bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Prognostic Utility of Breast Cancer Index to Stratify Distant Recurrence Risk in Invasive Lobular Carcinoma
Authors: Nunes Raquel , Sella Tal , Treuner Kai , Atkinson Jennifer M. , Wong Jenna , Zhang Yi , Exman Pedro , Dabbs David , Richardson Andrea L. , Schnabel Catherine A. , Sgroi Dennis C. , Oesterreich Steffi , Cimino-Mathews Ashley , Metzger Otto
Published: November 2024

AbstractPurpose:
The prognostic utility of Breast Cancer Index (BCI) for risk assessment of overall (0–10 years), early (0–5 years), and late (5–10 years) distant recurrence (DR) in hormone receptor–positive (HR+) invasive lobular carcinoma (ILC) was evaluated.
Experimental Design:
BCI gene expression analysis was performed blinded to clinical outcome utilizing tumor specimens from patients with HR+ ILC from a multi-institutional cohort. The primary endpoint was time to DR. Kaplan–Meier analyses of overall, early, and late DR risk were performed, and statistical significance was evaluated by log-rank test and Cox proportional hazards regression. The prognostic contribution of BCI in addition to clinicopathologic factors was evaluated by likelihood ratio analysis.
Results:
Analysis of 307 patients (99% ER+, 53% T1, 42% N+, 70% grade II) showed significant differences in DR over 10 years based on BCI risk categories. BCI low- and intermediate-risk patients demonstrated similar DR rates of 7.6% and 8.0%, respectively, compared with 27.0% for BCI high-risk patients. BCI was a significant independent prognostic factor for overall 10-year DR [HR = 4.09; 95% confidence interval (CI), 2.00–8.34; P = 0.0001] as well as for both early (HR = 8.19; 95% CI, 1.85–36.30; P = 0.0042) and late (HR = 3.04; 95% CI, 1.32–7.00; P = 0.0224) DR. In multivariate analysis, BCI remained the only statistically significant prognostic factor for DR (HR = 3.49; 95% CI, 1.28–9.54; P = 0.0150).
Conclusions:
BCI is an independent prognostic factor for ILC and significantly stratified patients for cumulative risk of 10-year, early, and late DR. BCI added prognostic value beyond clinicopathologic characteristics in this distinct subtype of breast cancer.
Data from A Phase I Study of LSZ102, an Oral Selective Estrogen Receptor Degrader, with or without Ribociclib or Alpelisib, in Patients with Estrogen Receptor–Positive Breast Cancer
Authors: Jhaveri Komal , Juric Dejan , Yap Yoon-Sim , Cresta Sara , Layman Rachel M. , Duhoux Francois P. , Terret Catherine , Takahashi Shunji , Huober Jens , Kundamal Nicole , Sheng Qing , Balbin Alejandro , Ji Yan , He Wei , Crystal Adam , De Vita Serena , Curigliano Giuseppe
Published: November 2024

AbstractPurpose:
Data are sparse for oral selective estrogen receptor (ER) degraders (SERD) in cancer treatment. The investigational oral SERD LSZ102 was assessed in monotherapy and combination use in a phase I study.
Patients and Methods:
A phase I, multicenter, open-label dose-escalation study (NCT02734615) of LSZ102 alone (arm A; n = 77) or with ribociclib (arm B; n = 78) or alpelisib (arm C; n = 43) in heavily pretreated adults with histologically confirmed ER-positive breast cancer and prior disease progression. Arm A received LSZ102 200–900 mg/day; arm B, LSZ102 200–600 mg/day plus ribociclib 300–600 mg/day; arm C, LSZ102 300–450 mg/day plus alpelisib 200–300 mg/day. Key outcomes were dose-limiting toxicities (DLT) in the first 28-day treatment cycle, adverse events (AE), laboratory parameters, pharmacokinetics, biopsy ER protein, and investigator-assessed clinical response (RECIST v1.1).
Results:
The most common AEs were gastrointestinal. Treatment-related serious AEs occurred in 10% of participants (19/198), mostly in arm C [10/43 (23%)]. DLTs occurred in: arm A, 5% (4/77); arm B, 3% (2/78); and arm C, 19% (8/43). LSZ102 exposure was slightly greater than dose proportional. On-treatment biopsy ER reductions were observed, with a trend toward an LSZ102 dose response. Objective response rates (95% confidence interval) were: arm A, 1.3% (0.0–7.0); arm B, 16.9% (9.3–27.1); and arm C, 7.0% (1.5–19.1), and clinical benefit rates 7.8% (2.9–16.2), 35.1% (24.5–46.8), and 20.9% (10.0–36.0), respectively.
Conclusions:
LSZ102 was well tolerated alone and with ribociclib and had a manageable safety profile with alpelisib. Preliminary clinical activity was observed in combination use.
Supp. Fig. 1 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 1
Supplementary Figure S5 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 S5
Supplementary Figure S2 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 S2
Supplemental Table 1 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

