bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental Table 4 from Validating Wave 1 (2014) Urinary Cotinine and TNE-2 Cut-points for Differentiating Wave 4 (2017) Cigarette Use from Non-use in the United States Using Data from the PATH Study
Authors: Edwards Kathryn C. , Khan Asia , Sharma Eva , Wang Lanqing , Feng June , Blount Benjamin C. , Sosnoff Connie S. , Smith Danielle M. , Goniewicz Maciej L. , Pearson Jennifer , Villanti Andrea C. , Delnevo Cristine D. , Bover-Manderski Michelle T. , Hatsukami Dorothy K. , Niaura Raymond , Everard Colm , Kimmel Heather L. , Duffy Kara , Rostron Brian L. , Del Valle-Pinero Arseima Y. , van Bemmel Dana M. , Stanton Cassandra A. , Hyland Andrew
Published: September 2023

Supplemental Table 4 provides prevalence rates of any tobacco use using TNE-2 cut-points.
Supplemental Table 1 from Validating Wave 1 (2014) Urinary Cotinine and TNE-2 Cut-points for Differentiating Wave 4 (2017) Cigarette Use from Non-use in the United States Using Data from the PATH Study
Authors: Edwards Kathryn C. , Khan Asia , Sharma Eva , Wang Lanqing , Feng June , Blount Benjamin C. , Sosnoff Connie S. , Smith Danielle M. , Goniewicz Maciej L. , Pearson Jennifer , Villanti Andrea C. , Delnevo Cristine D. , Bover-Manderski Michelle T. , Hatsukami Dorothy K. , Niaura Raymond , Everard Colm , Kimmel Heather L. , Duffy Kara , Rostron Brian L. , Del Valle-Pinero Arseima Y. , van Bemmel Dana M. , Stanton Cassandra A. , Hyland Andrew
Published: September 2023

Supplemental Table 1 provides demographic and tobacco use characteristics of exclusive and polytobacco users.
Supplemental Figure 1 from Validating Wave 1 (2014) Urinary Cotinine and TNE-2 Cut-points for Differentiating Wave 4 (2017) Cigarette Use from Non-use in the United States Using Data from the PATH Study
Authors: Edwards Kathryn C. , Khan Asia , Sharma Eva , Wang Lanqing , Feng June , Blount Benjamin C. , Sosnoff Connie S. , Smith Danielle M. , Goniewicz Maciej L. , Pearson Jennifer , Villanti Andrea C. , Delnevo Cristine D. , Bover-Manderski Michelle T. , Hatsukami Dorothy K. , Niaura Raymond , Everard Colm , Kimmel Heather L. , Duffy Kara , Rostron Brian L. , Del Valle-Pinero Arseima Y. , van Bemmel Dana M. , Stanton Cassandra A. , Hyland Andrew
Published: September 2023

Supplemental Figure 1 shows the analytic sample flow chart.
Data from Elevated EVL Methylation Level in the Normal Colon Mucosa Is a Potential Risk Biomarker for Developing Recurrent Adenomas
Authors: Yu Ming , Carter Kelly T. , Baker Kelsey K. , Redman Mary W. , Wang Ting , Vickers Kathy , Li Christopher I. , Cohen Stacey A. , Krane Mukta , Ose Jennifer , Gigic Biljana , Figueiredo Jane C. , Toriola Adetunji T. , Siegel Erin M. , Shibata David , Schneider Martin , Ulrich Cornelia M. , Dzubinski Lynda A. , Schoen Robert E. , Grady William M.
Published: September 2023

AbstractBackground:
Individuals with adenomatous colorectal polyps undergo repeated colonoscopy surveillance to identify and remove metachronous adenomas. However, many patients with adenomas do not develop recurrent adenomas. Better methods to evaluate who benefits from increased surveillance are needed. We evaluated the use of altered EVL methylation as a potential biomarker for risk of recurrent adenomas.
Methods:
Patients with ≥1 colonoscopy had EVL methylation (mEVL) measured with an ultra-accurate methylation-specific droplet digital PCR assay on normal colon mucosa. The association between EVL methylation levels and adenoma or colorectal cancer was evaluated using three case/control definitions in three models: unadjusted (model 1), adjusting for baseline characteristics (model 2), and an adjusted model excluding patients with colorectal cancer at baseline (model 3).
Results:
Between 2001 and 2020, 136 patients were included; 74 healthy patients and 62 patients with a history of colorectal cancer. Older age, never smoking, and baseline colorectal cancer were associated with higher levels of mEVL (P ≤ 0.05). Each log base 10 difference in mEVL was associated with an increased risk of adenoma(s) or cancer at/after baseline for model 1 [OR, 2.64; 95% confidence interval (CI), 1.09–6.36], and adenoma(s) or cancer after baseline for models 1 (OR, 2.01; 95% CI, 1.04–3.90) and model 2 (OR, 3.17; 95% CI, 1.30–7.72).
Conclusions:
Our results suggest that EVL methylation level detected in the normal colon mucosa has the potential to be a biomarker for monitoring the risk for recurrent adenomas.
Impact:
These findings support the potential utility of EVL methylation for improving the accuracy for assigning risk for recurrent colorectal adenomas and cancer.
Data from HSA Adductomics Reveals Sex Differences in NHL Incidence and Possible Involvement of Microbial Translocation
Authors: Grigoryan Hasmik , Imani Partow , Sacerdote Carlotta , Masala Giovanna , Grioni Sara , Tumino Rosario , Chiodini Paolo , Dudoit Sandrine , Vineis Paolo , Rappaport Stephen M.
Published: September 2023

