bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S2 from Detection of Recurrence through microRNA-371a-3p Serum Levels in a Follow-up of Stage I Testicular Germ Cell Tumors in the DRKS-00019223 Study
Authors: Belge Gazanfer , Dumlupinar Cansu , Nestler Tim , Klemke Markus , Törzsök Peter , Trenti Emanuela , Pichler Renate , Loidl Wolfgang , Che Yue , Hiester Andreas , Matthies Cord , Pichler Martin , Paffenholz Pia , Kluth Luis , Wenzel Mike , Sommer Jörg , Heinzelbecker Julia , Schriefer Philipp , Winter Alexander , Zengerling Friedemann , Kramer Mario Wolfgang , Lengert Marie , Frey Jana , Heidenreich Axel , Wülfing Christian , Radtke Arlo , Dieckmann Klaus-Peter
Published: January 2024

Supplementary Table S2. Follow-up schedule of clinical stage I nonseminoma patients used in the study (modified from Oldenburg et al., Ann. Oncol. 2022, and Kliesch et al. Urol. int. 2021)
Supplementary Table S1 from PDGFRβ Signaling Cooperates with β-Catenin to Modulate c-Abl and Biologic Behavior of Desmoid-Type Fibromatosis
Authors: Hu Jia , Hameed Meera R. , Agaram Narasimhan P. , Whiting Karissa A. , Qin Li-Xuan , Villano Anthony M. , O'Connor Rachael B. , Rozenberg Julian M. , Cohen Sonia , Prendergast Katherine , Kryeziu Sara , White Richard L. , Posner Mitchell C. , Socci Nicholas D. , Gounder Mrinal M. , Singer Samuel , Crago Aimee M.
Published: January 2024

Gene set enrichment analysis of pathways altered in desmoid cells after CTNNB1 knockdown
Supplementary Data 1 from PDGFRβ Signaling Cooperates with β-Catenin to Modulate c-Abl and Biologic Behavior of Desmoid-Type Fibromatosis
Authors: Hu Jia , Hameed Meera R. , Agaram Narasimhan P. , Whiting Karissa A. , Qin Li-Xuan , Villano Anthony M. , O'Connor Rachael B. , Rozenberg Julian M. , Cohen Sonia , Prendergast Katherine , Kryeziu Sara , White Richard L. , Posner Mitchell C. , Socci Nicholas D. , Gounder Mrinal M. , Singer Samuel , Crago Aimee M.
Published: January 2024

Supplemental Methods Tables, Supplemental Methods Figures, Supplemental Figures
Supplementary Table S9 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

The correlation between pretreatment PD-L1 CPS and clinical outcomes
Table S2 from Phase I/IIa Trial in Advanced Pancreatic Ductal Adenocarcinoma Treated with Cytotoxic Drug-Packaged, EGFR-Targeted Nanocells and Glycolipid-Packaged Nanocells
Authors: Ganju Vinod , Marx Gavin , Pattison Scott , Amaro-Mugridge Nancy B. , Zhao Jing-Ting , Williams Bryan R.G. , MacDiarmid Jennifer A. , Brahmbhatt Himanshu
Published: January 2024

Table S2: Measurement of PNU-159682 Packaged in EDVs
Supplementary Table S2 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

Adverse effects during induction chemoimmunotherapy and adjuvant immunotherapy
Supplementary Table S11 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

The comparison of patients of enrollment among three clinical trials
Supplementary Table S10 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

the Kaplan-Meier estimates of survival among different subgroups of PD-L1 CPS
Supplementary Table S7 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Table S7. Summary of Cox proportional hazards model for overall survival.
Supplementary Table S6 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Table S6. Summary of significantly changing TCR clones across the study cohort
Supplementary Figure S6 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

The Differential Expression of Various Genes between the Resistant and Sensitive Groups
Supplementary Figure S4 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

Kaplan-Meier estimates of survival across various subgroups with PD-L1 expression
Supplementary Table S14 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Table S14. Summary of Olink plasma proteomic analyses.
Supplementary Figure S2 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

Kaplan-Meier estimates of survival across various subgroups
Supplementary Figure S1 from Induction Toripalimab and Chemotherapy for Organ Preservation in Locally Advanced Laryngeal and Hypopharyngeal Cancer: A Single-Arm Phase II Clinical Trial
Authors: Ou Xiaomin , Zhai Ruiping , Wei Wenjun , Chen Jiaying , Ou Dan , Liao Tian , Xu Tingting , Zhu Yongxue , Wang Yulong , Huang Shenglin , Shi Rongliang , Wu Bin , Chen Tongzhen , Li Yuan , Yang Zhongyi , Zhou Changming , Liu Yuan , Jiang Ziting , Zeng Min , Liu Xin , Ji Dongmei , Ying Hongmei , Zhang Zhen , Hu Chaosu , Lu Xueguan , Ji Qinghai , He Xiayun , Wang Yu
Published: January 2024

