bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Inhibition of STAT6 with Antisense Oligonucleotides Enhances the Systemic Antitumor Effects of Radiotherapy and Anti–PD-1 in Metastatic Non–Small Cell Lung Cancer
Authors: He Kewen , Barsoumian Hampartsoum B. , Puebla-Osorio Nahum , Hu Yun , Sezen Duygu , Wasley Mark D. , Bertolet Genevieve , Zhang Jie , Leuschner Carola , Yang Liangpeng , Kettlun Leyton Claudia S. , Fowlkes Natalie Wall , Green Morgan Maureen , Hettrick Lisa , Chen Dawei , Masrorpour Fatemeh , Gu Meidi , Maazi Hadi , Revenko Alexey S. , Cortez Maria Angelica , Welsh James W.
Published: April 2023

Abstract
Diverse factors contribute to the limited clinical response to radiotherapy (RT) and immunotherapy in metastatic non–small cell lung cancer (NSCLC), among which is the ability of these tumors to recruit a retinue of suppressive immune cells—such as M2 tumor-associated macrophages (TAM)—thereby establishing an immunosuppressive tumor microenvironment that contributes to tumor progression and radio resistance. M2 TAMs are activated by the STAT6 signaling pathway. Therefore, we targeted STAT6 using an antisense oligonucleotide (ASO) along with hypofractionated RT (hRT; 3 fractions of 12 Gy each) to primary tumors in three bilateral murine NSCLC models (Lewis lung carcinoma, 344SQ-parental, and anti–PD-1–resistant 344SQ lung adenocarcinomas). We found that STAT6 ASO plus hRT slowed growth of both primary and abscopal tumors, decreased lung metastases, and extended survival. Interrogating the mechanism of action showed reduced M2 macrophage tumor infiltration, enhanced TH1 polarization, improved T-cell and macrophage function, and decreased TGFβ levels. The addition of anti–PD-1 further enhanced systemic antitumor responses. These results provide a preclinical rationale for the pursuit of an alternative therapeutic approach for patients with immune-resistant NSCLC.
Supplementary Figure 7 from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia
Authors: Roels Juliette , Thénoz Morgan , Szarzyńska Bronisława , Landfors Mattias , De Coninck Stien , Demoen Lisa , Provez Lien , Kuchmiy Anna , Strubbe Steven , Reunes Lindy , Pieters Tim , Matthijssens Filip , Van Loocke Wouter , Erarslan-Uysal Büşra , Richter-Pechańska Paulina , Declerck Ken , Lammens Tim , De Moerloose Barbara , Deforce Dieter , Van Nieuwerburgh Filip , Cheung Laurence C. , Kotecha Rishi S. , Mansour Marc R. , Ghesquière Bart , Van Camp Guy , Berghe Wim Vanden , Kowalczyk Jerzy R. , Szczepański Tomasz , Davé Utpal P. , Kulozik Andreas E. , Goossens Steven , Curtis David J. , Taghon Tom , Dawidowska Małgorzata , Degerman Sofie , Van Vlierberghe Pieter
Published: April 2023

Supplementary Figure 7
Supplementary Figure 2 from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia
Authors: Roels Juliette , Thénoz Morgan , Szarzyńska Bronisława , Landfors Mattias , De Coninck Stien , Demoen Lisa , Provez Lien , Kuchmiy Anna , Strubbe Steven , Reunes Lindy , Pieters Tim , Matthijssens Filip , Van Loocke Wouter , Erarslan-Uysal Büşra , Richter-Pechańska Paulina , Declerck Ken , Lammens Tim , De Moerloose Barbara , Deforce Dieter , Van Nieuwerburgh Filip , Cheung Laurence C. , Kotecha Rishi S. , Mansour Marc R. , Ghesquière Bart , Van Camp Guy , Berghe Wim Vanden , Kowalczyk Jerzy R. , Szczepański Tomasz , Davé Utpal P. , Kulozik Andreas E. , Goossens Steven , Curtis David J. , Taghon Tom , Dawidowska Małgorzata , Degerman Sofie , Van Vlierberghe Pieter
Published: April 2023