AbstractBackground:
The higher incidence of non–Hodgkin lymphoma (NHL) in males is not well understood. Although reactive oxygen species (ROS) have been implicated as causes of NHL, they cannot be measured directly in archived blood.
Methods:
We performed untargeted adductomics of stable ROS adducts in human serum albumin (HSA) from 67 incident NHL cases and 82 matched controls from the European Prospective Investigation into Cancer and Nutrition-Italy cohort. Regression and classification methods were employed to select features associated with NHL in all subjects and in males and females separately.
Results:
Sixty seven HSA-adduct features were quantified by liquid chromatography–high-resolution mass spectrometry at Cys34 (n = 55) and Lys525 (n = 12). Three features were selected for association with NHL in all subjects, while seven were selected for males and five for females with minimal overlap. Two selected features were more abundant in cases and seven in controls, suggesting that altered homeostasis of ROS may affect NHL incidence. Heat maps revealed differential clustering of features between sexes, suggesting differences in operative pathways.
Conclusions:
Adduct clusters dominated by Cys34 oxidation products and disulfides further implicate ROS and redox biology in the etiology of NHL. Sex differences in dietary and alcohol consumption also help to explain the limited overlap of feature selection between sexes. Intriguingly, a disulfide of methanethiol from enteric microbial metabolism was more abundant in male cases, thereby implicating microbial translocation as a potential contributor to NHL in males.
Impact:
Only two of the ROS adducts associated with NHL overlapped between sexes and one adduct implicates microbial translocation as a risk factor.
Data from Sex-specific Associations between Body Mass Index and Thyroid Cancer Incidence among Korean Adults
Authors: Kim Kyoung-Nam , Kim Kyungsik , Lee Sangjun , Park Sue K.
Published: September 2023

AbstractBackground:
The potential differences by sex in the association between body mass index (BMI) and thyroid cancer risk remain unconfirmed.
Methods:
Data from the National Health Insurance Service-National Health Screening Cohort (NHIS-HEALS; 2002–2015; population size = 510,619) and the Korean Multi-center Cancer Cohort (KMCC) data (1993–2015; population size = 19,026) were used. We constructed Cox regression models, adjusted for potential confounders, to evaluate the association between BMI and thyroid cancer incidence in each cohort, and assessed the consistency of the results.
Results:
In the NHIS-HEALS, 1,351 and 4,609 incident thyroid cancer cases occurred during the follow-up among men and women, respectively. Compared with BMI of 18.5–22.9 kg/m2, BMI of 23.0–24.9 [no. of cases = 410; HR, 1.25; 95% confidence interval (CI), 1.08–1.44], 25.0–29.9 (no. of cases = 522; HR, 1.32; 95% CI, 1.15–1.51), and ≥30.0 kg/m2 (no. of cases = 48; HR, 1.93; 95% CI, 1.42–2.61) were associated with an increased risk of incident thyroid cancer among males. Among females, BMI of 23.0–24.9 (no. of cases = 1,300; HR, 1.17; 95% CI, 1.09–1.26) and 25.0–29.9 (no. of cases = 1,406; HR, 1.20; 95% CI, 1.11–1.29) were associated with incident thyroid cancer. The analyses using the KMCC demonstrated results consistent with wider CIs.
Conclusions:
Sex differences in the associations between BMI and thyroid cancer incidence were observed in Korean cohorts.
Impact:
BMI <23 kg/m2 may help prevent incident thyroid cancer, especially among men.
Figure S2 from De Novo and Histologically Transformed Small-Cell Lung Cancer Is Sensitive to Lurbinectedin Treatment Through the Modulation of EMT and NOTCH Signaling Pathways
Authors: Chakraborty Subhamoy , Coleman Charles , Manoj Parvathy , Demircioglu Deniz , Shah Nisargbhai , de Stanchina Elisa , Rudin Charles M. , Hasson Dan , Sen Triparna
Published: September 2023

Figure S2. Lurbinectedin sensitivity (IC50) correlation with MYC expression and changes in expression of NE markers.
Supplementary Table S1 from A Bifunctional PARP-HDAC Inhibitor with Activity in Ewing Sarcoma
Authors: Ramos Louise , Truong Sarah , Zhai Beibei , Joshi Jay , Ghaidi Fariba , Lizardo Michael M. , Shyp Taras , Kung Sonia H.Y. , Rezakhanlou Alireza M. , Oo Htoo Zarni , Adomat Hans , Le Bihan Stephane , Collins Colin , Bacha Jeffrey , Brown Dennis , Langlands John , Shen Wang , Lallous Nada , Sorensen Poul H. , Daugaard Mads
Published: September 2023

Blood cell panel counts and weight loss percentage of in vivo toxicity study
Supplementary Figure S5 from A Bifunctional PARP-HDAC Inhibitor with Activity in Ewing Sarcoma
Authors: Ramos Louise , Truong Sarah , Zhai Beibei , Joshi Jay , Ghaidi Fariba , Lizardo Michael M. , Shyp Taras , Kung Sonia H.Y. , Rezakhanlou Alireza M. , Oo Htoo Zarni , Adomat Hans , Le Bihan Stephane , Collins Colin , Bacha Jeffrey , Brown Dennis , Langlands John , Shen Wang , Lallous Nada , Sorensen Poul H. , Daugaard Mads
Published: September 2023

Replicate graphs of spheroid assays and cell fluorescence data
Supplementary Figure S4 from A Bifunctional PARP-HDAC Inhibitor with Activity in Ewing Sarcoma
Authors: Ramos Louise , Truong Sarah , Zhai Beibei , Joshi Jay , Ghaidi Fariba , Lizardo Michael M. , Shyp Taras , Kung Sonia H.Y. , Rezakhanlou Alireza M. , Oo Htoo Zarni , Adomat Hans , Le Bihan Stephane , Collins Colin , Bacha Jeffrey , Brown Dennis , Langlands John , Shen Wang , Lallous Nada , Sorensen Poul H. , Daugaard Mads
Published: September 2023