Typical case with primary invasion to cervical esophagus
Supplementary Table S11 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Table S11.Summary of TCR clonotypic differential abundance analyses.
Supplementary Table S10 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Table S10. Summary of TCR sequencing characteristics for the cohort
Table 2 from Developing and Validating a Multivariable Prognostic-Predictive Classifier for Treatment Escalation of Oropharyngeal Squamous Cell Carcinoma: The PREDICTR-OPC Study
Authors: Mehanna Hisham , Rapozo Davy , von Zeidler Sandra V. , Harrington Kevin J. , Winter Stuart C. , Hartley Andrew , Nankivell Paul , Schache Andrew G. , Sloan Philip , Odell Edward W. , Thavaraj Selvam , Hunter Keith D. , Shah Ketan A. , Thomas Gareth J. , Long Anna , Amel-Kashipaz Rasoul , Brown Rachel M. , Conn Brendan , Hall Gillian L. , Matthews Paul , Weir Justin , Yeo Yen , Pring Miranda , West Catharine M.L. , McCaul James , Golusinski Pawel , Sitch Alice , Spruce Rachel , Batis Nikolaos , Bryant Jennifer L. , Brooks Jill M. , Jones Terence M. , Buffa Francesca , Haider Syed , Robinson Max
Published: January 2024

Clinical examples of the OS model.
Supplementary Figure S9 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Fig.S9 Comparison between plasma proteomic profiles across treatment timepoints and toxicity. Heatmaps
showing normalized protein expression (NPX) scores for 92 proteins evaluated using Olink analyses across all (A) baseline
(n=19) and (B) on-therapy (n=47) plasma samples from 28 patients. Panels indicating treatment timepoint and the presence
or absence of immunotherapy-related toxicity are displayed below the heatmaps.
Supplementary Data 1 from Developing and Validating a Multivariable Prognostic-Predictive Classifier for Treatment Escalation of Oropharyngeal Squamous Cell Carcinoma: The PREDICTR-OPC Study
Authors: Mehanna Hisham , Rapozo Davy , von Zeidler Sandra V. , Harrington Kevin J. , Winter Stuart C. , Hartley Andrew , Nankivell Paul , Schache Andrew G. , Sloan Philip , Odell Edward W. , Thavaraj Selvam , Hunter Keith D. , Shah Ketan A. , Thomas Gareth J. , Long Anna , Amel-Kashipaz Rasoul , Brown Rachel M. , Conn Brendan , Hall Gillian L. , Matthews Paul , Weir Justin , Yeo Yen , Pring Miranda , West Catharine M.L. , McCaul James , Golusinski Pawel , Sitch Alice , Spruce Rachel , Batis Nikolaos , Bryant Jennifer L. , Brooks Jill M. , Jones Terence M. , Buffa Francesca , Haider Syed , Robinson Max
Published: January 2024

Combined Supplementary Methods, Figures and Tables
Supplementary Figure S7 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Fig.S7 T cell receptor (TCR) clonotype dynamics in patients who developed immunotherapy-related toxicity. (A-J) Volcano plots showing significant TCR clonotypic expansions (red) and regressions (blue) following treatment with immunotherapy-containing agents in patients who developed immunotherapy
(IO) – associated pneumonitis. On-Tx, On-treatment.
Figure 4 from Developing and Validating a Multivariable Prognostic-Predictive Classifier for Treatment Escalation of Oropharyngeal Squamous Cell Carcinoma: The PREDICTR-OPC Study
Authors: Mehanna Hisham , Rapozo Davy , von Zeidler Sandra V. , Harrington Kevin J. , Winter Stuart C. , Hartley Andrew , Nankivell Paul , Schache Andrew G. , Sloan Philip , Odell Edward W. , Thavaraj Selvam , Hunter Keith D. , Shah Ketan A. , Thomas Gareth J. , Long Anna , Amel-Kashipaz Rasoul , Brown Rachel M. , Conn Brendan , Hall Gillian L. , Matthews Paul , Weir Justin , Yeo Yen , Pring Miranda , West Catharine M.L. , McCaul James , Golusinski Pawel , Sitch Alice , Spruce Rachel , Batis Nikolaos , Bryant Jennifer L. , Brooks Jill M. , Jones Terence M. , Buffa Francesca , Haider Syed , Robinson Max
Published: January 2024

