bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas
Authors: Gonzalez-Buendia Edgar , Zhao Junfei , Wang Lu , Mukherjee Subhas , Zhang Daniel , Arrieta Víctor A. , Feldstein Eric , Kane J. Robert , Kang Seong Jae , Lee-Chang Catalina , Mahajan Aayushi , Chen Li , Realubit Ronald , Karan Charles , Magnuson Lisa , Horbinski Craig , Marshall Stacy A. , Sarkaria Jann N. , Mohyeldin Ahmed , Nakano Ichiro , Bansal Mukesh , James Charles D. , Brat Daniel J. , Ahmed Atique , Canoll Peter , Rabadan Raul , Shilatifard Ali , Sonabend Adam M.
Published: November 2024

AbstractPurpose:
The epigenetic mechanisms involved in transcriptional regulation leading to malignant phenotype in gliomas remains poorly understood. Topoisomerase IIB (TOP2B), an enzyme that decoils and releases torsional forces in DNA, is overexpressed in a subset of gliomas. Therefore, we investigated its role in epigenetic regulation in these tumors.
Experimental Design:
To investigate the role of TOP2B in epigenetic regulation in gliomas, we performed paired chromatin immunoprecipitation sequencing for TOP2B and RNA-sequencing analysis of glioma cell lines with and without TOP2B inhibition and in human glioma specimens. These experiments were complemented with assay for transposase-accessible chromatin using sequencing, gene silencing, and mouse xenograft experiments to investigate the function of TOP2B and its role in glioma phenotypes.
Results:
We discovered that TOP2B modulates transcription of multiple oncogenes in human gliomas. TOP2B regulated transcription only at sites where it was enzymatically active, but not at all native binding sites. In particular, TOP2B activity localized in enhancers, promoters, and introns of PDGFRA and MYC, facilitating their expression. TOP2B levels and genomic localization was associated with PDGFRA and MYC expression across glioma specimens, which was not seen in nontumoral human brain tissue. In vivo, TOP2B knockdown of human glioma intracranial implants prolonged survival and downregulated PDGFRA.
Conclusions:
Our results indicate that TOP2B activity exerts a pleiotropic role in transcriptional regulation of oncogenes in a subset of gliomas promoting a proliferative phenotype.
Data from Single-Agent Ibrutinib for Rituximab-Refractory Waldenström Macroglobulinemia: Final Analysis of the Substudy of the Phase III InnovateTM Trial
Authors: Trotman Judith , Buske Christian , Tedeschi Alessandra , Matous Jeffrey V. , MacDonald David , Tam Constantine S. , Tournilhac Olivier , Ma Shuo , Treon Steven P. , Oriol Albert , Ping Jerry , Briso Eva M. , Arango-Hisijara Israel , Dimopoulos Meletios A.
Published: November 2024

AbstractPurpose:
The first report from the open-label substudy of the phase III iNNOVATE study (PCYC-1127; NCT02165397) demonstrated that single-agent ibrutinib was efficacious and well tolerated in patients with heavily pretreated, rituximab-refractory Waldenström macroglobulinemia. Results from the final analysis are now reported.
Patients and Methods:
Ibrutinib 420 mg was administered once daily to patients (N = 31) who failed to achieve at least a minor response (MR) or who relapsed <12 months after their last rituximab-containing therapy. Endpoints included progression-free survival (PFS) and overall response rate (ORR; MR or better) per independent review committee, hemoglobin improvement, overall survival (OS), and safety; serum IgM was also assessed.
Results:
After a median follow-up of 58 months (range: 9–61), median PFS was 39 months [95% confidence interval (CI): 25–not evaluable]; 60-month PFS rate was 40%. In MYD88L265P/CXCR4WHIM and MYD88L265P/CXCR4WT subtypes, median PFS was 18 months and not reached, respectively. In all patients, ORR was 87%; responses deepened over time with major response (≥ partial response) rates increasing from 61% at 6 months to 77% at 60 months. Median OS was not reached. Seventeen of 21 patients (81%) with baseline hemoglobin ≤11.0 g/dL had sustained hemoglobin improvement. Improvements in serum IgM levels were sustained, reaching a maximum median change of −37 g/L at 54 months. Ibrutinib maintained a manageable safety profile, with no new safety signals identified. There were no events of major hemorrhage or atrial fibrillation.
Conclusions:
In the final analysis from iNNOVATE, single-agent ibrutinib continued to show sustained efficacy in patients with heavily pretreated, rituximab-refractory Waldenström macroglobulinemia.
Supplementary Methods from Dual A2A/A2B Adenosine Receptor Antagonist M1069 Counteracts Immunosuppressive Mechanisms of Adenosine and Reduces Tumor Growth In Vivo
Authors: Schiemann Kai , Belousova Natalya , Matevossian Armine , Nallaparaju Kalyan C. , Kradjian Giorgio , Pandya Meghana , Chen Zhouxiang , Aral Esengul , Krauel Eva-Maria , Petrova Elissaveta , Boesler Carsten , Kitzing Thomas , Lecomte Marc , Wagner Christian , Blayo Anne Laure , Schann Stephan , Huck Bayard , Moisan Jacques , Zaynagetdinov Rinat
Published: November 2024

Supplementary Materials and Methods
Supp. Fig. 2 from Dual A2A/A2B Adenosine Receptor Antagonist M1069 Counteracts Immunosuppressive Mechanisms of Adenosine and Reduces Tumor Growth In Vivo
Authors: Schiemann Kai , Belousova Natalya , Matevossian Armine , Nallaparaju Kalyan C. , Kradjian Giorgio , Pandya Meghana , Chen Zhouxiang , Aral Esengul , Krauel Eva-Maria , Petrova Elissaveta , Boesler Carsten , Kitzing Thomas , Lecomte Marc , Wagner Christian , Blayo Anne Laure , Schann Stephan , Huck Bayard , Moisan Jacques , Zaynagetdinov Rinat
Published: November 2024

Supplementary Figure 2
Supplementary Figure S3 from Identification of ATP-Competitive Human CMG Helicase Inhibitors for Cancer Intervention that Disrupt CMG-Replisome Function
Authors: Xiang Shengyan , Craig Kendall C. , Luo Xingju , Welch Darcy L. , Ferreira Renan B. , Lawrence Harshani R. , Lawrence Nicholas J. , Reed Damon R. , Alexandrow Mark G.
Published: November 2024