EC50 values for cell binding
Supplemental 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

Target-dependent multifunctional cytokine production
Figure S5 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 5
Figure S4 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 4
Figure S1 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 1
Figure S3 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 Figure 3
Figure S2 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 Figure 2
Figure S4 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 4
Figure S3 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 3
Table S1-2 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

Supplementary Table S1. Structure and characterization of MTT1-8. Table S2. the sequence of human TLR7 and TLR8.
Figure S3 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 S3. Expression of CD40+DCs in PBMC. PBMC was treated with gradient concentrations of R848 and MTT-6 for 24 h, and the expression level of CD40 in DC cells (CD11b+CD11c+) was measured by flow cytometry, shown as the representative images.
Supplementary Table S2 from NAD+ Metabolic Enzyme Inhibitor as Radiosensitizer for Malignant Meningioma and its Modulation of P53 Expression
Authors: Lv Yifan , Deng Yuxuan , Feng Jie , Liu Jinqiu , Yang Mingxu , Pu Zhuonan , Zhang Shaodong , Wu Zhen , Ji Nan , Park Deric M. , Hao Huyu
Published: November 2024

Supplementary Table S2
Supplementary Figure S2 from NAD+ Metabolic Enzyme Inhibitor as Radiosensitizer for Malignant Meningioma and its Modulation of P53 Expression
Authors: Lv Yifan , Deng Yuxuan , Feng Jie , Liu Jinqiu , Yang Mingxu , Pu Zhuonan , Zhang Shaodong , Wu Zhen , Ji Nan , Park Deric M. , Hao Huyu
Published: November 2024

Supplementary Figure S2
Supplementary Figure S1 from NAD+ Metabolic Enzyme Inhibitor as Radiosensitizer for Malignant Meningioma and its Modulation of P53 Expression
Authors: Lv Yifan , Deng Yuxuan , Feng Jie , Liu Jinqiu , Yang Mingxu , Pu Zhuonan , Zhang Shaodong , Wu Zhen , Ji Nan , Park Deric M. , Hao Huyu
Published: November 2024

Supplementary Figure S1
Supplementary Data 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

Supplementary Methods and Results
Figure S8 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 S8
Figure S1 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 S1
Supplementary Table 6 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 MMAE to Sprague-Dawley rats.
Supplementary Table 3 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 MMAE toxicokinetic parameters following three i.v. bolus doses of T-mavg-MMAU DAR4 in male cynomolgus monkeys.
Supplementary Figure 5 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 T-mcvc-MMAE DAR4 and T-mavg-MMAU DAR8.
Supplementary Figure 4 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 T-mavg-MMAU DAR8.
Table S1 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 S1
Supplementary Figure 12 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.
Data 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