Multivariable survival modelling (trained with backward elimination using AIC) for composite (molecular biomarkers + clinical factors) and clinical factors only with OS. A–D, Assessment of composite and clinical only models in the validation cohort split into two and three risk groups. E–H, Assessment of composite and clinical only models’ predicted risk groups (low- and high-risk) stratified by surgery in the training (E and F) and validation cohorts (G and H). Risk groups in the validation cohort were created using the thresholds (two-group classification: median; three-group classification: tertiles) derived from the training set. In E, the estimate of HR (95% CI) was not possible due to absence of events in low, surgery+ group. Color key: same as Fig. 3.
Supplementary Figure S6 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Fig.S6 T cell receptor (TCR) clonotype dynamics across serial peripheral blood samples. (A-D) The dynamics
of individual TCR clones identified as either significantly increasing, significantly decreasing or not changing in abundance from
baseline to on-treatment sampling are shown for 4 representative patients. Across patients analyzed, no directionality bias was
observed in the panel of clones that did not significantly change in abundance between serial timepoints, towards either a
general increase or decrease. These results indicate that significant changes in observed clonotype dynamics between
baseline and on-treatment samples from this study cohort were not driven by the significant expansion of one or few high
abundance TCR clones.
Figure 2 from Developing and Validating a Multivariable Prognostic-Predictive Classifier for Treatment Escalation of Oropharyngeal Squamous Cell Carcinoma: The PREDICTR-OPC Study
Authors: Mehanna Hisham , Rapozo Davy , von Zeidler Sandra V. , Harrington Kevin J. , Winter Stuart C. , Hartley Andrew , Nankivell Paul , Schache Andrew G. , Sloan Philip , Odell Edward W. , Thavaraj Selvam , Hunter Keith D. , Shah Ketan A. , Thomas Gareth J. , Long Anna , Amel-Kashipaz Rasoul , Brown Rachel M. , Conn Brendan , Hall Gillian L. , Matthews Paul , Weir Justin , Yeo Yen , Pring Miranda , West Catharine M.L. , McCaul James , Golusinski Pawel , Sitch Alice , Spruce Rachel , Batis Nikolaos , Bryant Jennifer L. , Brooks Jill M. , Jones Terence M. , Buffa Francesca , Haider Syed , Robinson Max
Published: January 2024

A, Heatmaps summarizing the molecular and clinical data from training and validation sets. Rows contain clinical covariates and molecular biomarkers, while columns contain patients. Protein abundance H-scores (range: 0–300) were divided by 30 and Z transformed (μ = 0, σ = 1) for training and validation sets separately. Column order in each of the training and validation sets was determined by first sorting (low to high Z-score) on the protein biomarkers one by one (bottom up) and then OS event. B, Box plots displaying range of fitted coefficients including 25th percentile (Q1), median, and 75th percentile (Q3). To test the stability of the variables selected in the multivariable model, bootstrapping was performed on the training cohort (1,000 times) and Cox proportional hazards model was fitted with backward elimination on each subset. For each bootstrap iteration, coefficients of the resulting variables selected by the model are displayed in the box plots alongside their % frequency of inclusion over 1,000 iterations. Bootstrapping results confirmed the relative importance of variables in our original model (Supplementary Table S6), as these were ranked among the top recurrently selected variables over 1,000 iterations. Upper whisker of the box plots indicates: min (max(x), Q3 + 1.5 × IQR) and lower whisker indicates: max (min(x), Q1–1.5 × IQR) where IQR = Q3−Q1. Color key: TILS-3 = high, TILS-2 = moderate, TILS-1 = low.
Supplementary Figure S4 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Fig.S4 Associations between cfTL dynamics and outcomes according to immunotherapy
treatment regimen. The presence of a molecular response, as indicated by clearance of cfTL across any
sampled timepoint, was significantly associated with clinical benefit in (A) 19 patients treated with immune
checkpoint monotherapy (P = 0.02, Fisher’s exact test). Similar trends were observed in (B) 11 patients
treated with chemo-immunotherapy combination regimens. Associations between the presence (light blue)
or absence (coral) of a molecular response and survival outcomes in patients treated with (C, D) checkpoint monotherapy or (E, F) chemo-immunotherapy combination regimens, including cases with undetectable cfTL (grey).
Figure 1 from Developing and Validating a Multivariable Prognostic-Predictive Classifier for Treatment Escalation of Oropharyngeal Squamous Cell Carcinoma: The PREDICTR-OPC Study
Authors: Mehanna Hisham , Rapozo Davy , von Zeidler Sandra V. , Harrington Kevin J. , Winter Stuart C. , Hartley Andrew , Nankivell Paul , Schache Andrew G. , Sloan Philip , Odell Edward W. , Thavaraj Selvam , Hunter Keith D. , Shah Ketan A. , Thomas Gareth J. , Long Anna , Amel-Kashipaz Rasoul , Brown Rachel M. , Conn Brendan , Hall Gillian L. , Matthews Paul , Weir Justin , Yeo Yen , Pring Miranda , West Catharine M.L. , McCaul James , Golusinski Pawel , Sitch Alice , Spruce Rachel , Batis Nikolaos , Bryant Jennifer L. , Brooks Jill M. , Jones Terence M. , Buffa Francesca , Haider Syed , Robinson Max
Published: January 2024

Photomicrographs showing examples of the biomarkers in the predictive classifier: p16 immunohistochemistry (A–C), high-risk HPV in situ hybridization (D–F), survivin immunohistochemistry (G–I), and TILs (J–L). A, p16-positive tumor showing strong and diffuse nuclear and cytoplasmic staining. B, p16-negative tumor showing weak and diffuse cytoplasmic staining. C, p16-negative tumor with no staining. D–E, High-risk HPV-positive tumors showing diffuse nuclear and cytoplasmic staining (D) and punctate nuclear staining (E). F, High-risk HPV-negative tumor with no staining. G–I, Survivin staining showing tumors with high (G), medium (H), and low (I) H-scores. J–L, Cases with high (J), moderate (K), and low (L) TILs.
Supplementary Data1 from A Phase I/II Study of GSK525762 Combined with Fulvestrant in Patients with Hormone Receptor–positive/HER2-negative Advanced or Metastatic Breast Cancer
Authors: Cescon David W. , Hilton John , Morales Murilo Serafin , Layman Rachel M. , Pluard Timothy , Yeo Belinda , Park In Hae , Provencher Louise , Kim Sung-Bae , Im Young-Hyuck , Wyce Anastasia , Krishnatry Anu Shilpa , Hicks Kirsty , Zhang Qu , Barbash Olena , Khaled Ahmed , Horner Thierry , Dhar Arindam , Oliveira Mafalda , Sparano Joseph A.
Published: January 2024