Supplementary Figure S3
Supplementary Chemical Synthesis Methods from Identification of ATP-Competitive Human CMG Helicase Inhibitors for Cancer Intervention that Disrupt CMG-Replisome Function
Authors: Xiang Shengyan , Craig Kendall C. , Luo Xingju , Welch Darcy L. , Ferreira Renan B. , Lawrence Harshani R. , Lawrence Nicholas J. , Reed Damon R. , Alexandrow Mark G.
Published: November 2024

Supplementary Chemical Synthesis Methods
Supplemental Figure 8 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

Tumour growth in the huPBMC admixed anti-tumour study
Supplemental Figure 7 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

Serum levels of SC134-TCB in NSG mice
Supplemental Figure 5 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

SC134-TCB induced IFNy
Supplemental Figure 4 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

Maximum cytotoxicity
Supplementary Table 1 from Targeting Ovarian Cancer Stem Cells by Dual Inhibition of the Long Noncoding RNA HOTAIR and Lysine Methyltransferase EZH2
Authors: Wang Weini , Zhou Yanchi , Wang Ji , Zhang Shu , Ozes Ali , Gao Hongyu , Fang Fang , Wang Yue , Chu Xiaona , Liu Yunlong , Wan Jun , Mitra Anirban K. , O’Hagan Heather M. , Nephew Kenneth P.
Published: November 2024

Sequences
Figure S3 from Targeting Ovarian Cancer Stem Cells by Dual Inhibition of the Long Noncoding RNA HOTAIR and Lysine Methyltransferase EZH2
Authors: Wang Weini , Zhou Yanchi , Wang Ji , Zhang Shu , Ozes Ali , Gao Hongyu , Fang Fang , Wang Yue , Chu Xiaona , Liu Yunlong , Wan Jun , Mitra Anirban K. , O’Hagan Heather M. , Nephew Kenneth P.
Published: November 2024

Supplementary Figure 3
Figure S2 from Targeting Ovarian Cancer Stem Cells by Dual Inhibition of the Long Noncoding RNA HOTAIR and Lysine Methyltransferase EZH2
Authors: Wang Weini , Zhou Yanchi , Wang Ji , Zhang Shu , Ozes Ali , Gao Hongyu , Fang Fang , Wang Yue , Chu Xiaona , Liu Yunlong , Wan Jun , Mitra Anirban K. , O’Hagan Heather M. , Nephew Kenneth P.
Published: November 2024

Supplementary Figure 2
Figure 6 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

T cell–mediated cytokine production by SC134-TCB. A, Serum cytokine concentration after incubation of whole blood with SC134-TCB or huOKT3 for 5 and 24 hours from one representative donor of four analyzed. B, Cytokine detection in mouse sera 24 hours after one 100 μg SC134-TCB dose (DMS79 inoculation 8 days prior to pan-T and TCB dosing). Primary cell analysis of SC134-TCB–mediated T-cell activation. C, Reactivity measured by IFNγ ELISpot with normal primary human cells derived from the thymus and skin or (D) from cardiac and gastric tissues. DMS79 and PBMC only used as positive and negative controls, respectively. Representative data shown for two healthy PBMC donors.
Figure 4 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

Effective tumor control by SC134-TCB. A, Significant tumor-free survival in admixed antitumor study dosed with 100 μg SC134-TCB for 3 weeks. PBMC implanted with DMS79 cells at 1:1 ratio and a further two doses of PBMCs given on days 8 and 15. Log-rank Mantel–Cox P < 0.0001. Significant DMS79 tumor control by SC134-TCB treatment, with PBMCs dosed on days 3 and 18 (dotted lines), after tumor inoculation, at 5:1 ratio. Gray arrows show biweekly dosing of SC134-TCB (100 μg): (B) tumor volume (individual growth curves, shown in Supplementary Fig. S9A). Significance, mixed-effects model P = 0.013 and (C) OS, log-rank Mantel–Cox P = 0.0042, shown. D, Phenotyping data assessing the percentage of exhausted T cells (PD1+TIM3+) in terminal tumor samples. T cells were gated based on combined CD4 and CD8 staining (gating strategy depicted in Supplementary Fig. S9B). E, SC134-TCB detection in tumors compared with spleens in the SC134-TCB–dosed group (i.v.), paired t test, P = 0.0069. Each point represents an individual mouse. SC134-TCB–mediated T-cell infiltration and activation coincide with significant antitumor impact. F, Significant tumor control by SC134 with single PBMC administration (day 8) combined with SC134-TCB (100 μg at days 9, 11, and 15). Significance, two-way ANOVA, P = 0.0249; individual growth curves are shown in Supplementary Fig. S9C. G, Significantly increased T-cell presence and T-cell activation: (H) PD1+ and (I) CXCR3+ in tumors of SC134-TCB–treated mice. The presence of individual populations is evident from the IHC analysis of terminal tumor samples (Supplementary Fig. S9D).
Supplementary Table 2 from Novel Inhibition of Central Carbon Metabolism Pathways by Rac and CDC42 inhibitor MBQ167 and Paclitaxel
Authors: Cruz-Collazo Ailed M. , Katsara Olga , Grafals-Ruiz Nilmary , Colon Gonzalez Jessica , Dorta-Estremera Stephanie , Carlo Victor P. , Chorna Nataliya , Schneider Robert J. , Dharmawardhane Suranganie
Published: November 2024

Supplementary Table 2
Figure 3 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