Supplementary Figure 2
Supplementary Table 5 from SIRT5 Is a Druggable Metabolic Vulnerability in Acute Myeloid Leukemia
Authors: Yan Dongqing , Franzini Anca , Pomicter Anthony D. , Halverson Brayden J. , Antelope Orlando , Mason Clinton C. , Ahmann Jonathan M. , Senina Anna V. , Vellore Nadeem A. , Jones Courtney L. , Zabriskie Matthew S. , Than Hein , Xiao Michael J. , van Scoyk Alexandria , Patel Ami B. , Clair Phillip M. , Heaton William L. , Owen Shawn C. , Andersen Joshua L. , Egbert Christina M. , Reisz Julie A. , D'Alessandro Angelo , Cox James E. , Gantz Kevin C. , Redwine Hannah M. , Iyer Siddharth M. , Khorashad Jamshid S. , Rajabi Nima , Olsen Christian A. , O'Hare Thomas , Deininger Michael W.
Published: April 2023

The 1,287 genes targeted by the shRNA of the leukemia library.
Supplementary Table 4 from SIRT5 Is a Druggable Metabolic Vulnerability in Acute Myeloid Leukemia
Authors: Yan Dongqing , Franzini Anca , Pomicter Anthony D. , Halverson Brayden J. , Antelope Orlando , Mason Clinton C. , Ahmann Jonathan M. , Senina Anna V. , Vellore Nadeem A. , Jones Courtney L. , Zabriskie Matthew S. , Than Hein , Xiao Michael J. , van Scoyk Alexandria , Patel Ami B. , Clair Phillip M. , Heaton William L. , Owen Shawn C. , Andersen Joshua L. , Egbert Christina M. , Reisz Julie A. , D'Alessandro Angelo , Cox James E. , Gantz Kevin C. , Redwine Hannah M. , Iyer Siddharth M. , Khorashad Jamshid S. , Rajabi Nima , Olsen Christian A. , O'Hare Thomas , Deininger Michael W.
Published: April 2023

Next generation sequencing for 52 myeloid malignancies-related genes.
Table S7 from Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1
Authors: Koya Junji , Saito Yuki , Kameda Takuro , Kogure Yasunori , Yuasa Mitsuhiro , Nagasaki Joji , McClure Marni B. , Shingaki Sumito , Tabata Mariko , Tahira Yuki , Akizuki Keiichi , Kamiunten Ayako , Sekine Masaaki , Shide Kotaro , Kubuki Yoko , Hidaka Tomonori , Kitanaka Akira , Nakano Nobuaki , Utsunomiya Atae , Togashi Yosuke , Ogawa Seishi , Shimoda Kazuya , Kataoka Keisuke
Published: April 2023

Candidate pathogenic mutations detected by WES or targeted-seq in ATL and AC samples
Supplementary Table S1 from How to Provide the Needed Protection from COVID-19 to Patients with Hematologic Malignancies
Authors: Ribas Antoni , Dhodapkar Madhav V. , Campbell Katie M. , Davies Faith E. , Gore Steven D. , Levy Ronald , Greenberger Lee M.
Published: April 2023

Supplementary Table S1
Supplementary Table S3 from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary table S3 listed the potential KDM5A binding proteins identified by mass spectrometry.
Supplementary Table S1 from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary Table 1 listed the genes upregulated and downregulated after treatment with JQKD82 in MM1S cells for 48 h
Supplementary Figure S4 from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary Figure S4 shows that KDM5 inhibition of KDM5A knockdown downregulates MYC target genes in MM.
Supplementary Figure from Blockade or Deletion of IFNγ Reduces Macrophage Activation without Compromising CAR T-cell Function in Hematologic Malignancies
Authors: Bailey Stefanie R. , Vatsa Sonika , Larson Rebecca C. , Bouffard Amanda A. , Scarfò Irene , Kann Michael C. , Berger Trisha R. , Leick Mark B. , Wehrli Marc , Schmidts Andrea , Silva Harrison , Lindell Kevin A. , Demato Ashley , Gallagher Kathleen M.E. , Frigault Matthew J. , Maus Marcela V.
Published: April 2023

Supplementary Figure from Blockade or Deletion of IFNγ Reduces Macrophage Activation without Compromising CAR T-cell Function in Hematologic Malignancies
Supplementary Table from In Vivo Monitoring of Polycythemia Vera Development Reveals Carbonic Anhydrase 1 as a Potent Therapeutic Target
Authors: Murakami Shohei , Barroca Vilma , Perié Leïla , Bravard Anne , Bernardino-Sgherri Jacqueline , Tisserand Amandine , Devanand Caroline , Edmond Valérie , Magniez Aurélie , Tenreira Bento Sabrina , Torres Claire , Pasquier Florence , Plo Isabelle , Vainchenker William , Villeval Jean-Luc , Roméo Paul-Henri , Lewandowski Daniel
Published: April 2023