Supplementary information
Supplementary Figure S2 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Weksler Benny , Bahary Nathan , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Goel Akul , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Zaidi Ali H. , Forde Patrick M. , Anagnostou Valsamo
Published: January 2024

Supplementary Fig.S2 Overview of variants detected in plasma cell-free DNA. (A) The percentage of all classified plasma variants that were
assigned an origin of germline, tumor-derived or clonal haematopoiesis (CH)-derived. (B) The maximum mutant allele fraction (MAF) of
tumor-derived circulating tumor DNA (ctDNA) variants at baseline sampling, stratified by treatment (immunotherapy (IO) or chemo-immunotherapy (chemo-IO)) and clinical benefit (durable clinical benefit (DCB) or non-durable clinical benefit (NDB)). P values were calculated using
the Mann-Whitney U test. (C-F) Associations between baseline ctDNA maximal MAFs and survival outcomes according to progression-free
(PFS) and overall survival (OS) in patients treated with (C-D) immune checkpoint monotherapy and (E-F) chemo-immunotherapy combination regimens. *, P < 0.05
Figure S7 from Magnetic Resonance Imaging of Iron Metabolism with T2* Mapping Predicts an Enhanced Clinical Response to Pharmacologic Ascorbate in Patients with GBM
Authors: Petronek Michael S. , Monga Varun , Bodeker Kellie L. , Kwofie Michael , Lee Chu-Yu , Mapuskar Kranti A. , Stolwijk Jeffrey M. , Zaher Amira , Wagner Brett A. , Smith Mark C. , Vollstedt Sandy , Brown Heather , Chandler Meghan L. , Lorack Amanda C. , Wulfekuhle Jared S. , Sarkaria Jann N. , Flynn Ryan T. , Greenlee Jeremy D.W. , Howard Matthew A. , Smith Brian J. , Jones Karra A. , Buettner Garry R. , Cullen Joseph J. , St-Aubin Joel , Buatti John M. , Magnotta Vincent A. , Spitz Douglas R. , Allen Bryan G.
Published: January 2024

P-AscH- stimulates the release of iron as Fe2+ from ferritin.
Supplementary Data 1 from A Phase I Study of the CDK4/6 Inhibitor Palbociclib in Combination with Cetuximab and Radiotherapy for Locally Advanced Head and Neck Squamous Cell Carcinoma
Authors: Ngamphaiboon Nuttapong , Pattaranutaporn Poompis , Lukerak Somthawin , Siripoon Teerada , Jinawath Artit , Arsa Lalida , Shantavasinkul Prapimporn Ch. , Taonam Naphat , Trachu Narumol , Jinawath Natini , Kositwattanarerk Arpakorn , Sananmuang Thiparom , Jiarpinitnun Chuleeporn
Published: January 2024

Supplementary Data
Figure S6 from Magnetic Resonance Imaging of Iron Metabolism with T2* Mapping Predicts an Enhanced Clinical Response to Pharmacologic Ascorbate in Patients with GBM
Authors: Petronek Michael S. , Monga Varun , Bodeker Kellie L. , Kwofie Michael , Lee Chu-Yu , Mapuskar Kranti A. , Stolwijk Jeffrey M. , Zaher Amira , Wagner Brett A. , Smith Mark C. , Vollstedt Sandy , Brown Heather , Chandler Meghan L. , Lorack Amanda C. , Wulfekuhle Jared S. , Sarkaria Jann N. , Flynn Ryan T. , Greenlee Jeremy D.W. , Howard Matthew A. , Smith Brian J. , Jones Karra A. , Buettner Garry R. , Cullen Joseph J. , St-Aubin Joel , Buatti John M. , Magnotta Vincent A. , Spitz Douglas R. , Allen Bryan G.
Published: January 2024

Ferritin overexpression-induced Fe metabolic perturbations.
Supplementary Table S2 from Targeted Radiation Delivery before Haploidentical HCT for High-risk Leukemia or MDS Patients Yields Long-term Survivors
Authors: Orozco Johnnie J. , Vo Phuong T. , Gooley Ted A. , Haaf Robyn L. , Lundberg Sally J. , Hamlin Donald K. , Wilbur D. Scott , Matesan Manuela C. , Fisher Darrell R. , Gopal Ajay K. , Green Damian J. , Pagel John M. , Sandmaier Brenda M.
Published: January 2024