Replicate data of DNA damage assays
Supplementary Table S3 from Phase I trial of Ganitumab plus Dasatinib to Cotarget the Insulin-Like Growth Factor 1 Receptor and Src Family Kinase YES in Rhabdomyosarcoma
Authors: Akshintala Srivandana , Sundby R. Taylor , Bernstein Donna , Glod John W. , Kaplan Rosandra N. , Yohe Marielle E. , Gross Andrea M. , Derdak Joanne , Lei Haiyan , Pan Alexander , Dombi Eva , Palacio-Yance Isabel , Herrera Kailey R. , Miettinen Markku M. , Chen Helen X. , Steinberg Seth M. , Helman Lee J. , Mascarenhas Leo , Widemann Brigitte C. , Navid Fariba , Shern Jack F. , Heske Christine M.
Published: September 2023

Adverse events possibly probably or definitely related to dasatinib across all 28 cycles (maximum grade per patient)
Supplementary Dataset S1 from Phase I trial of Ganitumab plus Dasatinib to Cotarget the Insulin-Like Growth Factor 1 Receptor and Src Family Kinase YES in Rhabdomyosarcoma
Authors: Akshintala Srivandana , Sundby R. Taylor , Bernstein Donna , Glod John W. , Kaplan Rosandra N. , Yohe Marielle E. , Gross Andrea M. , Derdak Joanne , Lei Haiyan , Pan Alexander , Dombi Eva , Palacio-Yance Isabel , Herrera Kailey R. , Miettinen Markku M. , Chen Helen X. , Steinberg Seth M. , Helman Lee J. , Mascarenhas Leo , Widemann Brigitte C. , Navid Fariba , Shern Jack F. , Heske Christine M.
Published: September 2023

Fusion-positive RMS enhancer sites; Universal DNAase-hypersensitivity sites; YES1 and IGF1R region sets
Supplementary Table S5 from Activin A–Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2023

Supplementary Table S5. MC1, MC2 and MC3 secretome genesets.
Supplementary Figure S8 from Activin A–Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2023

Supplementary Figure S8: Activin A exposure in Fibroblasts and Macrophages clusters.
Supplementary Figure S7 from Activin A–Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2023

Supplementary Figure S7: ECM-remodeling CAFs and macrophages co-localize in CD8 T cells-depleted areas.
Supplementary Figure S5 from Activin A–Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2023

Supplementary Figure S5: TME2 is enriched in immunosuppressive macrophages, but devoid of immunoreactive CD8 T cells.
Supplementary Figure S3 from Activin A–Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2023

Supplementary Figure S3: Immunosuppressive TME2 are enriched in ECM-remodeling CAFs.
Supplementary Figure S2 from Activin A–Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2023

Supplementary Figure S2: Establishment of spatial transcriptional signatures for TMEs with distinct immune profiles.
Supplementary Video S2A from First-in-Human Study of the Radioligand 68Ga-N188 Targeting Nectin-4 for PET/CT Imaging of Advanced Urothelial Carcinoma
Authors: Duan Xiaojiang , Xia Lei , Zhang Zhuochen , Ren Yanan , Pomper Martin G. , Rowe Steven P. , Li Xuesong , Li Nan , Zhang Ning , Zhu Hua , Yang Zhi , Sheng Xinan , Yang Xing
Published: September 2023

40 min full dynamic Total-body PET imaging of Patient 1
Supplementary Methods S1 from First-in-Human Study of the Radioligand 68Ga-N188 Targeting Nectin-4 for PET/CT Imaging of Advanced Urothelial Carcinoma
Authors: Duan Xiaojiang , Xia Lei , Zhang Zhuochen , Ren Yanan , Pomper Martin G. , Rowe Steven P. , Li Xuesong , Li Nan , Zhang Ning , Zhu Hua , Yang Zhi , Sheng Xinan , Yang Xing
Published: September 2023

Supplementary Methods
Supplementary Figure S2 from KIT and PDGFRA Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial
Authors: Joensuu Heikki , Wardelmann Eva , Eriksson Mikael , Reichardt Annette , Hall Kirsten Sundby , Schütte Jochen , Cameron Silke , Hohenberger Peter , Sihto Harri , Jost Philipp J. , Lindner Lars H. , Bauer Sebastian , Nilsson Bengt , Kallio Raija , Pesonen Tommi , Reichardt Peter
Published: September 2023

Kaplan-Meier estimates of recurrence-free survival of patients with KIT exon 11 substitution mutation (A) and patients with KIT exon 9 mutation (B). The 5-year and 10-year survival rates are shown. Censored patients are indicated with a bar
Supplementary Figure S1 from KIT and PDGFRA Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial
Authors: Joensuu Heikki , Wardelmann Eva , Eriksson Mikael , Reichardt Annette , Hall Kirsten Sundby , Schütte Jochen , Cameron Silke , Hohenberger Peter , Sihto Harri , Jost Philipp J. , Lindner Lars H. , Bauer Sebastian , Nilsson Bengt , Kallio Raija , Pesonen Tommi , Reichardt Peter
Published: September 2023