Supplementary Table from In Vivo Monitoring of Polycythemia Vera Development Reveals Carbonic Anhydrase 1 as a Potent Therapeutic Target
Supplementary Data from In Vivo Monitoring of Polycythemia Vera Development Reveals Carbonic Anhydrase 1 as a Potent Therapeutic Target
Authors: Murakami Shohei , Barroca Vilma , Perié Leïla , Bravard Anne , Bernardino-Sgherri Jacqueline , Tisserand Amandine , Devanand Caroline , Edmond Valérie , Magniez Aurélie , Tenreira Bento Sabrina , Torres Claire , Pasquier Florence , Plo Isabelle , Vainchenker William , Villeval Jean-Luc , Roméo Paul-Henri , Lewandowski Daniel
Published: April 2023

Supplementary Data from In Vivo Monitoring of Polycythemia Vera Development Reveals Carbonic Anhydrase 1 as a Potent Therapeutic Target
Data from RETRACTED: In Vivo Monitoring of Polycythemia Vera Development Reveals Carbonic Anhydrase 1 as a Potent Therapeutic Target
Authors: Murakami Shohei , Barroca Vilma , Perié Leïla , Bravard Anne , Bernardino-Sgherri Jacqueline , Tisserand Amandine , Devanand Caroline , Edmond Valérie , Magniez Aurélie , Tenreira Bento Sabrina , Torres Claire , Pasquier Florence , Plo Isabelle , Vainchenker William , Villeval Jean-Luc , Roméo Paul-Henri , Lewandowski Daniel
Published: April 2023

Abstract
Current murine models of myeloproliferative neoplasms (MPNs) cannot examine how MPNs progress from a single bone marrow source to the entire hematopoietic system. Thus, using transplantation of knock-in JAK2V617F hematopoietic cells into a single irradiated leg, we show development of polycythemia vera (PV) from a single anatomic site in immunocompetent mice. Barcode experiments reveal that grafted JAK2V617F stem/progenitor cells migrate from the irradiated leg to nonirradiated organs such as the contralateral leg and spleen, which is strictly required for development of PV. Mutant cells colonizing the nonirradiated leg efficiently induce PV in nonconditioned recipient mice and contain JAK2V617F hematopoietic stem/progenitor cells that express high levels of carbonic anhydrase 1 (CA1), a peculiar feature also found in CD34+ cells from patients with PV. Finally, genetic and pharmacologic inhibition of CA1 efficiently suppresses PV development and progression in mice and decreases PV patients’ erythroid progenitors, strengthening CA1 as a potent therapeutic target for PV.
Significance:
Follow-up of hematopoietic malignancies from their initiating anatomic site is crucial for understanding their development and discovering new therapeutic avenues. We developed such an approach, used it to characterize PV progression, and identified CA1 as a promising therapeutic target of PV.

This article is highlighted in the In This Issue feature, p. 265
Supplementary Tables 2 and 3 from Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with Breast Cancer
Authors: Axelrod Margaret L. , Wang Yu , Xu Yaomin , Sun Xiaopeng , Bejan Cosmin A. , Gonzalez-Ericsson Paula I. , Nunnery Sara , Bergman Riley E. , Donaldson Joshua , Guerrero-Zotano Angel L. , Massa Chiara , Seliger Barbara , Sanders Melinda , Mayer Ingrid A. , Balko Justin M.
Published: April 2023

ICD and CPT codes used for synthetic derivative analyses.
Supplementary Figures 1-3 from Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with Breast Cancer
Authors: Axelrod Margaret L. , Wang Yu , Xu Yaomin , Sun Xiaopeng , Bejan Cosmin A. , Gonzalez-Ericsson Paula I. , Nunnery Sara , Bergman Riley E. , Donaldson Joshua , Guerrero-Zotano Angel L. , Massa Chiara , Seliger Barbara , Sanders Melinda , Mayer Ingrid A. , Balko Justin M.
Published: April 2023