Potent T cell–mediated tumor cell killing by SC134-TCB. SC134-TCB induced tumor cell killing. A, Cytotoxicity EC50 via LDH release and flow-based analysis in pan-T:DMS79 cocultures. B, Percentage maximum target cell death of DMS79 with SC134-TCB and isotype control B12-TCB at 10 nmol/L. C, Increased killing by SC134-TCB (LDH release) at higher E:T ratios. Open symbols denote background killing by isotype control B12-TCB. D, LDH release from two target cell lines: high-expressor DMS79 and moderate-expressor DMS153. SC134-TCB induced T-cell activation. E, EC50 via CD69 staining shown for DMS79 and DMS153. F, Percentage maximum activation with SC134-TCB and isotype control B12-TCB at 10 nmol/L. G, Activation of CD4 and CD8 T-cell subsets from one effector donor. H, SC134-TCB induced CD4 and CD8 T-cell proliferation (day 3) determined by Ki67 staining. Representative donor shown. I, Target-dependent multifunctional cytokine production by SC134-TCB in DMS79 cocultures with enriched T cells. T cells used at an E:T of 5:1, for all assays. Median or representative data shown for three or more human donors.
Figure 2 from SC134-TCB Targeting Fucosyl-GM1, a T Cell–Engaging Antibody with Potent Antitumor Activity in Preclinical Small Cell Lung Cancer Models
Authors: Dave Foram , Vaghela Poonam , Heath Bryony , Dunster Zuzana , Dubinina Elena , Thakker Dhruma , Mann Katie , Chadwick Joe , Cane Gaëlle , Kaira Bubacarr G. , Mohammed Omar J. , Choudhury Ruhul , Paston Samantha , Parsons Tina , Vankemmelbeke Mireille , Durrant Lindy
Published: November 2024

SC134-TCB effectively binds SCLC cell lines and T cells. A, Schematic drawing of the SC134-TCB format. Targeting regions of h134 in combination with scFv of huOKT3 were used. Stars denote “short tandem repeat” modification for Fc silencing. SCLC cell binding by SC134-TCB: (B) DMS79 cell binding of SC134-TCB and parental h134. C, Histograms of top concentration (50 nmol/L) SC134-TCB binding (black) to three target-positive cell lines DMS79, DMS153, and H740 compared with secondary antibody–only control (gray). D, Pan–T-cell binding of B12-TCB, SC134-TCB, and parental anti-CD3 (huOKT3). MFI assessed via flow cytometry. MFI, median fluorescence intensity. (A, Created with BioRender.com.)
Supplementary Tables S1-S11 from YAP1 Suppression by ZDHHC7 Is Associated with Ferroptosis Resistance and Poor Prognosis in Ovarian Clear Cell Carcinoma
Authors: Furutake Yoko , Yamaguchi Ken , Yamanoi Koji , Kitamura Sachiko , Takamatsu Shiro , Taki Mana , Ukita Masayo , Hosoe Yuko , Murakami Ryusuke , Abiko Kaoru , Horie Akihito , Hamanishi Junzo , Baba Tsukasa , Matsumura Noriomi , Mandai Masaki
Published: November 2024

Table S1 to S11
Figure S7 from YAP1 Suppression by ZDHHC7 Is Associated with Ferroptosis Resistance and Poor Prognosis in Ovarian Clear Cell Carcinoma
Authors: Furutake Yoko , Yamaguchi Ken , Yamanoi Koji , Kitamura Sachiko , Takamatsu Shiro , Taki Mana , Ukita Masayo , Hosoe Yuko , Murakami Ryusuke , Abiko Kaoru , Horie Akihito , Hamanishi Junzo , Baba Tsukasa , Matsumura Noriomi , Mandai Masaki
Published: November 2024

Raw data of immunoblotting.
Figure S5 from YAP1 Suppression by ZDHHC7 Is Associated with Ferroptosis Resistance and Poor Prognosis in Ovarian Clear Cell Carcinoma
Authors: Furutake Yoko , Yamaguchi Ken , Yamanoi Koji , Kitamura Sachiko , Takamatsu Shiro , Taki Mana , Ukita Masayo , Hosoe Yuko , Murakami Ryusuke , Abiko Kaoru , Horie Akihito , Hamanishi Junzo , Baba Tsukasa , Matsumura Noriomi , Mandai Masaki
Published: November 2024

Supplementary Figure 5
Figure S1 from YAP1 Suppression by ZDHHC7 Is Associated with Ferroptosis Resistance and Poor Prognosis in Ovarian Clear Cell Carcinoma
Authors: Furutake Yoko , Yamaguchi Ken , Yamanoi Koji , Kitamura Sachiko , Takamatsu Shiro , Taki Mana , Ukita Masayo , Hosoe Yuko , Murakami Ryusuke , Abiko Kaoru , Horie Akihito , Hamanishi Junzo , Baba Tsukasa , Matsumura Noriomi , Mandai Masaki
Published: November 2024

Supplementary Figure 1
Figure S5 from A DXd/TLR7-Agonist Dual-Conjugate Anti-HER2 ADC Exerts Robust Antitumor Activity Through Tumor Cell Killing and Immune Activation
Authors: Yue Hangtian , Xu Hui , Ma Lanping , Li Xiyuan , Yang Biyu , Wang Xiyuan , Zeng Qingzhong , Li Han , Zhang Deqiang , Geng Meiyu , Meng Tao , Xie Zuoquan
Published: November 2024

Figure S5. Tumor weight and flow cytometry analysis of tumor infiltrating leukocytes in EMT6-HER2 tumor model. (A) Tumor weight of Fig. 5A. (B-D) Gating strategy for flow cytometry analysis of immune subset in tumor samples. (E-H) EMT6-HER2 tumor were treated with control (0.9%NaCl), trastuzumab (1 mg/kg), Tras-DXd (1 mg/kg), or Tras-DXd-MTL1 (1 mg/kg) for 2 days (n=5), and immune subsets in tumor tissue were analyzed by flow cytometry, and the proportion macrophages (E), CD86+ macrophages (F), CD206+ macrophages (G), and CD3+T cells (H) were shown. The data were shown as mean ± SEM, One-way ANOVA (A, E-G) with Tukey’s correction were used for multiple comparisons. ns, not significant, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.
Figure S2 from A DXd/TLR7-Agonist Dual-Conjugate Anti-HER2 ADC Exerts Robust Antitumor Activity Through Tumor Cell Killing and Immune Activation
Authors: Yue Hangtian , Xu Hui , Ma Lanping , Li Xiyuan , Yang Biyu , Wang Xiyuan , Zeng Qingzhong , Li Han , Zhang Deqiang , Geng Meiyu , Meng Tao , Xie Zuoquan
Published: November 2024

Figure S2. HEK293T-luci cells expressing the NF-κB reporter system were treated with TNF-α (40 ng/ml), MTT-5 (10 µM), R848 (10 µM) and control (0.1%DMSO) for 24 h. The data were shown as mean ± SEM, and one-way ANOVA was used for multiple comparisons. ns, not significant, ****P < 0.0001.
Figure S7 from Tumor Microenvironment Reprogramming Improves Nanomedicine-Based Chemo-Immunotherapy in Sarcomas
Authors: Charalambous Antonia , Mpekris Fotios , Panagi Myrofora , Voutouri Chrysovalantis , Michael Christina , Gabizon Alberto A. , Stylianopoulos Triantafyllos
Published: November 2024