Kaplan-Meier estimates of recurrence-free survival (A, C) and overall survival (B, D) of patients with KIT exon 11 deletion mutation (A, B) and patients with KIT exon 11 indel mutation (C, D)
Supplementary Table S2 from Early Clearance of Plasma Epidermal Growth Factor Receptor Mutations as a Predictor of Outcome on Osimertinib in Advanced Non–Small Cell Lung Cancer; Exploratory Analysis from AURA3 and FLAURA
Authors: Gray Jhanelle E. , Ahn Myung-Ju , Oxnard Geoffrey R. , Shepherd Frances A. , Imamura Fumio , Cheng Ying , Okamoto Isamu , Cho Byoung Chul , Lin Meng-Chih , Wu Yi-Long , Majem Margarita , Gautschi Oliver , Boyer Michael , Bulusu Krishna C. , Markovets Aleksandra , Barrett J. Carl , Hodge Rachel , McKeown Astrid , Hartmaier Ryan J. , Chmielecki Juliann , Papadimitrakopoulou Vassiliki A. , Ramalingam Suresh S.
Published: September 2023

Univariable and multivariable analyses for OS from the AURA3 trial (ctDNA evaluable population, n = 291) and FLAURA trial (ctDNA evaluable population, n = 499).
Supplementary Figure S6 from Early Clearance of Plasma Epidermal Growth Factor Receptor Mutations as a Predictor of Outcome on Osimertinib in Advanced Non–Small Cell Lung Cancer; Exploratory Analysis from AURA3 and FLAURA
Authors: Gray Jhanelle E. , Ahn Myung-Ju , Oxnard Geoffrey R. , Shepherd Frances A. , Imamura Fumio , Cheng Ying , Okamoto Isamu , Cho Byoung Chul , Lin Meng-Chih , Wu Yi-Long , Majem Margarita , Gautschi Oliver , Boyer Michael , Bulusu Krishna C. , Markovets Aleksandra , Barrett J. Carl , Hodge Rachel , McKeown Astrid , Hartmaier Ryan J. , Chmielecki Juliann , Papadimitrakopoulou Vassiliki A. , Ramalingam Suresh S.
Published: September 2023

Kaplan–Meier estimates showing investigator-assessed PFS in FLAURA trial patients by clearance or non-clearance of plasma EGFRm status at Weeks 3 or 6 in patients who had baseline detectable plasma EGFRm. For comparison, patients with baseline non-detectable plasma EGFRm are included. A, Osimertinib arm by Week 3 plasma EGFRm status (n = 238). B, Comparator EGFR-TKI arm by Week 3 plasma EGFRm status (n = 243). C, Osimertinib arm by Week 6 plasma EGFRm status (n = 240). D, Comparator EGFR-TKI arm by Week 6 plasma EGFRm status (n = 235). Censored data are indicated by tick marks. Abbreviations: CI, confidence interval; EGFRm, epidermal growth factor receptor mutation (ex19del or L858R); NC, not calculable; mPFS, median PFS; TKI, tyrosine kinase inhibitor.
Supplementary Table S2 from Thyroid Cancers Exhibit Oncogene-Enhanced Macropinocytosis that Is Restrained by IGF1R and Promote Albumin–Drug Conjugate Response
Authors: Hu Huiyu , Ng Thomas S.C. , Kang Mikyung , Scott Ella , Li Ran , Quintana Jeremy M. , Matvey Dylan , Vantaku Venkata R. , Weissleder Ralph , Parangi Sareh , Miller Miles A.
Published: September 2023

Pharmacologic screening, over-representation analysis, and gene expression of macropinocytosis screen hits
Supplementary Table S1 from Thyroid Cancers Exhibit Oncogene-Enhanced Macropinocytosis that Is Restrained by IGF1R and Promote Albumin–Drug Conjugate Response
Authors: Hu Huiyu , Ng Thomas S.C. , Kang Mikyung , Scott Ella , Li Ran , Quintana Jeremy M. , Matvey Dylan , Vantaku Venkata R. , Weissleder Ralph , Parangi Sareh , Miller Miles A.
Published: September 2023

Biological and chemical reagents and their sources
Supplementary Figure S6 from Thyroid Cancers Exhibit Oncogene-Enhanced Macropinocytosis that Is Restrained by IGF1R and Promote Albumin–Drug Conjugate Response
Authors: Hu Huiyu , Ng Thomas S.C. , Kang Mikyung , Scott Ella , Li Ran , Quintana Jeremy M. , Matvey Dylan , Vantaku Venkata R. , Weissleder Ralph , Parangi Sareh , Miller Miles A.
Published: September 2023

IGF1R and IGF1 expression in four individual ATC patients, and IGF1 expression in myeloid cell subsets
Supplementary Figure S5 from Thyroid Cancers Exhibit Oncogene-Enhanced Macropinocytosis that Is Restrained by IGF1R and Promote Albumin–Drug Conjugate Response
Authors: Hu Huiyu , Ng Thomas S.C. , Kang Mikyung , Scott Ella , Li Ran , Quintana Jeremy M. , Matvey Dylan , Vantaku Venkata R. , Weissleder Ralph , Parangi Sareh , Miller Miles A.
Published: September 2023

IGF1R inhibition augments macropinocytosis and is blocked by IGF1
Supplemental Table 4 from The GENIE BPC NSCLC Cohort: A Real-World Repository Integrating Standardized Clinical and Genomic Data for 1,846 Patients with Non–Small Cell Lung Cancer
Authors: Choudhury Noura J. , Lavery Jessica A. , Brown Samantha , de Bruijn Ino , Jee Justin , Tran Thinh Ngoc , Rizvi Hira , Arbour Kathryn C. , Whiting Karissa , Shen Ronglai , Hellmann Matthew , Bedard Philippe L. , Yu Celeste , Leighl Natasha , LeNoue-Newton Michele , Micheel Christine , Warner Jeremy L. , Ginsberg Michelle S. , Plodkowski Andrew , Girshman Jeffrey , Sawan Peter , Pillai Shirin , Sweeney Shawn M. , Kehl Kenneth L. , Panageas Katherine S. , Schultz Nikolaus , Schrag Deborah , Riely Gregory J.
Published: September 2023