Supplementary Figure 1. Expression of immune related genes in the peripheral blood is associated with good outcome following NAC. Supplementary Figure 2. Monocytes are most abundant in blood of patients with good outcomes following NAC. Supplementary Figure 3. Monocytes are most abundant in blood of patients with good outcomes following NAC.
Figure SF1 from Bintrafusp Alfa, an Anti-PD-L1:TGFβ Trap Fusion Protein, in Patients with ctDNA-positive, Liver-limited Metastatic Colorectal Cancer
Authors: Morris Van K. , Overman Michael J. , Lam Michael , Parseghian Christine M. , Johnson Benny , Dasari Arvind , Raghav Kanwal , Kee Bryan K. , Huey Ryan , Wolff Robert A. , Shen John Paul , Li June , Zorrilla Isabel , Tzeng Ching-Wei D. , Tran Cao Hop S. , Chun Yun Shin , Newhook Timothy E. , Vauthey Nicolas , Duose Dzifa , Luthra Raja , Haymaker Cara , Kopetz Scott
Published: April 2023

Supplemental Figure S1
Appendix 1 from Prospective Associations of Hemoglobin A1c and c-peptide with Risk of Diabetes-related Cancers in the Cancer Prevention Study-II Nutrition Cohort
Authors: Campbell Peter T. , Newton Christina C. , Jacobs Eric J. , McCullough Marjorie L. , Wang Ying , Rees-Punia Erika , Guinter Mark A. , Murphy Neil , Koshiol Jill , Dehal Ahmed N. , Rohan Thomas , Strickler Howard , Petrick Jessica , Gunter Marc , Zhang Xuehong , McGlynn Katherine A. , Pollak Michael , Patel Alpa V. , Gapstur Susan M.
Published: April 2023

lab methods and qc
Supplementary Figure FS2 from Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis
Authors: Yao Lijun , Jayasinghe Reyka G. , Lee Brian H. , Bhasin Swati S. , Pilcher William , Doxie Deon Bryant , Gonzalez-Kozlova Edgar , Dasari Surendra , Fiala Mark A. , Pita-Juarez Yered , Strausbauch Michael , Kelly Geoffrey , Thomas Beena E. , Kumar Shaji K. , Cho Hearn Jay , Anderson Emilie , Wendl Michael C. , Dawson Travis , D'souza Darwin , Oh Stephen T. , Cheloni Giulia , Li Ying , DiPersio John F. , Rahman Adeeb H. , Dhodapkar Kavita M. , Kim-Schulze Seunghee , Vij Ravi , Vlachos Ioannis S. , Mehr Shaadi , Hamilton Mark , Auclair Daniel , Kourelis Taxiarchis , Avigan David , Dhodapkar Madhav V. , Gnjatic Sacha , Bhasin Manoj K. , Ding Li
Published: April 2023

Correlation of expression of canonical cell type markers across different modalities
Supplementary Figure FS1 from Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis
Authors: Yao Lijun , Jayasinghe Reyka G. , Lee Brian H. , Bhasin Swati S. , Pilcher William , Doxie Deon Bryant , Gonzalez-Kozlova Edgar , Dasari Surendra , Fiala Mark A. , Pita-Juarez Yered , Strausbauch Michael , Kelly Geoffrey , Thomas Beena E. , Kumar Shaji K. , Cho Hearn Jay , Anderson Emilie , Wendl Michael C. , Dawson Travis , D'souza Darwin , Oh Stephen T. , Cheloni Giulia , Li Ying , DiPersio John F. , Rahman Adeeb H. , Dhodapkar Kavita M. , Kim-Schulze Seunghee , Vij Ravi , Vlachos Ioannis S. , Mehr Shaadi , Hamilton Mark , Auclair Daniel , Kourelis Taxiarchis , Avigan David , Dhodapkar Madhav V. , Gnjatic Sacha , Bhasin Manoj K. , Ding Li
Published: April 2023

Expression of cell type markers in CITE-seq and comparison of cell subset abundance between technical replicates and across different centers
Supplementary Table S5 from A Preclinical and Phase Ib Study of Palbociclib plus Nab-Paclitaxel in Patients with Metastatic Adenocarcinoma of the Pancreas
Authors: Hidalgo Manuel , Garcia-Carbonero Rocio , Lim Kian-Huat , Messersmith Wells A. , Garrido-Laguna Ignacio , Borazanci Erkut , Lowy Andrew M. , Medina Rodriguez Laura , Laheru Daniel , Salvador-Barbero Beatriz , Malumbres Marcos , Shields David J. , Grossman Joseph E. , Huang Xin , Tammaro Meggan , Martini Jean-François , Yu Yanke , Kern Kenneth , Macarulla Teresa
Published: April 2023