Figure S7
Figure S4 from Tumor Microenvironment Reprogramming Improves Nanomedicine-Based Chemo-Immunotherapy in Sarcomas
Authors: Charalambous Antonia , Mpekris Fotios , Panagi Myrofora , Voutouri Chrysovalantis , Michael Christina , Gabizon Alberto A. , Stylianopoulos Triantafyllos
Published: November 2024

Figure S4
Figure S3 from Tumor Microenvironment Reprogramming Improves Nanomedicine-Based Chemo-Immunotherapy in Sarcomas
Authors: Charalambous Antonia , Mpekris Fotios , Panagi Myrofora , Voutouri Chrysovalantis , Michael Christina , Gabizon Alberto A. , Stylianopoulos Triantafyllos
Published: November 2024

Figure S3
Figure S2 from Tumor Microenvironment Reprogramming Improves Nanomedicine-Based Chemo-Immunotherapy in Sarcomas
Authors: Charalambous Antonia , Mpekris Fotios , Panagi Myrofora , Voutouri Chrysovalantis , Michael Christina , Gabizon Alberto A. , Stylianopoulos Triantafyllos
Published: November 2024

Figure S2
Supplementary Table 7 from Trastuzumab-MMAU Antibody-Auristatin Conjugates: Valine-Glucoserine Linker with Stabilized Maleimide Conjugation Improves In Vivo Efficacy and Tolerability
Authors: Goldberg Shalom D. , Satomaa Tero , Aina Olulanu , Aitio Olli , Burke Krista , Dudkin Vadim , Geist Brian , Irrechukwu Onyi , Hänninen Anna-Liisa , Heiskanen Annamari , Helin Jari , Hiltunen Jukka O. , Kinyamu-Akunda Jacqueline , Klein Donna M. , Kohli Neeraj , Kotiranta Titta , Lähteenmäki Tuula , Niemelä Ritva , Pitkänen Virve , Pynnönen Henna , Rittase William , Wiley Kristen , Zhou Junguo , Saarinen Juhani
Published: November 2024

Mean plasma MMAE toxicokinetic estimates following weekly i.v. doses of free MMAU to Sprague-Dawley rats.
Supplementary Table 2 from Trastuzumab-MMAU Antibody-Auristatin Conjugates: Valine-Glucoserine Linker with Stabilized Maleimide Conjugation Improves In Vivo Efficacy and Tolerability
Authors: Goldberg Shalom D. , Satomaa Tero , Aina Olulanu , Aitio Olli , Burke Krista , Dudkin Vadim , Geist Brian , Irrechukwu Onyi , Hänninen Anna-Liisa , Heiskanen Annamari , Helin Jari , Hiltunen Jukka O. , Kinyamu-Akunda Jacqueline , Klein Donna M. , Kohli Neeraj , Kotiranta Titta , Lähteenmäki Tuula , Niemelä Ritva , Pitkänen Virve , Pynnönen Henna , Rittase William , Wiley Kristen , Zhou Junguo , Saarinen Juhani
Published: November 2024

Individual and mean serum total antibody toxicokinetic parameters following three i.v. bolus doses of T-mavg-MMAU DAR4 in male cynomolgus monkeys.
Supplementary Figure 9 from Trastuzumab-MMAU Antibody-Auristatin Conjugates: Valine-Glucoserine Linker with Stabilized Maleimide Conjugation Improves In Vivo Efficacy and Tolerability
Authors: Goldberg Shalom D. , Satomaa Tero , Aina Olulanu , Aitio Olli , Burke Krista , Dudkin Vadim , Geist Brian , Irrechukwu Onyi , Hänninen Anna-Liisa , Heiskanen Annamari , Helin Jari , Hiltunen Jukka O. , Kinyamu-Akunda Jacqueline , Klein Donna M. , Kohli Neeraj , Kotiranta Titta , Lähteenmäki Tuula , Niemelä Ritva , Pitkänen Virve , Pynnönen Henna , Rittase William , Wiley Kristen , Zhou Junguo , Saarinen Juhani
Published: November 2024

Effect of cysteine protease inhibitor E-64 on lysosomal degradation of T-mavg-MMAU DAR8 and T-mcvc-MMAE DAR4.
Supplementary Figure 7 from Trastuzumab-MMAU Antibody-Auristatin Conjugates: Valine-Glucoserine Linker with Stabilized Maleimide Conjugation Improves In Vivo Efficacy and Tolerability
Authors: Goldberg Shalom D. , Satomaa Tero , Aina Olulanu , Aitio Olli , Burke Krista , Dudkin Vadim , Geist Brian , Irrechukwu Onyi , Hänninen Anna-Liisa , Heiskanen Annamari , Helin Jari , Hiltunen Jukka O. , Kinyamu-Akunda Jacqueline , Klein Donna M. , Kohli Neeraj , Kotiranta Titta , Lähteenmäki Tuula , Niemelä Ritva , Pitkänen Virve , Pynnönen Henna , Rittase William , Wiley Kristen , Zhou Junguo , Saarinen Juhani
Published: November 2024

Digestion of T-mcvc-MMAE DAR4 with recombinant cathepsin B.
Table S2 from Inhibition of SUMOylation Induces Adaptive Antitumor Immunity against Pancreatic Cancer through Multiple Effects on the Tumor Microenvironment
Authors: Erdem Suna , Lee Hyojae James , Shankara Narayanan Jayanth Surya Narayanan , Tharuka Mohottige Don Neranjan , De la Torre Jorge , Ren Tianchen , Kuang Yixuan , Abeywardana Tharindumala , Li Kevin , Berger Allison J. , Lowy Andrew M. , White Rebekah R. , Chen Yuan
Published: November 2024