Supplemental Table 4
Supplemental Table 2 from The GENIE BPC NSCLC Cohort: A Real-World Repository Integrating Standardized Clinical and Genomic Data for 1,846 Patients with Non–Small Cell Lung Cancer
Authors: Choudhury Noura J. , Lavery Jessica A. , Brown Samantha , de Bruijn Ino , Jee Justin , Tran Thinh Ngoc , Rizvi Hira , Arbour Kathryn C. , Whiting Karissa , Shen Ronglai , Hellmann Matthew , Bedard Philippe L. , Yu Celeste , Leighl Natasha , LeNoue-Newton Michele , Micheel Christine , Warner Jeremy L. , Ginsberg Michelle S. , Plodkowski Andrew , Girshman Jeffrey , Sawan Peter , Pillai Shirin , Sweeney Shawn M. , Kehl Kenneth L. , Panageas Katherine S. , Schultz Nikolaus , Schrag Deborah , Riely Gregory J.
Published: September 2023

Supplemental Table 2
Supplemental Fig. 3 from The GENIE BPC NSCLC Cohort: A Real-World Repository Integrating Standardized Clinical and Genomic Data for 1,846 Patients with Non–Small Cell Lung Cancer
Authors: Choudhury Noura J. , Lavery Jessica A. , Brown Samantha , de Bruijn Ino , Jee Justin , Tran Thinh Ngoc , Rizvi Hira , Arbour Kathryn C. , Whiting Karissa , Shen Ronglai , Hellmann Matthew , Bedard Philippe L. , Yu Celeste , Leighl Natasha , LeNoue-Newton Michele , Micheel Christine , Warner Jeremy L. , Ginsberg Michelle S. , Plodkowski Andrew , Girshman Jeffrey , Sawan Peter , Pillai Shirin , Sweeney Shawn M. , Kehl Kenneth L. , Panageas Katherine S. , Schultz Nikolaus , Schrag Deborah , Riely Gregory J.
Published: September 2023

Supplemental Figure 3: PFS estimates for patients with NSCLC treated with standard first- and second-line therapies.
Supplementary Data 2 from Treatment Response in First-Line Metastatic Pancreatic Ductal Adenocarcinoma Is Stratified By a Composite Index of Tumor Proliferation and CD8 T-Cell Infiltration
Authors: Beatty Gregory L. , Delman Devora , Yu Jiayi , Liu Mingen , Li Joey H. , Zhang Liti , Lee Jae W. , Chang Renee B. , Bahary Nathan , Kennedy Eugene P. , Wang-Gillam Andrea , Rossi Gabriela R. , Garrido-Laguna Ignacio
Published: September 2023

DEG Table for R vs NR (mRNAseq)
Supplementary Table S4 from CDK4/6-MEK Inhibition in MPNSTs Causes Plasma Cell Infiltration, Sensitization to PD-L1 Blockade, and Tumor Regression
Authors: Kohlmeyer Jordan L. , Lingo Joshua J. , Kaemmer Courtney A. , Scherer Amanda , Warrier Akshaya , Voigt Ellen , Raygoza Garay Juan A. , McGivney Gavin R. , Brockman Qierra R. , Tang Amy , Calizo Ana , Pollard Kai , Zhang Xiaochun , Hirbe Angela C. , Pratilas Christine A. , Leidinger Mariah , Breheny Patrick , Chimenti Michael S. , Sieren Jessica C. , Monga Varun , Tanas Munir R. , Meyerholz David K. , Darbro Benjamin W. , Dodd Rebecca D. , Quelle Dawn E.
Published: September 2023

Supplementary Table S4. Primers for qRT-PCR analyses
Supplementary Table S2 from CDK4/6-MEK Inhibition in MPNSTs Causes Plasma Cell Infiltration, Sensitization to PD-L1 Blockade, and Tumor Regression
Authors: Kohlmeyer Jordan L. , Lingo Joshua J. , Kaemmer Courtney A. , Scherer Amanda , Warrier Akshaya , Voigt Ellen , Raygoza Garay Juan A. , McGivney Gavin R. , Brockman Qierra R. , Tang Amy , Calizo Ana , Pollard Kai , Zhang Xiaochun , Hirbe Angela C. , Pratilas Christine A. , Leidinger Mariah , Breheny Patrick , Chimenti Michael S. , Sieren Jessica C. , Monga Varun , Tanas Munir R. , Meyerholz David K. , Darbro Benjamin W. , Dodd Rebecca D. , Quelle Dawn E.
Published: September 2023

Supplementary Table S2. Antibodies and dyes used for immunophenotyping by flow cytometry.
Supplementary Table S1 from CDK4/6-MEK Inhibition in MPNSTs Causes Plasma Cell Infiltration, Sensitization to PD-L1 Blockade, and Tumor Regression
Authors: Kohlmeyer Jordan L. , Lingo Joshua J. , Kaemmer Courtney A. , Scherer Amanda , Warrier Akshaya , Voigt Ellen , Raygoza Garay Juan A. , McGivney Gavin R. , Brockman Qierra R. , Tang Amy , Calizo Ana , Pollard Kai , Zhang Xiaochun , Hirbe Angela C. , Pratilas Christine A. , Leidinger Mariah , Breheny Patrick , Chimenti Michael S. , Sieren Jessica C. , Monga Varun , Tanas Munir R. , Meyerholz David K. , Darbro Benjamin W. , Dodd Rebecca D. , Quelle Dawn E.
Published: September 2023