Summary of PFS and OS by Mutation Status.
Figure SF4 from Safety, Tolerability, and Pharmacokinetics of TAK-931, a Cell Division Cycle 7 Inhibitor, in Patients with Advanced Solid Tumors: A Phase I First-in-Human Study
Authors: Kuboki Yasutoshi , Shimizu Toshio , Yonemori Kan , Kojima Takashi , Kondo Shunsuke , Koganemaru Shigehiro , Iwasa Satoru , Harano Kenichi , Koyama Takafumi , Lu Vickie , Zhou Xiaofei , Niu Huifeng , Yanai Tomoko , Garcia-Ribas Ignacio , Doi Toshihiko , Yamamoto Noboru
Published: April 2023

(A) Best percent change from baseline in tumor size for all patients in schedule A. (B) and (C) computed tomography scans from patients in schedule A at screening (left panels) and 9 weeks post-dose (right panels); (B) patient with duodenal cancer treated with TAK-931 30 mg; (C) patient with esophageal cancer treated with TAK-931 50 mg. Yellow arrows indicate target lesions.
Figure S3 from Boosting of Waned Humoral and Cellular Responses to SARS-CoV-2 Variants of Concern Among Patients with Cancer
Authors: McKenzie Duncan R. , Graham Rosalind , Lechmere Thomas , Domingo-Vila Clara , Alaguthurai Thanussuyah , Arman Celeste , Pollock Emily , Gousis Charalampos , Kakkassery Helen , Carpenter Esme , Kurshan Ashwini , Vidler Jennifer , Kulasekararaj Austin , Patten Piers , North Bernard V. , Tree Timothy , Doores Katie J. , Hayday Adrian C. , Irshad Sheeba
Published: April 2023

S3. Boosted serological responses and persistent T cell responses following SARS-CoV-2 vaccination dose
Supplementary Figure S7 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer
Authors: Chen Hao , Cresswell Gregory M. , Libring Sarah , Ayers Mitchell G. , Miao Jinmin , Zhang Zhong-Yin , Solorio Luis , Ratliff Timothy L. , Wendt Michael K.
Published: April 2023

The gating ancestry for the populations in the study of 4T1 model
Supplementary Figure S5 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer
Authors: Chen Hao , Cresswell Gregory M. , Libring Sarah , Ayers Mitchell G. , Miao Jinmin , Zhang Zhong-Yin , Solorio Luis , Ratliff Timothy L. , Wendt Michael K.
Published: April 2023

Corresponding representative dot plots for the quantification in figure 2D-F and additional myeloid composition analysis in the study of D2.A1 model.
Supplementary Table TS3 from Circulating Tumor DNA Monitoring Reveals Molecular Progression before Radiologic Progression in a Real-life Cohort of Patients with Advanced Non–small Cell Lung Cancer
Authors: Frank Malene S. , Andersen Christina S.A. , Ahlborn Lise B. , Pallisgaard Niels , Bodtger Uffe , Gehl Julie
Published: April 2023

Representativeness of study participants
Supplementary Table S2 from Avian Paramyxovirus 4 Antitumor Activity Leads to Complete Remissions and Long-term Protective Memory in Preclinical Melanoma and Colon Carcinoma Models
Authors: Javaheri Aryana , Bykov Yonina , Mena Ignacio , García-Sastre Adolfo , Cuadrado-Castano Sara
Published: April 2023

RT-qPCR Primers' sequences
Figure S9 from Impaired Antitumor Immune Response in MYCN-amplified Neuroblastoma Is Associated with Lack of CCL2 Secretion and Poor Dendritic Cell Recruitment
Authors: Kacher Jamila , Manches Olivier , Aspord Caroline , Sartelet Hervé , Chaperot Laurence
Published: April 2023

Supplementary figure 9 shows IL-12 and IL-8 contents in supernatants after activation of PBMC in co-culture with NB cell lines.
Figure S2 from Impaired Antitumor Immune Response in MYCN-amplified Neuroblastoma Is Associated with Lack of CCL2 Secretion and Poor Dendritic Cell Recruitment
Authors: Kacher Jamila , Manches Olivier , Aspord Caroline , Sartelet Hervé , Chaperot Laurence
Published: April 2023