Supplementary Table S2: Recipient - Donor Characteristics
Figure S4 from Magnetic Resonance Imaging of Iron Metabolism with T2* Mapping Predicts an Enhanced Clinical Response to Pharmacologic Ascorbate in Patients with GBM
Authors: Petronek Michael S. , Monga Varun , Bodeker Kellie L. , Kwofie Michael , Lee Chu-Yu , Mapuskar Kranti A. , Stolwijk Jeffrey M. , Zaher Amira , Wagner Brett A. , Smith Mark C. , Vollstedt Sandy , Brown Heather , Chandler Meghan L. , Lorack Amanda C. , Wulfekuhle Jared S. , Sarkaria Jann N. , Flynn Ryan T. , Greenlee Jeremy D.W. , Howard Matthew A. , Smith Brian J. , Jones Karra A. , Buettner Garry R. , Cullen Joseph J. , St-Aubin Joel , Buatti John M. , Magnotta Vincent A. , Spitz Douglas R. , Allen Bryan G.
Published: January 2024

Doxycycline induces ferritin heavy chain overexpression.
Supplementary Table S1 from Targeted Radiation Delivery before Haploidentical HCT for High-risk Leukemia or MDS Patients Yields Long-term Survivors
Authors: Orozco Johnnie J. , Vo Phuong T. , Gooley Ted A. , Haaf Robyn L. , Lundberg Sally J. , Hamlin Donald K. , Wilbur D. Scott , Matesan Manuela C. , Fisher Darrell R. , Gopal Ajay K. , Green Damian J. , Pagel John M. , Sandmaier Brenda M.
Published: January 2024

Supplementary Table S1: Study Representativeness Table
Figure S2 from Magnetic Resonance Imaging of Iron Metabolism with T2* Mapping Predicts an Enhanced Clinical Response to Pharmacologic Ascorbate in Patients with GBM
Authors: Petronek Michael S. , Monga Varun , Bodeker Kellie L. , Kwofie Michael , Lee Chu-Yu , Mapuskar Kranti A. , Stolwijk Jeffrey M. , Zaher Amira , Wagner Brett A. , Smith Mark C. , Vollstedt Sandy , Brown Heather , Chandler Meghan L. , Lorack Amanda C. , Wulfekuhle Jared S. , Sarkaria Jann N. , Flynn Ryan T. , Greenlee Jeremy D.W. , Howard Matthew A. , Smith Brian J. , Jones Karra A. , Buettner Garry R. , Cullen Joseph J. , St-Aubin Joel , Buatti John M. , Magnotta Vincent A. , Spitz Douglas R. , Allen Bryan G.
Published: January 2024

Predictive power of T2* in patients receiving standard-of-care therapy.
Figure S1 from Magnetic Resonance Imaging of Iron Metabolism with T2* Mapping Predicts an Enhanced Clinical Response to Pharmacologic Ascorbate in Patients with GBM
Authors: Petronek Michael S. , Monga Varun , Bodeker Kellie L. , Kwofie Michael , Lee Chu-Yu , Mapuskar Kranti A. , Stolwijk Jeffrey M. , Zaher Amira , Wagner Brett A. , Smith Mark C. , Vollstedt Sandy , Brown Heather , Chandler Meghan L. , Lorack Amanda C. , Wulfekuhle Jared S. , Sarkaria Jann N. , Flynn Ryan T. , Greenlee Jeremy D.W. , Howard Matthew A. , Smith Brian J. , Jones Karra A. , Buettner Garry R. , Cullen Joseph J. , St-Aubin Joel , Buatti John M. , Magnotta Vincent A. , Spitz Douglas R. , Allen Bryan G.
Published: January 2024

T2* relaxation in GBM and normal tissue.
Data from ERK1/2 Phosphorylation Predicts Survival in Recurrent Glioblastoma Following Intracerebral and Adjuvant PD-1/CTLA-4 Immunotherapy: A REMARK-guided Analysis
Authors: Arrieta Víctor A. , Duerinck Johnny , Burdett Kirsten B. , Habashy Karl J. , Geens Wietse , Gould Andrew , Schwarze Julia K. , Dmello Crismita , Kim Kwang-Soo , Saganty Ruth , Chen Li , Moscona Alberto , McCord Matthew , Lee-Chang Catalina , Horbinski Craig M. , Zhang Hui , Stupp Roger , Neyns Bart , Sonabend Adam M.
Published: January 2024