Supplementary Table S1. Antibody sources and conditions for western blotting, IF, and IHC
Supplementary Figure S2 from CDK4/6-MEK Inhibition in MPNSTs Causes Plasma Cell Infiltration, Sensitization to PD-L1 Blockade, and Tumor Regression
Authors: Kohlmeyer Jordan L. , Lingo Joshua J. , Kaemmer Courtney A. , Scherer Amanda , Warrier Akshaya , Voigt Ellen , Raygoza Garay Juan A. , McGivney Gavin R. , Brockman Qierra R. , Tang Amy , Calizo Ana , Pollard Kai , Zhang Xiaochun , Hirbe Angela C. , Pratilas Christine A. , Leidinger Mariah , Breheny Patrick , Chimenti Michael S. , Sieren Jessica C. , Monga Varun , Tanas Munir R. , Meyerholz David K. , Darbro Benjamin W. , Dodd Rebecca D. , Quelle Dawn E.
Published: September 2023

Supplementary Figure S2. Dual CDK4/6-MEK inhibition synergistically suppresses the growth of some, but not all, MPNST PDXs in immune deficient mice
Supplementary Data 1 from Efficacy and Quality-of-Life Following Involved Nodal Radiotherapy for Head and Neck Squamous Cell Carcinoma: The INRT-AIR Phase II Clinical Trial
Authors: Sher David J. , Moon Dominic H. , Vo Dat , Wang Jing , Chen Liyuan , Dohopolski Michael , Hughes Randall , Sumer Baran D. , Ahn Chul , Avkshtol Vladimir
Published: September 2023

Includes Supp Figure 1, Supp Table 1 (representativeness table) and Supp Methods
Supplementary Table S3 from A Phase I/II Trial of HER2 Vaccine–Primed Autologous T-Cell Infusions in Patients with Treatment Refractory HER2–Overexpressing Breast Cancer
Authors: Disis Mary L. , Dang Yushe , Coveler Andrew L. , Childs Jennifer S. , Higgins Doreen M. , Liu Ying , Zhou Jing , Mackay Sean , Salazar Lupe G.
Published: September 2023

Immunologic parameters pre-treatment between PR+SD and PD patients.
Supplementary Table S2 from A Phase I/II Trial of HER2 Vaccine–Primed Autologous T-Cell Infusions in Patients with Treatment Refractory HER2–Overexpressing Breast Cancer
Authors: Disis Mary L. , Dang Yushe , Coveler Andrew L. , Childs Jennifer S. , Higgins Doreen M. , Liu Ying , Zhou Jing , Mackay Sean , Salazar Lupe G.
Published: September 2023

Detailed adverse events.
Supplementary Table S1 from A Phase I/II Trial of HER2 Vaccine–Primed Autologous T-Cell Infusions in Patients with Treatment Refractory HER2–Overexpressing Breast Cancer
Authors: Disis Mary L. , Dang Yushe , Coveler Andrew L. , Childs Jennifer S. , Higgins Doreen M. , Liu Ying , Zhou Jing , Mackay Sean , Salazar Lupe G.
Published: September 2023

Representativeness of study participants.
Supplementary Figure S1 from A Phase I/II Trial of HER2 Vaccine–Primed Autologous T-Cell Infusions in Patients with Treatment Refractory HER2–Overexpressing Breast Cancer
Authors: Disis Mary L. , Dang Yushe , Coveler Andrew L. , Childs Jennifer S. , Higgins Doreen M. , Liu Ying , Zhou Jing , Mackay Sean , Salazar Lupe G.
Published: September 2023

Flow chart of participants.
Supplementary Table 3 from A Prognostic Model Based on Residual Cancer Burden and Tumor-Infiltrating Lymphocytes on Residual Disease after Neoadjuvant Therapy in HER2+ Breast Cancer
Authors: Miglietta Federica , Ragazzi Moira , Fernandes Bethania , Griguolo Gaia , Massa Davide , Girardi Fabio , Bottosso Michele , Bisagni Alessandra , Zarrilli Giovanni , Porra Francesca , Iannaccone Daniela , Dore Leocadia , Gaudio Mariangela , Santandrea Giacomo , Fassan Matteo , Lo Mele Marcello , De Sanctis Rita , Zambelli Alberto , Bisagni Giancarlo , Guarneri Valentina , Dieci Maria Vittoria
Published: September 2023

Supplementary Table 3 – Multivariate Cox analysis for disease-free survival (DFS) in patients with residual disease (RD) after surgery
Supplementary Table 2 from A Prognostic Model Based on Residual Cancer Burden and Tumor-Infiltrating Lymphocytes on Residual Disease after Neoadjuvant Therapy in HER2+ Breast Cancer
Authors: Miglietta Federica , Ragazzi Moira , Fernandes Bethania , Griguolo Gaia , Massa Davide , Girardi Fabio , Bottosso Michele , Bisagni Alessandra , Zarrilli Giovanni , Porra Francesca , Iannaccone Daniela , Dore Leocadia , Gaudio Mariangela , Santandrea Giacomo , Fassan Matteo , Lo Mele Marcello , De Sanctis Rita , Zambelli Alberto , Bisagni Giancarlo , Guarneri Valentina , Dieci Maria Vittoria
Published: September 2023

Supplementary Table 2 - Representativeness of Study Participants
Supplementary Figure 3 from A Prognostic Model Based on Residual Cancer Burden and Tumor-Infiltrating Lymphocytes on Residual Disease after Neoadjuvant Therapy in HER2+ Breast Cancer
Authors: Miglietta Federica , Ragazzi Moira , Fernandes Bethania , Griguolo Gaia , Massa Davide , Girardi Fabio , Bottosso Michele , Bisagni Alessandra , Zarrilli Giovanni , Porra Francesca , Iannaccone Daniela , Dore Leocadia , Gaudio Mariangela , Santandrea Giacomo , Fassan Matteo , Lo Mele Marcello , De Sanctis Rita , Zambelli Alberto , Bisagni Giancarlo , Guarneri Valentina , Dieci Maria Vittoria
Published: September 2023