Abstract
While A2A adenosine receptor (AR) was considered as a major contributor to adenosine-mediated immunosuppression, A2B, having the lowest affinity to adenosine, has also emerged as a potential contributor to tumor promotion. Therefore, in adenosine-rich tumor microenvironment (TME), where A2B could be complementary and/or compensatory to A2A, simultaneous targeting of A2A and A2B ARs can provide higher potential for cancer immunotherapy. We developed M1069—a highly selective dual antagonist of the A2A and A2B AR. In assays with primary human and murine immune cells, M1069 rescued IL2 production from T cells (A2A dependent) and inhibited VEGF production by myeloid cells (A2B dependent) in adenosine-high settings. M1069 also demonstrated superior suppression of the secretion of protumorigenic cytokines CXCL1, CXCL5, and rescue of IL12 secretion from adenosine-differentiated dendritic cells compared to an A2A-selective antagonist (A2Ai). In a one-way mixed lymphocyte reaction (MLR) assay, adenosine-differentiated human and murine dendritic cells treated with M1069 demonstrated superior T-cell stimulatory activity compared to dendritic cells differentiated in presence of A2Ai. In vivo, M1069 decreased tumor growth as a monotherapy and enhanced antitumor activity of bintrafusp alfa (BA) or cisplatin in syngeneic adenosinehi/CD73hi 4T1 breast tumor model, but not in the CD73 knockout 4T1 tumor model or in adenosinelow/CD73low MC38 murine colon carcinoma model. In summary, our dual A2A/A2B AR antagonist M1069 may counteract immune-suppressive mechanisms of high concentrations of adenosine in vitro and in vivo and enhance the antitumor activity of other agents, including BA and cisplatin.
Data 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

Abstract
The human CMG helicase (Cdc45-MCM-GINS) is a novel target for anticancer therapy. Tumor-specific weaknesses in the CMG are caused by oncogene-driven changes that adversely affect CMG function, and CMG activity is required for recovery from replicative stresses such as chemotherapy. Herein, we developed an orthogonal biochemical screening approach and identified CMG inhibitors (CMGi) that inhibit ATPase and helicase activities in an ATP-competitive manner at low micromolar concentrations. Structure–activity information, in silico docking, and testing with synthetic chemical compounds indicate that CMGi require specific chemical elements and occupy ATP-binding sites and channels within minichromosome maintenance (MCM) subunits leading to the ATP clefts, which are likely used for ATP/ADP ingress or egress. CMGi are therefore MCM complex inhibitors (MCMi). Biologic testing shows that CMGi/MCMi inhibit cell growth and DNA replication using multiple molecular mechanisms distinct from other chemotherapy agents. CMGi/MCMi block helicase assembly steps that require ATP binding/hydrolysis by the MCM complex, specifically MCM ring assembly on DNA and GINS recruitment to DNA-loaded MCM hexamers. During the S-phase, inhibition of MCM ATP binding/hydrolysis by CMGi/MCMi causes a “reverse allosteric” dissociation of Cdc45/GINS from the CMG that destabilizes replisome components Ctf4, Mcm10, and DNA polymerase-α, -δ, and -ε, resulting in DNA damage. CMGi/MCMi display selective toxicity toward multiple solid tumor cell types with K-Ras mutations, targeting the CMG and inducing DNA damage, Parp cleavage, and loss of viability. This new class of CMGi/MCMi provides a basis for small chemical development of CMG helicase-targeted anticancer compounds with distinct mechanisms of action.
Data 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

Abstract
The emergence of trastuzumab deruxtecan (T-DXd), a new-generation antibody–drug conjugate (ADC), has profoundly altered the therapeutic paradigm for HER2-positive solid tumors, demonstrating remarkable clinical benefits. However, the combined outcomes of T-DXd with immunotherapy agents remain ambiguous. In this study, we introduce Tras-DXd-MTL1, an innovative HER2 targeting ADC that integrates the topoisomerase inhibitor DXd and a toll like receptor 7 (TLR7) agonist MTT5, linked to trastuzumab via a GGFG tetrapeptide linker. Mechanistically, Tras-DXd-MTL1 retains the DNA-damaging and cell-killing properties of topoisomerase inhibitors while simultaneously enhancing the immune response within the tumor microenvironment. This is achieved by promoting immune cell infiltration and activating dendritic cells and CD8+T cells via MTT5. In vivo evaluation of Tras-DXd-MTL1’s antitumor potency revealed a notably superior performance compared with the T-DXd (Tras-DXd) or Tras-MTL1 in immunocompetent mice with trastuzumab-resistant EMT6-HER2 tumor and immunodeficient mice with JIMT-1 tumor. This improved efficacy is primarily attributed to its dual functions of immune stimulation and cytotoxicity. Our findings highlight the potential of incorporating immunostimulatory agents into ADC design to potentiate antitumor effects and establish durable immune memory, thereby reducing tumor recurrence risks. Therefore, our study offers a novel strategy for the design of immune-activating ADCs and provides a potential approach for targeting solid tumors with different levels of HER2 expression.
Data 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