Supplementary figure 2 shows flow cytometry gating strategy for cell subsets identification (CCR2 phenotyping)
Supplemental Figures 1-7, Tables 1-3 from Patients with Lung Cancer of Different Racial Backgrounds Harbor Distinct Immune Cell Profiles
Authors: Xu Yitian , Zhang Licheng , Thaiparambil Jose , Mai Sunny , Perera Dimuthu Nuwan , Zhang Jilu , Pan Ping-Ying , Coarfa Cristian , Ramos Kenneth , Chen Shu-Hsia , El-Zein Randa
Published: April 2023

Supplemental Figure 1, CD45 staining of normal adjacent tissue of 5 AA and 5 CA patients. Supplemental Figure 2, survival curves for CA and AA patients (A), from patients with different smoking histories (B), and CA and AA patients with different smoking histories (C). D, immune population comparisons between patients with different smoking histories without stratification by race. Supplemental Figure 3, survival rate (A) and curves (B) for male and female patients. C, survival curves for male and female CA and AA patients. D, immune population comparisons between male and female patients without stratification by race. Supplemental Figure 4, survival rate (A) and curves (B) patients with different tumor types. C, survival curves for CA and AA patients with different tumor types. D, immune population comparisons between patients with different tumor types without stratification by race. Supplemental Figure 5, immune population comparisons between CA and AA patients after stratifying by tumor type. Supplemental Figure 6, immune population comparisons between patients with different survival status without (A) or with (B) stratification by race. Supplemental Figure 7, immune population comparisons between patients at different disease stages without (A) or with (B) stratification by race. Supplemental Table 1, antibody list. Supplemental Table 2, number of samples processed for IMC evaluation of different tumor sub-types. Supplemental Table 3, number of samples processed for IMC evaluation of different disease stages.
Supplementary Material S7 from Diagnostic Accuracy of Blood-based Biomarkers for Pancreatic Cancer: A Systematic Review and Meta-analysis
Authors: Kane Laura E. , Mellotte Gregory S. , Mylod Eimear , O'Brien Rebecca M. , O'Connell Fiona , Buckley Croí E. , Arlow Jennifer , Nguyen Khanh , Mockler David , Meade Aidan D. , Ryan Barbara M. , Maher Stephen G.
Published: April 2023

Complete extracted dataset
Figure S1 from Cell-free DNA Predicts Prolonged Response to Multi-agent Chemotherapy in Pancreatic Ductal Adenocarcinoma
Authors: Christenson Eric S. , Lim Su Jin , Durham Jennifer , De Jesus-Acosta Ana , Bever Katherine , Laheru Daniel , Ryan Amy , Agarwal Parul , Scharpf Robert B. , Le Dung T. , Wang Hao
Published: April 2023

Supplemental Figure 1. Pairwise scatterplots comparing protein and cfDNA biomarkers for Post-treatment time point and % change pre-treatment to post-treatment. To determine the relationship between the different protein and cfDNA biomarkers we created pairwise scatterplots for the post-treatment time point (panel A) and % change (panel B). These data demonstrated good agreement between different cfDNA variables while the protein based showed variable correlations with cfDNA variables as outlined in Supplemental Table 3.
Supplementary Table S9 from Mixed Response to Cancer Immunotherapy is Driven by Intratumor Heterogeneity and Differential Interlesion Immune Infiltration
Authors: Morinaga Takao , Inozume Takashi , Kawazu Masahito , Ueda Youki , Sax Nicolas , Yamashita Kazuo , Kawashima Shusuke , Nagasaki Joji , Ueno Toshihide , Lin Jason , Ohara Yuuki , Kuwata Takeshi , Yukami Hiroki , Kawazoe Akihito , Shitara Kohei , Honobe-Tabuchi Akiko , Ohnuma Takehiro , Kawamura Tatsuyoshi , Umeda Yoshiyasu , Kawahara Yu , Nakamura Yasuhiro , Kiniwa Yukiko , Morita Ayako , Ichihara Eiki , Kiura Katsuyuki , Enokida Tomohiro , Tahara Makoto , Hasegawa Yoshinori , Mano Hiroyuki , Suzuki Yutaka , Nishikawa Hiroyoshi , Togashi Yosuke
Published: April 2023

