. , Batista Oliva Isabela , Claiborne Daniel T. , Vogel Peter , Liu Lijun , Liu Qin , Nefedova Yulia , Cassel Joel , Auslander Noam , Kossenkov Andrew V. , Karanicolas John , Murphy Maureen E.
Published: September 2024

Evaluating the association between AA, Y107H variant, and cancer risk.
Supplementary Figures S1-10 from Targeting N-linked Glycosylation for the Therapy of Aggressive Lymphomas
Authors: Scheich Sebastian , Chen Jiji , Liu Jiamin , Schnutgen Frank , Enssle Julius C. , Ceribelli Michele , Thomas Craig J. , Choi Jaewoo , Morris Vivian , Hsiao Tony , Nguyen Hang , Wang Boya , Bolomsky Arnold , Phelan James D. , Corcoran Sean , Urlaub Henning , Young Ryan M. , Haupl Bjorn , Wright George W. , Huang Da Wei , Ji Yanlong , Yu Xin , Xu Weihong , Yang Yandan , Zhao Hong , Muppidi Jagan , Pan Kuan-Ting , Oellerich Thomas , Staudt Louis M.
Published: September 2024

Supplemental Figure 1. IRF4-GFP knock-in reporter cell lines. Supplemental Figure 2. IRF4-GFP CRISPR screen in adult T-cell lymphoma and screen controls. Supplemental Figure 3. The OST is essential for DLBCL. Supplemental Figure 4. The role of the OST complex in radiation chimeras. Supplemental Figure 5. The B-cell receptor is glycosylated by the OST complex. Supplemental Figure 6. B-cell receptor deglycosylation leads to higher surface expression. Supplemental Figure 7. B-cell receptor deglycosylation leads to signaling changes in proximal BCR signaling components. Supplemental Figure 8. BCR deglycosylation leads to recruitment of CD22 on the cell surface to the BCR and signaling alterations in GCB DLBCL. Supplemental Figure 9. BCR internalization and My-T-BCR formation in glycosylation deficient cells. Supplemental Figure 10. NGI-1 synergizes with BTK and PI3K inhibitors.
Figure S7 from Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy GX. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Helena , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: September 2024

Increasing IL3Rα/βc ratios and enforced hexamer signaling lead to reduced differentiation in in vivo engraftments.