Table S2
Fig. S7 from Inhibition of SUMOylation Induces Adaptive Antitumor Immunity against Pancreatic Cancer through Multiple Effects on the Tumor Microenvironment
Authors: Erdem Suna , Lee Hyojae James , Shankara Narayanan Jayanth Surya Narayanan , Tharuka Mohottige Don Neranjan , De la Torre Jorge , Ren Tianchen , Kuang Yixuan , Abeywardana Tharindumala , Li Kevin , Berger Allison J. , Lowy Andrew M. , White Rebekah R. , Chen Yuan
Published: November 2024

Fig. S7
Fig. S6 from Inhibition of SUMOylation Induces Adaptive Antitumor Immunity against Pancreatic Cancer through Multiple Effects on the Tumor Microenvironment
Authors: Erdem Suna , Lee Hyojae James , Shankara Narayanan Jayanth Surya Narayanan , Tharuka Mohottige Don Neranjan , De la Torre Jorge , Ren Tianchen , Kuang Yixuan , Abeywardana Tharindumala , Li Kevin , Berger Allison J. , Lowy Andrew M. , White Rebekah R. , Chen Yuan
Published: November 2024

Fig. S6
Supplementary Figure 13 from Trastuzumab-MMAU Antibody-Auristatin Conjugates: Valine-Glucoserine Linker with Stabilized Maleimide Conjugation Improves In Vivo Efficacy and Tolerability
Authors: Goldberg Shalom D. , Satomaa Tero , Aina Olulanu , Aitio Olli , Burke Krista , Dudkin Vadim , Geist Brian , Irrechukwu Onyi , Hänninen Anna-Liisa , Heiskanen Annamari , Helin Jari , Hiltunen Jukka O. , Kinyamu-Akunda Jacqueline , Klein Donna M. , Kohli Neeraj , Kotiranta Titta , Lähteenmäki Tuula , Niemelä Ritva , Pitkänen Virve , Pynnönen Henna , Rittase William , Wiley Kristen , Zhou Junguo , Saarinen Juhani
Published: November 2024

Digestion of lintuzumab-mcvc-MMAE DAR4 (lintuzumab vedotin) by cynomolgus monkey liver microsomes at pH 4.5.
Fig. S5 from Inhibition of SUMOylation Induces Adaptive Antitumor Immunity against Pancreatic Cancer through Multiple Effects on the Tumor Microenvironment
Authors: Erdem Suna , Lee Hyojae James , Shankara Narayanan Jayanth Surya Narayanan , Tharuka Mohottige Don Neranjan , De la Torre Jorge , Ren Tianchen , Kuang Yixuan , Abeywardana Tharindumala , Li Kevin , Berger Allison J. , Lowy Andrew M. , White Rebekah R. , Chen Yuan
Published: November 2024

Fig.S5
Supplementary Figure 11 from Trastuzumab-MMAU Antibody-Auristatin Conjugates: Valine-Glucoserine Linker with Stabilized Maleimide Conjugation Improves In Vivo Efficacy and Tolerability
Authors: Goldberg Shalom D. , Satomaa Tero , Aina Olulanu , Aitio Olli , Burke Krista , Dudkin Vadim , Geist Brian , Irrechukwu Onyi , Hänninen Anna-Liisa , Heiskanen Annamari , Helin Jari , Hiltunen Jukka O. , Kinyamu-Akunda Jacqueline , Klein Donna M. , Kohli Neeraj , Kotiranta Titta , Lähteenmäki Tuula , Niemelä Ritva , Pitkänen Virve , Pynnönen Henna , Rittase William , Wiley Kristen , Zhou Junguo , Saarinen Juhani
Published: November 2024

Lysosomal degradation of non-hydrolyzed Cys-mavg-MMAU linker-payload molecule.
Fig. S3 from Inhibition of SUMOylation Induces Adaptive Antitumor Immunity against Pancreatic Cancer through Multiple Effects on the Tumor Microenvironment
Authors: Erdem Suna , Lee Hyojae James , Shankara Narayanan Jayanth Surya Narayanan , Tharuka Mohottige Don Neranjan , De la Torre Jorge , Ren Tianchen , Kuang Yixuan , Abeywardana Tharindumala , Li Kevin , Berger Allison J. , Lowy Andrew M. , White Rebekah R. , Chen Yuan
Published: November 2024

Fig. S3
Supplementary Table from Emerging Tumor-Agnostic Molecular Targets
Authors: Bhamidipati Dedipya , Schram Alison M.
Published: November 2024

Supplementary Table
Data from Targeting Ovarian Cancer Stem Cells by Dual Inhibition of the Long Noncoding RNA HOTAIR and Lysine Methyltransferase EZH2
Authors: Wang Weini , Zhou Yanchi , Wang Ji , Zhang Shu , Ozes Ali , Gao Hongyu , Fang Fang , Wang Yue , Chu Xiaona , Liu Yunlong , Wan Jun , Mitra Anirban K. , O’Hagan Heather M. , Nephew Kenneth P.
Published: November 2024

Abstract
The persistence of cancer stem cells (CSC) is believed to contribute to resistance to platinum-based chemotherapy and disease relapse in ovarian cancer, the fifth leading cause of cancer-related death among US women. HOXC transcript antisense RNA (HOTAIR) is a long, noncoding RNA (lncRNA) overexpressed in high-grade serous ovarian cancer and linked to chemoresistance. However, HOTAIR impacts chromatin dynamics in ovarian CSCs. Oncogenic lncRNA’s contributions to drug-resistant disease are incompletely understood. Here, we generated HOTAIR knockout (KO) high-grade serous ovarian cancer cell lines using paired CRISPR guide RNA design to investigate the function of HOTAIR. We show the loss of HOTAIR function resensitized ovarian cancer cells to platinum treatment and decreased the population of ovarian CSCs. Furthermore, HOTAIR KO inhibited the development of stemness-related phenotypes, including spheroid formation ability and expression of key stemness-associated genes ALDH1A1, NOTCH3, SOX9, and PROM1. HOTAIR KO altered the cellular transcriptome and chromatin accessibility landscape of multiple oncogenic-associated genes and pathways, including the NF-kB pathway. HOTAIR functions as an oncogene by recruiting enhancer of zeste homolog 2 (EZH2) to catalyze H3K27 trimethylation to suppress downstream tumor suppressor genes, and it was of interest to inhibit both HOTAIR and EZH2. In vivo, combining a HOTAIR inhibitor with an EZH2 inhibitor and platinum chemotherapy decreased tumor formation and increased survival. These results suggest a key role for HOTAIR in ovarian CSCs and malignant potential. Targeting HOTAIR in combination with epigenetic therapies may represent a therapeutic strategy to ameliorate ovarian cancer progression and resistance to platinum-based chemotherapy.
Supplemental Table 3 from Plasma Concentrations of Multiple Oxysterols and Risk of Colorectal Adenomas
Authors: Passarelli Michael N. , McDonald Jeffrey G. , Thompson Bonne M. , Pomares-Millan Hugo , Palys Thomas J. , Rees Judy R. , Barry Elizabeth L.
Published: November 2024