Sequencing summary.
Supplementary Table S7 from Mixed Response to Cancer Immunotherapy is Driven by Intratumor Heterogeneity and Differential Interlesion Immune Infiltration
Authors: Morinaga Takao , Inozume Takashi , Kawazu Masahito , Ueda Youki , Sax Nicolas , Yamashita Kazuo , Kawashima Shusuke , Nagasaki Joji , Ueno Toshihide , Lin Jason , Ohara Yuuki , Kuwata Takeshi , Yukami Hiroki , Kawazoe Akihito , Shitara Kohei , Honobe-Tabuchi Akiko , Ohnuma Takehiro , Kawamura Tatsuyoshi , Umeda Yoshiyasu , Kawahara Yu , Nakamura Yasuhiro , Kiniwa Yukiko , Morita Ayako , Ichihara Eiki , Kiura Katsuyuki , Enokida Tomohiro , Tahara Makoto , Hasegawa Yoshinori , Mano Hiroyuki , Suzuki Yutaka , Nishikawa Hiroyoshi , Togashi Yosuke
Published: April 2023

Tested clonotypes.
Supplementary Figures S1, Tables S1-S2 from GLS1 is a Protective Factor in Patients with Ovarian Clear Cell Carcinoma and its Expression Does Not Correlate with ARID1A-mutated Tumors
Authors: Clemente Valentino , Hoshino Asumi , Shetty Mihir , Nelson Andrew , Erickson Britt K. , Baker Ruth , Rubin Nathan , Khalifa Mahmoud , Weroha S. John , Lou Emil , Bazzaro Martina
Published: April 2023

Figure S1, Table S1, Table S2
Supplementary Table S1 from Mixed Response to Cancer Immunotherapy is Driven by Intratumor Heterogeneity and Differential Interlesion Immune Infiltration
Authors: Morinaga Takao , Inozume Takashi , Kawazu Masahito , Ueda Youki , Sax Nicolas , Yamashita Kazuo , Kawashima Shusuke , Nagasaki Joji , Ueno Toshihide , Lin Jason , Ohara Yuuki , Kuwata Takeshi , Yukami Hiroki , Kawazoe Akihito , Shitara Kohei , Honobe-Tabuchi Akiko , Ohnuma Takehiro , Kawamura Tatsuyoshi , Umeda Yoshiyasu , Kawahara Yu , Nakamura Yasuhiro , Kiniwa Yukiko , Morita Ayako , Ichihara Eiki , Kiura Katsuyuki , Enokida Tomohiro , Tahara Makoto , Hasegawa Yoshinori , Mano Hiroyuki , Suzuki Yutaka , Nishikawa Hiroyoshi , Togashi Yosuke
Published: April 2023

Melanoma patient characteristics.
Supplementary Table 2 from Remodeling of the Tumor Microenvironment Through PAK4 Inhibition Sensitizes Tumors to Immune Checkpoint Blockade
Authors: Abril-Rodriguez Gabriel , Torrejon Davis Y. , Karin Daniel , Campbell Katie M. , Medina Egmidio , Saco Justin D. , Galvez Mildred , Champhekar Ameya S. , Perez-Garcilazo Ivan , Baselga-Carretero Ignacio , Singh Jas , Comin-Anduix Begoña , Puig-Saus Cristina , Ribas Antoni
Published: April 2023

Supplemental Table 2: Differential gene expression analysis between B16 KO and WT cells in vitro. Showing genes with q < 0.05 and log2FC > 1 or < -1.
Data File DS1 from Targeting Lymphoma-associated Macrophage Expansion via CSF1R/JAK Inhibition is a Therapeutic Vulnerability in Peripheral T-cell Lymphomas
Authors: Gao Xin , Kady Nermin , Wang Chenguang , Abdelrahman Suhaib , Gann Peter , Sverdlov Maria , Wolfe Ashley , Brown Noah , Reneau John , Robida Aaron M. , Murga-Zamalloa Carlos , Wilcox Ryan A.
Published: April 2023

TME gene sets
Suppl Fig FS1 from A Phase I Trial of VEGF-A Inhibition Combined with PD-L1 Blockade for Recurrent Glioblastoma
Authors: Chiu Daniel , Qi Jingjing , Thin Tin Htwe , Garcia-Barros Monica , Lee Brian , Hahn Mary , Mandeli John , Belani Puneet , Nael Kambiz , Rashidipour Omid , Ghatan Saadi , Hadjipanayis Constantinos G. , Yong Raymund L. , Germano Isabelle M. , Brody Rachel , Tsankova Nadejda M. , Gnjatic Sacha , Kim-Schulze Seunghee , Hormigo Adília
Published: April 2023