Supplementary Figure 3 – Matched evaluation of baseline TIL (b-TILs) and residual (RD-TILs) in the overall RD cohort (Fig. 3a), the high RD-TILs cohort (Fig. 3b) and in the low RD-TILs cohort (Fig. 3c).
Supplementary Figure 1 from A Prognostic Model Based on Residual Cancer Burden and Tumor-Infiltrating Lymphocytes on Residual Disease after Neoadjuvant Therapy in HER2+ Breast Cancer
Authors: Miglietta Federica , Ragazzi Moira , Fernandes Bethania , Griguolo Gaia , Massa Davide , Girardi Fabio , Bottosso Michele , Bisagni Alessandra , Zarrilli Giovanni , Porra Francesca , Iannaccone Daniela , Dore Leocadia , Gaudio Mariangela , Santandrea Giacomo , Fassan Matteo , Lo Mele Marcello , De Sanctis Rita , Zambelli Alberto , Bisagni Giancarlo , Guarneri Valentina , Dieci Maria Vittoria
Published: September 2023

Supplementary Figure 1 - Kaplan–Meier curves of overall survival according to RCB classes and RD-TILs.
Table S3 from Results of an Open-label, Phase Ia/b Study of Pembrolizumab plus Olaratumab in Patients with Unresectable, Locally Advanced, or Metastatic Soft-Tissue Sarcoma
Authors: Schöffski Patrick , Bahleda Rastislav , Wagner Andrew J. , Burgess Melissa A. , Junker Niels , Chisamore Michael , Peterson Patrick , Szpurka Anna M. , Ceccarelli Matteo , Tap William D.
Published: September 2023

Table S3: Pharmacokinetic parameters after a 60-minute IV infusion of olaratumab on Day 1 and Day 8 of Cycle 1 and Cycle 3 with pembrolizumab.
Table S2 from Results of an Open-label, Phase Ia/b Study of Pembrolizumab plus Olaratumab in Patients with Unresectable, Locally Advanced, or Metastatic Soft-Tissue Sarcoma
Authors: Schöffski Patrick , Bahleda Rastislav , Wagner Andrew J. , Burgess Melissa A. , Junker Niels , Chisamore Michael , Peterson Patrick , Szpurka Anna M. , Ceccarelli Matteo , Tap William D.
Published: September 2023

Table S2: Dose reduction, delay, and omission due to AE.
Figure S2 from Results of an Open-label, Phase Ia/b Study of Pembrolizumab plus Olaratumab in Patients with Unresectable, Locally Advanced, or Metastatic Soft-Tissue Sarcoma
Authors: Schöffski Patrick , Bahleda Rastislav , Wagner Andrew J. , Burgess Melissa A. , Junker Niels , Chisamore Michael , Peterson Patrick , Szpurka Anna M. , Ceccarelli Matteo , Tap William D.
Published: September 2023

Figure S2: Waterfall plot for percent change in tumor size in cohort 1, cohort 2, and the dose-expansion cohort.
Table S6 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2023

Dosing and schedule of abemaciclib and LY3214996
Table S5 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2023

Statistics from DESeq2
Table S4 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2023

Table of mice enrolled in drug study
Table S2 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2023

Raw log2LFQ values for kinases profiled by MIB/MS
Figure S13 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2023

Etv4, Dusp6, Phlda1, and Dusp4 mRNA expression
Figure S12 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2023

Ki67 Mouse IHC Analysis
Data from First-in-Human Study of the Radioligand 68Ga-N188 Targeting Nectin-4 for PET/CT Imaging of Advanced Urothelial Carcinoma
Authors: Duan Xiaojiang , Xia Lei , Zhang Zhuochen , Ren Yanan , Pomper Martin G. , Rowe Steven P. , Li Xuesong , Li Nan , Zhang Ning , Zhu Hua , Yang Zhi , Sheng Xinan , Yang Xing
Published: September 2023

AbstractPurpose:
Nectin-4 is an emerging biomarker for cancer diagnosis and therapy. Recently, enfortumab vedotin (EV) was approved by the FDA as the first nectin-4 targeting antibody–drug conjugate for treating advanced urothelial carcinoma (UC). A PET imaging method to noninvasively quantify nectin-4 expression level would potentially help to select patients most likely to respond to EV and predict the response.
Experimental Design:
In this study, we designed a bicyclic peptide-based nectin-4 targeting radiotracer 68Ga-N188. Initially, we performed preclinical evaluations of 68Ga-N188 in UC cell lines and xenograft mouse models. Next, we performed the translational study in healthy volunteers and a pilot cohort of patients with advanced UC on uEXPLORER total-body PET/CT.
Results:
In the preclinical study, 68Ga-N188 showed high affinity to nectin-4, specific uptake in a nectin-4(+) xenograft mouse model, and suitable pharmacokinetic and safety profiles. In the translational study, 2 healthy volunteers and 14 patients with advanced UC were enrolled. The pharmacokinetic profile was determined for 68Ga-N188, and the nectin-4 relative expression level in different organs was quantitatively imaged.
Conclusions:
A clear correlation between PET SUV value and nectin-4 expression was observed, supporting the application of 68Ga-N188 PET as a companion diagnostic tool for optimizing treatments that target nectin-4.