Abstract
Sarcomas are a heterogeneous group of rare cancers that originate in soft tissues or bones. Their complexity and tendency for metastases make treatment challenging, highlighting the need for new therapeutic approaches to improve patient survival. The difficulties in treating these cancers primarily stem from abnormalities within the tumor microenvironment (TME), which leads to reduced blood flow and oxygen levels in tumors. Consequently, this hampers the effective delivery of drugs to tumors and diminishes treatment efficacy despite higher toxic doses of chemotherapy. In this study, we tested the mechanotherapeutic ketotifen combined with either pegylated liposomal doxorubicin (PLD) or pegylated liposomal coencapsulated alendronate–doxorubicin (PLAD) plus anti–programmed cell death protein 1 antibody in mouse models of fibrosarcoma and osteosarcoma. We found that ketotifen successfully reprogrammed the TME by reducing tumor stiffness and increasing perfusion, proven by changes measured by shear-wave elastography and contrast-enhanced ultrasound, respectively, and enhanced the therapeutic efficacy of our nanomedicine-based chemo-immunotherapy protocols. Furthermore, we observed a trend toward improved antitumor responses when nano-chemotherapy is given alongside anti–programmed cell death protein 1 and when the immunomodulator alendronate was present in the treatment. We next investigated the mechanisms of action of this combination. Ketotifen combined with nanomedicine-based chemo-immunotherapy increased T-cell infiltration, specifically cytotoxic CD8+ T cells and CD4+ T helper cells, and decreased the number of regulatory T cells. In addition, the combination also altered the polarization of tumor-associated macrophages, favoring the M1 immune-supportive phenotype over the M2 immunosuppressive phenotype. Collectively, our findings provide evidence that ketotifen-induced TME reprogramming can improve the efficacy of nanomedicine-based chemo-immunotherapy in sarcomas.
Data from Emerging Tumor-Agnostic Molecular Targets
Authors: Bhamidipati Dedipya , Schram Alison M.
Published: November 2024

Abstract
Advances in tumor molecular profiling have uncovered shared genomic and proteomic alterations across tumor types that can be exploited therapeutically. A biomarker-driven, disease-agnostic approach to oncology drug development can maximize the reach of novel therapeutics. To date, eight drug–biomarker pairs have been approved for the treatment of patients with advanced solid tumors with specific molecular profiles. Emerging biomarkers with the potential for clinical actionability across tumor types include gene fusions involving NRG1, FGFR1/2/3, BRAF, and ALK and mutations in TP53 Y220C, KRAS G12C, FGFR2/3, and BRAF non-V600 (class II). We explore the growing evidence for clinical actionability of these biomarkers in patients with advanced solid tumors.
Supplemental Table 4 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 4. PIPs from BKMR models.
Supplemental Table 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 Table 2. Sensitivity analyses that modify models from Table 2 to adjust for additional variables.
Supplementary Table 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 Table S2: Differences in demographic, socioeconomic and behavioral/life style factors between participants with Lactobacillus-dominant microbiota and non-Lactobacillus-dominant microbiota.
Data 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