AbstractPurpose:
Evidence suggests that MAPK pathway activation, as measured by ERK1/2 phosphorylation (p-ERK), predicts overall survival (OS) in patients with recurrent glioblastoma receiving anti-PD-1 therapy. We aimed to validate these findings in independent cohorts.
Experimental Design:
In a 24-patient clinical trial on recurrent glioblastoma and high-grade gliomas, we examined the link between p-ERK levels and OS. Patients received intravenous nivolumab, followed by maximal safe resection and an intracerebral injection of either ipilimumab alone or combined with nivolumab. Biweekly adjuvant nivolumab was then administered up to five times (NCT03233152). Using REporting recommendations for tumor MARKER prognostic studies (REMARK) criteria, we conducted independent analyses for p-ERK quantification and statistical evaluations. Additional comparative analysis included prior cohorts, totaling 65 patients. Cox proportional hazards models and meta-analysis were employed to assess p-ERK as a predictive biomarker after immunotherapy.
Results:
Lower median p-ERK+ cell density was observed compared with prior studies, likely due to variable tissue processing across cohorts. Nonetheless, high p-ERK was associated with prolonged OS, particularly in isocitrate dehydrogenase wild-type glioblastomas (P = 0.036). Median OS for high and low p-ERK patients were 55.6 and 30 weeks, respectively. Multivariable analysis reinforced p-ERK's significance in survival prediction (P = 0.011). Upon p-ERK normalization across cohorts (n = 65), meta-analysis supported the survival benefit of elevated tumor p-ERK levels (P = 0.0424).
Conclusions:
This study strengthens the role of p-ERK as a predictive biomarker for OS in patients with glioblastoma on immune checkpoint blockade. Future research should focus on further validation in prospective trials and the standardization of preanalytical variables influencing p-ERK quantification.
Data from SAR-096: Phase II Clinical Trial of Ribociclib in Combination with Everolimus in Advanced Dedifferentiated Liposarcoma (DDL) and Leiomyosarcoma (LMS)
Authors: Movva Sujana , Matloob Sahar , Handorf Elizabeth A. , Choy Edwin , Merriam Priscilla , Flieder Douglas B. , Cai Kathy Q. , Zhou Yan , Tetzlaff Eric D. , Pagan Cheyenne , Barker Emma , Veggeberg Rosanna , Zumpano Delia , Rink Lori , von Mehren Margaret , George Suzanne
Published: January 2024

AbstractPurpose:
Dedifferentiated liposarcoma (DDL) and leiomyosarcoma (LMS) are two common subtypes of soft-tissue sarcoma, a rare group of diseases for which new treatments are needed. Chemotherapy remains the standard option for advanced disease. Targeting cyclin-dependent kinase 4 and 6 (CDK4/6) in DDL and mTOR in LMS is of biologic interest. When combined, the CDK4 inhibitor ribociclib and the mTOR inhibitor everolimus have shown synergistic growth inhibition in multiple tumor models, suggesting that this combination could be beneficial in patients.
Patients and Methods:
This was a single arm, open label, multicenter phase II study of the combination of ribociclib and everolimus. Patients were enrolled into one of two cohorts: DDL or LMS with intact Rb. The primary endpoint was progression-free rate (PFR) at 16 weeks. Secondary endpoints included progression-free survival (PFS) and overall survival, safety and biomarker analyses.
Results:
In the DDL cohort, 33.3% [95% confidence interval (CI), 15.6%–55.3%] of patients were progression-free at 16 weeks. Median PFS in this cohort was 15.4 weeks (95% CI, 8–36 weeks) with 2 partial responses. In the LMS cohort the PFR at 16 weeks was 29.2% (95% CI, 12.6%–51.1%). Median PFS in this cohort was 15.7 weeks (95% CI, 7.7–NA). Most common toxicities included fatigue (66.7%), anorexia (43.8%), and hyperglycemia (43.8%). Concordance between Rb testing methodologies was poor.
Conclusions:
The combination of ribociclib and everolimus demonstrates activity in DDL with prolonged stable disease (≥16 weeks) meeting the primary endpoint. Notably partial responses were observed. The primary endpoint was not reached in the LMS cohort. The combination was well tolerated with expected side effects.
Data from CDK4/6 Inhibition Sensitizes Intracranial Tumors to PD-1 Blockade in Preclinical Models of Brain Metastasis
Authors: Nayyar Naema , de Sauvage Magali A. , Chuprin Jane , Sullivan Emily M. , Singh Mohini , Torrini Consuelo , Zhang Britney S. , Bandyopadhyay Sushobhana , Daniels Keith A. , Alvarez-Breckenridge Christopher , Dahal Ashish , Brehm Michael A. , Brastianos Priscilla K.
Published: January 2024

AbstractPurpose:
Brain metastases are associated with high morbidity and are often resistant to immune checkpoint inhibitors. We evaluated whether CDK4/6 inhibitor (CDKi) abemaciclib can sensitize intracranial tumors to programmed cell death protein 1 (PD-1) inhibition in mouse models of melanoma and breast cancer brain metastasis.
Experimental Design:
Treatment response was evaluated in vivo using immunocompetent mouse models of brain metastasis bearing concurrent intracranial and extracranial tumors. Treatment effect on intracranial and extracranial tumor–immune microenvironments (TIME) was evaluated using immunofluorescence, multiplex immunoassays, high-parameter flow cytometry, and T-cell receptor profiling. Mice with humanized immune systems were evaluated using flow cytometry to study the effect of CDKi on human T-cell development.
Results:
We found that combining abemaciclib with PD-1 inhibition reduced tumor burden and improved overall survival in mice. The TIME, which differed on the basis of anatomic location of tumors, was altered with CDKi and PD-1 inhibition in an organ-specific manner. Combination abemaciclib and anti–PD-1 treatment increased recruitment and expansion of CD8+ effector T-cell subsets, depleted CD4+ regulatory T (Treg) cells, and reduced levels of immunosuppressive cytokines in intracranial tumors. In immunodeficient mice engrafted with human immune systems, abemaciclib treatment supported development and maintenance of CD8+ T cells and depleted Treg cells.
Conclusions:
Our results highlight the distinct properties of intracranial and extracranial tumors and support clinical investigation of combination CDK4/6 and PD-1 inhibition in patients with brain metastases.