See related commentary by Jiang et al., p. 3259
Supplementary Figure 9 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 2023

Figure S9. (A) Left Panels: representative images of triple IHC staining of Na+/K+-ATPase (green), Integrin αv (red), and Gal-3 (brown) in the orthotopic tumor samples from the indicated group of mice; bars, 100 µm. Middle panel: IF of Golgi stained by GM130 in the prostate tumor foci; bars, 10 µm. White boxes indicate areas enlarged at the right. (B) Quantification of Golgi fragments per cell in tumor foci from samples in A; median ± SD. (C) ATF6 IF in the orthotopic tumor samples from the indicated group of mice; bars, 20 µm. Areas of mice prostate epithelium is highlighted by dotted lines. (D) Quantification of ATF6 IF intensity from samples in C; median ± SD. For all graphs: pairwise comparisons using Wilcoxon rank sum exact test, p-adjusted using Benjamini-Hochberg; ****p<0.0001, **p<0.01, and *p<0.05; n indicates the number of foci counted. (E) IF staining of the prostate tumor foci from the indicated group of mice to visualize Na+/K+-ATPase (magenta), Integrin αv (red), and Gal-3 (green); bars, 10 µm. (F, G) Quantification of IF intensity of Integrin αv (F) and Gal-3 (G) at the PM in samples from C; median ± SD.
Supplementary Figure 7 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 2023

Figure S7. (A, B) Alcohol dehydrogenase (ADH1A) and Aldehyde dehydrogenase (ALDH2) W-B of the lysate of PC-3 (A) and DU145 (B) cells. Asterisks indicate the bands corresponding to the appropriate proteins.
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 2023

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.
Movie S4 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 2023

PC-3 cell treated with HCQ, stained for Integrin αv (red), Gal-3 (green), EEA1 (magenta). Areas of 3-color colocalization are highlighted with white. Surfaces were reconstructed by Imaris.
SupplementaryTable S7 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Normalized CTA expression from NCI-H209 cell, xenografts, and chemo-treated xenografts (related to Figure 5f)
Supplementary Table S8 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Oligos and Primer Sequences
Supplementary Table S6 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Normalized differentially expressed genes between subclones (related to Figure 5a)
Supplementary Fig S2 from Chromatin-Associated SIN3B Protects Cancer Cells from Genotoxic Stress-Induced Apoptosis and Dictates DNA Damage Repair Pathway Choice
Authors: Morales-Valencia Jorge , Petit Coralie , Calderon Alexander , Saini Siddharth , David Gregory
Published: September 2023

SIN3B protects from drug-induced cytotoxicity, independently of its ability to interact with its cognate partners.
Supplementary Table S5 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Normalized gene expression across NCI-H209 subclones (related to Figure 4)
Supplementary Fig S1 from Chromatin-Associated SIN3B Protects Cancer Cells from Genotoxic Stress-Induced Apoptosis and Dictates DNA Damage Repair Pathway Choice
Authors: Morales-Valencia Jorge , Petit Coralie , Calderon Alexander , Saini Siddharth , David Gregory
Published: September 2023

SIN3B protects against DNA damage-induced apoptosis.
Table S2 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Table S2. NormLinear: provides normalized RPPA data in linear values.
Figure S5 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Figure S5. ERK Score correlates with Tumor Stage and ATA Risk Group in thyroid cancer.
Supplementary Figure S6 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Expression and validation of AP-1 family genes in late tumor development.
Supplementary Figure S5 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Cell cycle stage assignment of the SCLC cells from the autochthonous model.
Figure S3 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Figure S3. Sensitivity to BRAF inhibition does not correlate with fibronectin, α5β1 integrin, c-MET, or FAK/Src levels. BRAF inhibition increases fibronectin expression and secretion, which is blocked by ERK1/2 inhibition.
Figure S2 from Fibronectin Contributes to a BRAF Inhibitor–driven Invasive Phenotype in Thyroid Cancer through EGR1, Which Can Be Blocked by Inhibition of ERK1/2
Authors: Hicks Hannah M. , Pozdeyev Nikita , Sams Sharon B. , Pugazhenthi Umarani , Bales Elise S. , Hofmann Marie-Claude , McKenna Logan R. , Schweppe Rebecca E.
Published: September 2023

Figure S2. BRAF inhibition increases fibronectin expression and secretion, which is blocked by ERK1/2 inhibition.
Supplementary Figure S10 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Graphic displaying the sample makeup of the three NCI-H209 sample arms.
Supplementary Figure S1 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Authors: Wollenzien Hannah , Afeworki Tecleab Yohannes , Szczepaniak-Sloane Robert , Restaino Anthony , Kareta Michael S.
Published: September 2023

Validation of the autochthonous barcoding model.
Supplementary Figure 6 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 2023

Mineralization assay co-cultured with MCF7 cells.
Supplementary Figure 4 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 2023

Extraction of c-Jun-regulated bone metastasis gene signatures from the MCF7 cell lines.
Supplementary Table S5 from Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma
Authors: Wang Xin , Kutschat Ana P. , Aggrey-Fynn Joana , Hamdan Feda H. , Graham Rondell P. , Wixom Alexander Q. , Souto Yara , Ladigan-Badura Swetlana , Yonkus Jennifer A. , Abdelrahman Amro M. , Alva-Ruiz Roberto , Gaedcke Jochen , Ströbel Philipp , Kosinsky Robyn Laura , Wegwitz Florian , Hermann Patrick , Truty Mark J. , Siveke Jens T. , Hahn Stephan A. , Hessmann Elisabeth , Johnsen Steven A. , Najafova Zeynab
Published: September 2023

Supplementary Table S5 contains list of genes associated with L3.6pl TP63 dependent enhancers.