Supplemental Table 3. Subgroup analyses by treatment assignment.
Supplemental Figure 2 from Plasma Concentrations of Multiple Oxysterols and Risk of Colorectal Adenomas
Authors: Passarelli Michael N. , McDonald Jeffrey G. , Thompson Bonne M. , Pomares-Millan Hugo , Palys Thomas J. , Rees Judy R. , Barry Elizabeth L.
Published: November 2024

Supplemental Figure 2. Exposure-response functions from BKMR models of any colorectal adenoma risk.
Supplemental Figure 1 from Plasma Concentrations of Multiple Oxysterols and Risk of Colorectal Adenomas
Authors: Passarelli Michael N. , McDonald Jeffrey G. , Thompson Bonne M. , Pomares-Millan Hugo , Palys Thomas J. , Rees Judy R. , Barry Elizabeth L.
Published: November 2024

Supplemental Figure 1. Synthesis of selected oxysterols from cholesterol.
Supplementary Table S5 from Viewing Native American Cervical Cancer Disparities through the Lens of the Vaginal Microbiome: A Pilot Study
Authors: Łaniewski Paweł , Joe Tawnjerae R. , Jimenez Nicole R. , Eddie Tristen L. , Bordeaux Skyler J. , Quiroz Verity , Peace Donna J. , Cui Haiyan , Roe Denise J. , Caporaso J. Gregory , Lee Naomi R. , Herbst-Kralovetz Melissa M.
Published: November 2024

Supplementary Table S5: Differences in global health and perceived stress measurements between Native and non-Native participants.
Supplementary Table S4 from Viewing Native American Cervical Cancer Disparities through the Lens of the Vaginal Microbiome: A Pilot Study
Authors: Łaniewski Paweł , Joe Tawnjerae R. , Jimenez Nicole R. , Eddie Tristen L. , Bordeaux Skyler J. , Quiroz Verity , Peace Donna J. , Cui Haiyan , Roe Denise J. , Caporaso J. Gregory , Lee Naomi R. , Herbst-Kralovetz Melissa M.
Published: November 2024

Supplementary Table S4: Differences in global health and perceived stress measurements between hrHPV-positive and hrHPV-negative participants.
Supplementary Table S1 from Viewing Native American Cervical Cancer Disparities through the Lens of the Vaginal Microbiome: A Pilot Study
Authors: Łaniewski Paweł , Joe Tawnjerae R. , Jimenez Nicole R. , Eddie Tristen L. , Bordeaux Skyler J. , Quiroz Verity , Peace Donna J. , Cui Haiyan , Roe Denise J. , Caporaso J. Gregory , Lee Naomi R. , Herbst-Kralovetz Melissa M.
Published: November 2024

Supplementary Table S1: 16S rRNA sequencing data.
Supplementary Figure S2 from Viewing Native American Cervical Cancer Disparities through the Lens of the Vaginal Microbiome: A Pilot Study
Authors: Łaniewski Paweł , Joe Tawnjerae R. , Jimenez Nicole R. , Eddie Tristen L. , Bordeaux Skyler J. , Quiroz Verity , Peace Donna J. , Cui Haiyan , Roe Denise J. , Caporaso J. Gregory , Lee Naomi R. , Herbst-Kralovetz Melissa M.
Published: November 2024

Supplementary Figure S2: BV-associated bacteria positively correlate with each other and negatively correlate with Lactobacillus species, including L. crispatus and L. jensenii.
Supplementary Figure S1 from Viewing Native American Cervical Cancer Disparities through the Lens of the Vaginal Microbiome: A Pilot Study
Authors: Łaniewski Paweł , Joe Tawnjerae R. , Jimenez Nicole R. , Eddie Tristen L. , Bordeaux Skyler J. , Quiroz Verity , Peace Donna J. , Cui Haiyan , Roe Denise J. , Caporaso J. Gregory , Lee Naomi R. , Herbst-Kralovetz Melissa M.
Published: November 2024

Supplementary Figure S1: Vaginal microbiota profiles cluster based on Lactobacillus dominance and not clinical or sociodemographic factors.
Figure S6 from Blocking CX3CR1+ Tumor-Associated Macrophages Enhances the Efficacy of Anti-PD1 Therapy in Hepatocellular Carcinoma
Authors: Xiang Xiaonan , Wang Kai , Zhang Hui , Mou Haibo , Shi Zhixiong , Tao Yaoye , Song Hongliang , Lian Zhengxing , Wang Shuai , Lu Di , Wei Xuyong , Xie Haiyang , Zheng Shusen , Wang Jianguo , Xu Xiao
Published: November 2024

Supplementary Fig S6. PGE2 released by tumor cells under immune attack promotes CX3CR1 upregulation on macrophages
Supplementary Table 4 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Immune cell densities across tissue sites. Mean densities of immune cell subsets as determined by flow cytometry are displayed across tumor-free and tumor-involved tissues. Means were calculated across all collected patient tissues with the number of included data points shown as ‘n’. Table values are colorized from least dense (blue) to most dense (red).
Figure S8 from A Single-Cell Analysis of the NK-Cell Landscape Reveals That Dietary Restriction Boosts NK-Cell Antitumor Immunity via Eomesodermin
Authors: He Junming , Chen Donglin , Xiong Wei , Wang Yuande , Chen Shasha , Yang Meixiang , Dong Zhongjun
Published: November 2024

The less accessible loci found in cluster 3.
Figure S6 from A Single-Cell Analysis of the NK-Cell Landscape Reveals That Dietary Restriction Boosts NK-Cell Antitumor Immunity via Eomesodermin
Authors: He Junming , Chen Donglin , Xiong Wei , Wang Yuande , Chen Shasha , Yang Meixiang , Dong Zhongjun
Published: November 2024