Abstract
Oxysterols are metabolites of cholesterol that regulate the homeostasis of cholesterol, fatty acids, and glucose. These metabolites are generated throughout the body, either enzymatically or from oxidative stress, and are detectable in peripheral circulation. We previously reported that circulating 27-hydroxycholesterol (27-OHC), an endogenous selective estrogen receptor modulator, may be a risk factor for colorectal adenomas. Here, in addition to 27-OHC, we report on four other circulating oxysterols: 25-hydroxycholesterol, 24(S)-hydroxycholesterol, 7ɑ-hydroxycholesterol, and 4β-hydroxycholesterol. Oxysterol concentrations were measured using liquid chromatography/mass spectrometry from fasting plasma collected at baseline from 1,246 participants of the Vitamin D/Calcium Polyp Prevention Study, a multicenter adenoma chemoprevention trial. To evaluate multiple oxysterols simultaneously, we used both log-linear regression and Bayesian kernel machine regression models developed for analyses of complex mixtures adjusted for potential confounding factors. Higher circulating 7ɑ-hydroxycholesterol was associated with higher adenoma risk (Bayesian kernel machine regression–based multivariable-adjusted risk ratios (RR; for the 75th vs. 25th percentile, 1.22; 95% credible interval, CI, 1.04–1.42). In contrast, higher circulating 4β-hydroxycholesterol was associated with lower risk of these polyps (RR, 0.84; 95% CI, 0.71–0.99). The positive association with advanced adenoma risk that we previously reported for circulating 27-OHC persisted when controlling for other oxysterols (RR, 1.26; 95% CI, 0.98–1.62), including among those with advanced adenomas at baseline (RR, 1.75; 95% CI, 1.01–3.06).

Prevention Relevance: Circulating concentrations of multiple oxysterols measured at the time of an initial colorectal adenoma diagnosis may be risk factors for subsequent incidence of these lesions. Novel colorectal cancer prevention strategies may target oxysterol formation.
Table S2 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

Table S2
Figure S7 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
Figure S3 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 Figure S3. The effect of CX3CR1 neutralizing antibody on macrophages
Figure S1 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 Figure S1. Flow cytometry and FACS gating strategy
Supplementary Table 2 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

Flow cytometry antibodies.
Supplementary Table 1 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

Patient primary tumor clinical characteristics. Tumors were negative for HER2 expression unless otherwise shown. * Inflammatory breast cancer; # First primary breast cancer; § Second primary breast cancer
Figure S5 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 treatment enriches the Eomes expression and functional DP NK cells by suppressing mTORC1 signaling.
Supplementary Figure 9 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

Whole slide multiplex immunofluorescence representative images. Whole slide composite images (left) of staining for CD3 (green), CD8 (orange), FOXP3 (yellow), CD20 (cyan), CD68 (magenta), pan-CK (gray), DAPI (blue). Tissue segmentation (right) for each whole slide image is shown for cancer islands (red), stroma (green), extending 100um bands (multiple colors) and adjacent tumor-free tissue. Representative whole slides are shown for tumor-involved bone (A, B), brain (C, D), liver (E, F), lung (G, H), and skin (I, J). Scale bars are shown.
Supplementary Figure 8 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 representative images and analysis strategy. Representative images of a tumor-involved liver are shown. A, A composite image, B, phenotyped image, and C, tissue segmented image. Individual markers are shown at higher magnification for pan-CK (D), CD3 (E), CD8 (F), CD68 (G), CD20 (H), FOXP3 (I), DAPI alone (J), and as a composite image (K). L, Segmented cells were phenotyped as CD3+ CD8- T cells (green), CD8+ T cells (orange), CD3+ CD8- FOXP3+ Tregs (yellow), CD20+ B cells (cyan), and CD68+ macrophages (magenta). Unclassified segmented cells are not shown. Scale bars are shown.
Supplementary Figure 7 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

Paired analysis of tissue immune cell densities between organ sites. Densities of immune cell subsets as determined by flow cytometry are plotted connecting matched A, lung and liver, B, lung and skin, C, liver and skin tissues across tumor-free and tumor-involved tissues. Statistics generated by paired student t-tests. Calculated p values are displayed.
Figure S3 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

Single-cell RNA sequencing analysis the expression of CD27 and CD11b in NK cell clusters from DR-fed mice.
Supplementary Figure 6 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

Paired analysis of immune densities between tumor-free and tumor-involved tissues. Densities of immune cell subsets as determined by flow cytometry are plotted connecting matched tumor-free (blue) and tumor-involved (red) tissues. Statistics generated by paired student t-tests. Calculated p values are displayed.
Figure S2 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

Trajectory analysis NK cell development from normal diet or DR-fed mice.
Supplementary Figure 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

Detailed comparison of immune densities between different organ sites of metastatic or non-metastatic tissue. 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 Kruskal–Wallis test by ranks. Calculated p values are displayed as *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001.
Figure S1 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