See related commentary by Margolin, p. 257
Data from Negative Hyperselection of Patients with HER2+ and RAS Wild-Type Metastatic Colorectal Cancer Receiving Dual HER2 Blockade: the PRESSING-HER2 Study
Authors: Randon Giovanni , Nakamura Yoshiaki , Yaeger Rona , Lonardi Sara , Cremolini Chiara , Elez Elena , Nichetti Federico , Ghelardi Filippo , Nasca Vincenzo , Bergamo Francesca , Conca Veronica , Ros Javier , Bando Hideaki , Maddalena Giulia , Oldani Simone , Prisciandaro Michele , Raimondi Alessandra , Schrock Alexa B. , Agnelli Luca , Walch Henry , Yoshino Takayuki , Pietrantonio Filippo
Published: January 2024

AbstractPurpose:
To demonstrate the negative prognostic impact of a panel of genomic alterations (PRESSING-HER2 panel) and lack of HER2 amplification by next-generation sequencing (NGS) in patients with HER2+, RAS wild-type metastatic colorectal cancer receiving dual HER2 blockade.
Experimental Design:
The PRESSING-HER2 panel of HER2 mutations/rearrangements and RTK/MAPK mutations/amplifications was assessed by NGS. HER2 amplification was confirmed by NGS if copy-number variation (CNV) was ≥ 6. With a case–control design, hypothesizing 30% and 5% PRESSING-HER2 positivity in resistant [progression-free survival (PFS) <4 months and no RECIST response] versus sensitive cohorts, respectively, 35 patients were needed per group.
Results:
PRESSING-HER2 alterations included HER2 mutations/rearrangements, EGFR amplification, and BRAF mutations and had a prevalence of 27% (9/33) and 3% (1/35) in resistant versus sensitive patients (P = 0.005) and 63% predictive accuracy. Overall, HER2 nonamplified status by NGS had 10% prevalence. Median PFS and overall survival (OS) were worse in PRESSING-HER2+ versus negative (2.2 vs. 5.3 months, P < 0.001; 5.4 vs. 14.9 months, P = 0.001) and in HER2 nonamplified versus amplified (1.6 vs. 5.2 months, P < 0.001; 7.4 vs. 12.4 months, P = 0.157). These results were confirmed in multivariable analyses [PRESSING-HER2 positivity: PFS HR = 3.06, 95% confidence interval (CI), 1.40–6.69, P = 0.005; OS HR = 2.93, 95% CI, 1.32–6.48, P = 0.007]. Combining PRESSING-HER2 and HER2 CNV increased the predictive accuracy to 75%.
Conclusions:
PRESSING-HER2 panel and HER2 nonamplified status by NGS warrant validation as potential predictive markers in this setting.

See related commentary by Raghav et al., p. 260
Data from Detection of Recurrence through microRNA-371a-3p Serum Levels in a Follow-up of Stage I Testicular Germ Cell Tumors in the DRKS-00019223 Study
Authors: Belge Gazanfer , Dumlupinar Cansu , Nestler Tim , Klemke Markus , Törzsök Peter , Trenti Emanuela , Pichler Renate , Loidl Wolfgang , Che Yue , Hiester Andreas , Matthies Cord , Pichler Martin , Paffenholz Pia , Kluth Luis , Wenzel Mike , Sommer Jörg , Heinzelbecker Julia , Schriefer Philipp , Winter Alexander , Zengerling Friedemann , Kramer Mario Wolfgang , Lengert Marie , Frey Jana , Heidenreich Axel , Wülfing Christian , Radtke Arlo , Dieckmann Klaus-Peter
Published: January 2024

AbstractPurpose:
Surveillance of clinical stage I (CSI) testicular germ cell tumors (GCT) is hampered by low sensitivity and specificity of current biomarkers for detecting relapses. This study evaluated if serum levels of microRNA371a-3p (M371 test) can: (i) Accurately detect relapses, (ii) detect relapses earlier than conventional technology, and (iii) if elevated postoperative M371 levels may predict relapse.
Experimental Design:
In a multicentric setting, 258 patients with testicular CSI GCT were prospectively followed by surveillance for a median time of 18 months with serial measurements of serum M371 levels, in addition to standard diagnostic techniques. Diagnostic characteristics of M371 for detecting relapses were calculated using ROC curve analysis.
Results:
Thirty-nine patients recurred (15.1%), all with elevated M371 levels; eight without relapse had elevations, too. The test revealed the following characteristics: area under the ROC curve of 0.993, sensitivity 100%, specificity 96.3%, positive predictive value 83%, negative predictive value 100%. Earlier relapse detection with the test was found in 28%, with non-significant median time gain to diagnosis. Postoperative M371 levels did not predict future relapse.
Conclusions:
The sensitivity and specificity of the M371 test for detecting relapses in CSI GCTs are much superior to those of conventional diagnostics. However, post-orchiectomy M371 levels are not predictive of relapse, and there is no significant earlier relapse detection with the test. In all, there is clear evidence for the utility of the M371 test for relapse detection suggesting it may soon be ready for implementation into routine follow-up schedules for patients with testicular GCT.
Supplementary File 8 from WNT4 Regulates Cellular Metabolism via Intracellular Activity at the Mitochondria in Breast and Gynecologic Cancers
Authors: Sottnik Joseph L. , Shackleford Madeleine T. , Robinson Sydney K. , Villagomez Fabian R. , Bahnassy Shaymaa , Oesterreich Steffi , Hu Junxiao , Madak-Erdogan Zeynep , Riggins Rebecca B. , Corr Bradley R. , Cook Linda S. , Treviño Lindsey S. , Bitler Benjamin G. , Sikora Matthew J.
Published: January 2024