T-bet deficiency does not impact NK cell activation.
Figure S4 from A Single-Cell Analysis of the NK-Cell Landscape Reveals That Dietary Restriction Boosts NK-Cell Antitumor Immunity via Eomesodermin
Authors: He Junming , Chen Donglin , Xiong Wei , Wang Yuande , Chen Shasha , Yang Meixiang , Dong Zhongjun
Published: November 2024

DR-fed mice maintained their ability to suppress the growth of lung melanoma tumor cells, despite CD8 T cell depletion.
Supplementary Figure 5 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Statistical comparison of immune subset densities across metastatic and non-metastatic tissues. Densities of immune cell subsets compared across organ sites within A, general immune cell subsets and B, complex immune cell subsets. Statistics generated by Wilcoxon rank sum tests.
Supplementary Figure 3 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Detailed comparison of immune densities between metastatic and non-metastatic tissue samples of the same organ type. Densities of immune cell subsets within A, CD8+ T cells, B, CD4+ T cells, C, B cells, D, NK cells, E, DCs, and F, myeloid cells in tumor-free (blue) and tumor-involved (red) tissues assayed by flow cytometry. Statistics generated by Wilcoxon rank sum tests. Calculated p values are displayed as *, p < 0.05
Supplementary Figure 15 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Comparison of immune subset composition between organ sites. Frequencies of complex immune cell subsets compared across tumor-free and tumor-involved organ sites within A, CD8+ T cells, B, CD4+ T cells, C, B cells, D, NK cells, and E, monocytes. Statistics generated by Wilcoxon rank sum tests. Calculated p values are displayed as *, p < 0.05; **, p < 0.01; ***, p < 0.001.
Supplementary Figure 14 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Immune subset composition across different organ sites. Frequencies of complex immune cell subsets within A, CD8+ T cells, B, CD4+ T cells, C, B cells, D, NK cells, and E, monocytes. Statistics generated by Kruskal–Wallis test by ranks. Calculated p values are displayed as *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001.
Supplementary Figure 13 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Unsupervised analysis of immune densities across different sites of metastasis. Determination of optimal cluster numbers for unsupervised clustering by finding A, the elbow point of the total within sum of square and B, the highest value of gap statistics from 1 to 25 clusters. C, UMAP 2D space projection of all the samples with “pam” clustering results. D, Heatmap of immune densities annotated with tumor involvement and specimen sites. The samples (columns) in the heatmap were split by clustering results and ordered by cases. The immune densities (rows) in the heatmap were clustered by hierarchical clustering. E, Cluster features visualized by bubble plot with Wilcoxon rank sum tests. The statistics were obtained by comparing the samples within each cluster to all the other clusters. The higher densities within each cluster were represented by red bubbles and the lower ones were represented by blue bubbles. F, Relative sample distribution of specimen sites crossing different clusters. G, Sample distribution of all the cases crossing different clusters. Comparison of H, ER score (%) and I, PR score (%) crossing different clusters. J, Sample distribution of HER2 score crossing different clusters. The HER2 score of all the samples in cluster 4 were not evaluated. K, Comparison of Ki-67% crossing different clusters. Statistics generated by Fisher’s exact test (F, G, J), Kruskal–Wallis test by ranks (H, I, K) and Wilcoxon rank sum tests (E). Calculated p values are displayed as *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001.
Supplementary Figure 12 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Evaluation of dendritic cell enrichment and PD-L1 expression across organ sites. A, Densities of conventional DC subsets, B, frequencies of conventional DC subsets amongst total conventional DCs, C, percentage of each DC subset expressing PD-L1, D, and percentage of monocyte subsets expressing PD-L1 were compared across tumor-free and tumor-involved organ sites. Statistics generated by Wilcoxon rank sum tests.
Supplementary Figure 10 from Organ-Specific Immune Setpoints Underlie Divergent Immune Profiles across Metastatic Sites in Breast Cancer
Authors: Egelston Colt A. , Guo Weihua , Simons Diana L. , Ye Jian , Avalos Christian , Solomon Shawn T. , Nwangwu Mary , Nelson Michael S. , Tan Jiayi , Bacon Eliza R. , Ihle Kena , Schmolze Daniel , Tumyan Lusine , Waisman James R. , Lee Peter P.
Published: November 2024

Multiplex immunofluorescence quantification of immune densities in metastatic tissues. A, Densities of phenotype immune cells were compared between tumor-free and tumor-involved tissues across different organ sites. B, Pathologist evaluation of percentage of tissue area considered tumor-involved. C, Percentages of ‘clean tumor’ within tissue identified to be composed by stroma. Percentages of total stroma as contributed by 100um proximal stroma (D) and 200um proximal stroma (E) as compared to within tumor area alone. F, Representative composite images are shown for tumor-involved tissues of each organ type. Scale bars represent 100 μm. Statistics generated by Wilcoxon rank sum tests (A, D, E) or Kruskal–Wallis test by ranks (B, C). Calculated p values are displayed as *, p < 0.05; **, p < 0.01; ***.
Supplementary Table S4 from CD36+ Proinflammatory Macrophages Interact with ZCCHC12+ Tumor Cells in Papillary Thyroid Cancer Promoting Tumor Progression and Recurrence
Authors: Zhang Xin , Guo Limei , Tian Wenyu , Yang Ying , Yin Yue , Qiu Yaruo , Wang Weixuan , Li Yang , Zhang Guangze , Zhao Xuyang , Wang Guangxi , Lin Zhiqiang , Yang Meng , Zhao Wei , Lu Dan
Published: November 2024

Supplementary Table S4 The relationship between SPP1 expression and clinicpathologic characteristics in patients with PTC.
Table S8 from The Spatial Structure of the Tumor Immune Microenvironment Can Explain and Predict Patient Response in High-Grade Serous Carcinoma
Authors: Van Kleunen Lucy B. , Ahmadian Mansooreh , Post Miriam D. , Wolsky Rebecca J. , Rickert Christian , Jordan Kimberly R. , Hu Junxiao , Richer Jennifer K. , Brubaker Lindsay W. , Marjon Nicole , Behbakht Kian , Sikora Matthew J. , Bitler Benjamin G. , Clauset Aaron
Published: November 2024