Gene Ontology (GO) enrichment analysis on differential marker expression patterns in clusters of NK cells under dietary restriction (DR) compared to control.
Supplementary Figure 18 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

Differences in T cell effector features between tumor-free and tumor-involved tissues. Frequencies of A, non-naïve CD8+ T cells and B, non-naïve CD4+ T cells expressing PD-1, CD69, CD127, KLRG1, TIGIT, and CTLA-4 were compared between tumor-free and tumor-involved tissue sites. The capacity for C, non-naïve CD8+ T cells and D, non-naïve CD4+ T cells to produce IFN-γ, TNF-α, and IL-2 was also assessed. Statistics generated by Wilcoxon rank sum tests.
Supplementary Figure 17 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 composition differences between tumor-free and tumor-involved tissues. Matchstick plots depict p-values of significant differences between tumor-free and tumor-involved A, bone B, brain and C, skin lung tumor-involved tissues for all immune subsets densities and frequencies assessed. Negative log10 transformed p-values are displayed and sorted from most significant to least significant within the tumor-free tissues. Yellow lines indicate a greater density/frequency in tumor-involved tissue as compared to tumor-free tissues, while green lines indicate a greater density/frequency in tumor-free tissue as compared to tumor-involved tissues. Frequencies of complex immune cell subsets within D, CD8+ T cells, E, CD4+ T cells, F, monocytes. G, Frequencies of HLA-DR low cells amongst monocyte subsets. Frequencies of TIGIT+ and CTLA-4+ Tregs amongst non-H, naïve CD4+ T cells and I, Tregs. Statistics generated by Wilcoxon rank sum tests. Calculated p values are displayed as *, p < 0.05; **, p < 0.01.
Supplementary Figure 11 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 immune densities in segmented tissue areas across different organ sites. Densities of phenotype immune cells within segmented areas were compared across tumor-involved organ sites as shown (A, B). Statistics generated by Kruskal–Wallis test by ranks (A ) and Wilcoxon rank sum tests (B). Calculated p values are displayed as *, p < 0.05.
Supplementary Table S2 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 S2 Clinicopathological characteristics of patients for scRNA-seq data.
Supplementary Table S1 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

Table S1 Primers used for quantitative real-time PCR.
Supplementary Fig S8 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 S8
Table S7 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 S7. Results of 5-fold cross-validation with hyperparameter selection. Results across the 15 models evaluated for overall survival and progression-free survival across 5-folds with random forest hyperparameter selection.
Figure S7 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

Fig S7. Random forest predictive performance results with features derived from missing cell types all treated as NA. Main text Figure 6 repeated with missing cell types handled differently in data preprocessing.
Supplementary Data 4 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

Quality inspection form of IHH4
Supplementary Data 3 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

Quality inspection form of BCPAP
Supplementary Data 2 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

Cell line authentication of IHH4
Figure S23 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

Fig S23. Survival analysis of unsupervised clustering of samples. Using all the features for the samples, unsupervised KMeans clustering was performed to identify tumors with similar feature patterns with the intent of comparing survival outcomes between clusters. As prior work has identified four molecular subtypes of HGSC, we limited the analysis to four clusters (cluster 0 n = 30; cluster 1 n = 27; cluster 2 n = 12; and cluster 3 n = 8). (A) Survival analyses did not show a significant difference in PFS between clusters (Table S16). (B) However, there was a significant difference (53.5 months vs. 85 months) in OS between clusters 0 (n = 30) and 1 (n = 27) (HR = 2.182, P = 0.007) (Table S16).
Figure S22 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

Fig S22. Random forest feature importance results split by feature type - PFS. Feature importance results for progression-free survival show in Figure 7B, split by feature type and split by subtype for spatial network features.
Figure S20 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

Fig S20. Random forest feature importance results for only primary tumor samples. Main text Figure 7 with random forest models trained only on primary tumor samples for the same binary outcome variables of low vs. high OS and PFS (n = 69).
Figure S19 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

Fig S19. Random forest predictive performance results for only primary tumor samples. Main text Figure 6 repeated with random forest models trained only on primary tumor samples for the same binary outcome variables of low vs. high OS and PFS (n = 69).