Full RPPA dataset and analyses
Supplementary File 7 from WNT4 Regulates Cellular Metabolism via Intracellular Activity at the Mitochondria in Breast and Gynecologic Cancers
Authors: Sottnik Joseph L. , Shackleford Madeleine T. , Robinson Sydney K. , Villagomez Fabian R. , Bahnassy Shaymaa , Oesterreich Steffi , Hu Junxiao , Madak-Erdogan Zeynep , Riggins Rebecca B. , Corr Bradley R. , Cook Linda S. , Treviño Lindsey S. , Bitler Benjamin G. , Sikora Matthew J.
Published: January 2024

Cell line rs3820282 genotyping
Supplementary File 5 from WNT4 Regulates Cellular Metabolism via Intracellular Activity at the Mitochondria in Breast and Gynecologic Cancers
Authors: Sottnik Joseph L. , Shackleford Madeleine T. , Robinson Sydney K. , Villagomez Fabian R. , Bahnassy Shaymaa , Oesterreich Steffi , Hu Junxiao , Madak-Erdogan Zeynep , Riggins Rebecca B. , Corr Bradley R. , Cook Linda S. , Treviño Lindsey S. , Bitler Benjamin G. , Sikora Matthew J.
Published: January 2024

Consensus WNT4 target metabolites
Supplementary File 4 from WNT4 Regulates Cellular Metabolism via Intracellular Activity at the Mitochondria in Breast and Gynecologic Cancers
Authors: Sottnik Joseph L. , Shackleford Madeleine T. , Robinson Sydney K. , Villagomez Fabian R. , Bahnassy Shaymaa , Oesterreich Steffi , Hu Junxiao , Madak-Erdogan Zeynep , Riggins Rebecca B. , Corr Bradley R. , Cook Linda S. , Treviño Lindsey S. , Bitler Benjamin G. , Sikora Matthew J.
Published: January 2024

WNT4-OE and inhibitor metabolomics analyses
Supplemental Figure 3 from WNT4 Regulates Cellular Metabolism via Intracellular Activity at the Mitochondria in Breast and Gynecologic Cancers
Authors: Sottnik Joseph L. , Shackleford Madeleine T. , Robinson Sydney K. , Villagomez Fabian R. , Bahnassy Shaymaa , Oesterreich Steffi , Hu Junxiao , Madak-Erdogan Zeynep , Riggins Rebecca B. , Corr Bradley R. , Cook Linda S. , Treviño Lindsey S. , Bitler Benjamin G. , Sikora Matthew J.
Published: January 2024

RPPA networks in full cohort dataset
FIGURE 8 from WNT4 Regulates Cellular Metabolism via Intracellular Activity at the Mitochondria in Breast and Gynecologic Cancers
Authors: Sottnik Joseph L. , Shackleford Madeleine T. , Robinson Sydney K. , Villagomez Fabian R. , Bahnassy Shaymaa , Oesterreich Steffi , Hu Junxiao , Madak-Erdogan Zeynep , Riggins Rebecca B. , Corr Bradley R. , Cook Linda S. , Treviño Lindsey S. , Bitler Benjamin G. , Sikora Matthew J.
Published: January 2024

WNT4 variant genotype is associated with metabolic remodeling in gynecologic tumors, mirroring ILC signaling. A–C, Points represent total network score for the listed RPPA targets for individual tumors based on rs3820282 genotype. Red bar = median score; P-value from Mann–Whitney t test. A, Tumor scores for AMPK-associated network. B, Tumor scores for phospho-AMPK only. C, Tumor scores for glucose metabolism-associated network. D, Scatterplot of network scores in A and C; correlation from full dataset, that is, WT and Var samples combined. E–G, Network scores as in A–C from n = 58 stage I endometrioid-type endometrial tumors; networks generated independently from full dataset. E, Tumor scores for metabolic signaling network associated with AMPK and lipid metabolism signaling. F, Tumor scores for phospho-AMPKα1 only. G, Tumor scores for glucose metabolism-associated network. H, Points represent AMPK network score for individual tumors based on rs3820282 genotype and race/ethnicity groups. *, adj.P < 0.1, ANOVA with Welch correction. Cells were transfected with siRNA for 72 hours prior to immunoblotting, with ovarian cancer cell lines (I) and ILC cell lines (J). Representative band from total protein staining shown as loading control.