Table S8. Univariate Cox regression results with features derived from missing cell types all treated as NA. Univariate Cox regression results for OS and PFS for all features if all missing data values replaced with NA.
Supplementary Fig S6 from CD36+ Proinflammatory Macrophages Interact with ZCCHC12+ Tumor Cells in Papillary Thyroid Cancer Promoting Tumor Progression and Recurrence
Authors: Zhang Xin , Guo Limei , Tian Wenyu , Yang Ying , Yin Yue , Qiu Yaruo , Wang Weixuan , Li Yang , Zhang Guangze , Zhao Xuyang , Wang Guangxi , Lin Zhiqiang , Yang Meng , Zhao Wei , Lu Dan
Published: November 2024

Supplementary Figure S6
Supplementary Fig S5 from CD36+ Proinflammatory Macrophages Interact with ZCCHC12+ Tumor Cells in Papillary Thyroid Cancer Promoting Tumor Progression and Recurrence
Authors: Zhang Xin , Guo Limei , Tian Wenyu , Yang Ying , Yin Yue , Qiu Yaruo , Wang Weixuan , Li Yang , Zhang Guangze , Zhao Xuyang , Wang Guangxi , Lin Zhiqiang , Yang Meng , Zhao Wei , Lu Dan
Published: November 2024

Supplementary Figure S5
Table S5 from The Spatial Structure of the Tumor Immune Microenvironment Can Explain and Predict Patient Response in High-Grade Serous Carcinoma
Authors: Van Kleunen Lucy B. , Ahmadian Mansooreh , Post Miriam D. , Wolsky Rebecca J. , Rickert Christian , Jordan Kimberly R. , Hu Junxiao , Richer Jennifer K. , Brubaker Lindsay W. , Marjon Nicole , Behbakht Kian , Sikora Matthew J. , Bitler Benjamin G. , Clauset Aaron
Published: November 2024

Table S5. Univariate Cox regression main text results. Univariate Cox regression results for OS and PFS for all features.
Supplementary Fig S4 from CD36+ Proinflammatory Macrophages Interact with ZCCHC12+ Tumor Cells in Papillary Thyroid Cancer Promoting Tumor Progression and Recurrence
Authors: Zhang Xin , Guo Limei , Tian Wenyu , Yang Ying , Yin Yue , Qiu Yaruo , Wang Weixuan , Li Yang , Zhang Guangze , Zhao Xuyang , Wang Guangxi , Lin Zhiqiang , Yang Meng , Zhao Wei , Lu Dan
Published: November 2024

Supplementary Figure S4
Table S4 from The Spatial Structure of the Tumor Immune Microenvironment Can Explain and Predict Patient Response in High-Grade Serous Carcinoma
Authors: Van Kleunen Lucy B. , Ahmadian Mansooreh , Post Miriam D. , Wolsky Rebecca J. , Rickert Christian , Jordan Kimberly R. , Hu Junxiao , Richer Jennifer K. , Brubaker Lindsay W. , Marjon Nicole , Behbakht Kian , Sikora Matthew J. , Bitler Benjamin G. , Clauset Aaron
Published: November 2024

Table S4. Definitions of cellular phenotypes identified with unsupervised clustering.
Supplementary Fig S3 from CD36+ Proinflammatory Macrophages Interact with ZCCHC12+ Tumor Cells in Papillary Thyroid Cancer Promoting Tumor Progression and Recurrence
Authors: Zhang Xin , Guo Limei , Tian Wenyu , Yang Ying , Yin Yue , Qiu Yaruo , Wang Weixuan , Li Yang , Zhang Guangze , Zhao Xuyang , Wang Guangxi , Lin Zhiqiang , Yang Meng , Zhao Wei , Lu Dan
Published: November 2024

Supplementary Figure S3
Table S2 from The Spatial Structure of the Tumor Immune Microenvironment Can Explain and Predict Patient Response in High-Grade Serous Carcinoma
Authors: Van Kleunen Lucy B. , Ahmadian Mansooreh , Post Miriam D. , Wolsky Rebecca J. , Rickert Christian , Jordan Kimberly R. , Hu Junxiao , Richer Jennifer K. , Brubaker Lindsay W. , Marjon Nicole , Behbakht Kian , Sikora Matthew J. , Bitler Benjamin G. , Clauset Aaron
Published: November 2024

Table S2. Mass correction parameters. Configuration parameters used for multiplexed imaging correction.
Table S15 from The Spatial Structure of the Tumor Immune Microenvironment Can Explain and Predict Patient Response in High-Grade Serous Carcinoma
Authors: Van Kleunen Lucy B. , Ahmadian Mansooreh , Post Miriam D. , Wolsky Rebecca J. , Rickert Christian , Jordan Kimberly R. , Hu Junxiao , Richer Jennifer K. , Brubaker Lindsay W. , Marjon Nicole , Behbakht Kian , Sikora Matthew J. , Bitler Benjamin G. , Clauset Aaron
Published: November 2024

Table S15. Ranking of feature importance in the random forest model main text results. Ranking of median Gini importance values for all features across 500 evaluations predicting OS and PFS.
Supplementary Fig S15 from CD36+ Proinflammatory Macrophages Interact with ZCCHC12+ Tumor Cells in Papillary Thyroid Cancer Promoting Tumor Progression and Recurrence
Authors: Zhang Xin , Guo Limei , Tian Wenyu , Yang Ying , Yin Yue , Qiu Yaruo , Wang Weixuan , Li Yang , Zhang Guangze , Zhao Xuyang , Wang Guangxi , Lin Zhiqiang , Yang Meng , Zhao Wei , Lu Dan
Published: November 2024

Supplementary Figure S15
Table S14 from The Spatial Structure of the Tumor Immune Microenvironment Can Explain and Predict Patient Response in High-Grade Serous Carcinoma
Authors: Van Kleunen Lucy B. , Ahmadian Mansooreh , Post Miriam D. , Wolsky Rebecca J. , Rickert Christian , Jordan Kimberly R. , Hu Junxiao , Richer Jennifer K. , Brubaker Lindsay W. , Marjon Nicole , Behbakht Kian , Sikora Matthew J. , Bitler Benjamin G. , Clauset Aaron
Published: November 2024

Table S14. Ranking of feature importance in the random forest model for only primary tumor samples. Ranking of median Gini importance values for all features across 500 evaluations predicting OS and PFS, with the model trained only on primary tumor samples.