Sex as a variable of survival
Table ST2 from Phase I Trial of Intravenous Mistletoe Extract in Advanced Cancer
Authors: Paller Channing J. , Wang Lin , Fu Wei , Kumar Rajendra , Durham Jennifer N. , Azad Nilofer S. , Laheru Daniel A. , Browner Ilene , Kachhap Sushant K. , Boyapati Kavya , Odeny Thomas , Armstrong Deborah K. , Meyer Christian F. , Gaillard Stephanie , Brahmer Julie R. , Page Ivelisse , Wang Hao , Diaz Luis A.
Published: April 2023

Table S2 shows treatment-related adverse events by dose level
Figure S4 from Phase I Trial of Intravenous Mistletoe Extract in Advanced Cancer
Authors: Paller Channing J. , Wang Lin , Fu Wei , Kumar Rajendra , Durham Jennifer N. , Azad Nilofer S. , Laheru Daniel A. , Browner Ilene , Kachhap Sushant K. , Boyapati Kavya , Odeny Thomas , Armstrong Deborah K. , Meyer Christian F. , Gaillard Stephanie , Brahmer Julie R. , Page Ivelisse , Wang Hao , Diaz Luis A.
Published: April 2023

Figure S4 shows functional assessment of cancer therapy - general over time by response
Figure S12 from Phase I Trial of Intravenous Mistletoe Extract in Advanced Cancer
Authors: Paller Channing J. , Wang Lin , Fu Wei , Kumar Rajendra , Durham Jennifer N. , Azad Nilofer S. , Laheru Daniel A. , Browner Ilene , Kachhap Sushant K. , Boyapati Kavya , Odeny Thomas , Armstrong Deborah K. , Meyer Christian F. , Gaillard Stephanie , Brahmer Julie R. , Page Ivelisse , Wang Hao , Diaz Luis A.
Published: April 2023

Figure S12 shows functional well-being over time by response
Supplementary Table ST2 from Antibody Binding and Neutralization of Live SARS-CoV-2 Variants Including BA.4/5 Following Booster Vaccination of Patients with B-cell Malignancies
Authors: Chang Andres , Akhtar Akil , Lai Lilin , Orellana-Noia Victor M. , Linderman Susanne L. , McCook-Veal Ashley A. , Switchenko Jeffrey M. , Saini Manpreet , Valanparambil Rajesh M. , Blum Kristie A. , Allen Pamela B. , Lechowicz Mary Jo , Romancik Jason T. , Ayers Amy , Leal Alyssa , O'Leary Colin B. , Churnetski Michael C. , Baird Katelin , Kives Melissa , Wrammert Jens , Nooka Ajay K. , Koff Jean L. , Dhodapkar Madhav V. , Suthar Mehul S. , Cohen Jonathon B. , Ahmed Rafi
Published: April 2023

Supplemental Table 2. Clinical characteristics of NHL/CLL patients with high anti-spike IgG titers prior to booster vaccination
Supplementary Table ST1 from Antibody Binding and Neutralization of Live SARS-CoV-2 Variants Including BA.4/5 Following Booster Vaccination of Patients with B-cell Malignancies
Authors: Chang Andres , Akhtar Akil , Lai Lilin , Orellana-Noia Victor M. , Linderman Susanne L. , McCook-Veal Ashley A. , Switchenko Jeffrey M. , Saini Manpreet , Valanparambil Rajesh M. , Blum Kristie A. , Allen Pamela B. , Lechowicz Mary Jo , Romancik Jason T. , Ayers Amy , Leal Alyssa , O'Leary Colin B. , Churnetski Michael C. , Baird Katelin , Kives Melissa , Wrammert Jens , Nooka Ajay K. , Koff Jean L. , Dhodapkar Madhav V. , Suthar Mehul S. , Cohen Jonathon B. , Ahmed Rafi
Published: April 2023

Supplemental Table 1. Clinical and vaccination characteristics of NHL/CLL patients in this study
Supplementary Figure S2 from Complex Patterns of Genomic Heterogeneity Identified in 42 Tumor Samples and ctDNA of a Pulmonary Atypical Carcinoid Patient
Authors: Robb Tamsin J. , Tsai Peter , Fitzgerald Sandra , Shields Paula , Houseman Pascalene S. , Patel Rachna , Fan Vicky , Curran Ben , Tse Rexson , Ting Jacklyn , Kramer Nicole , Woodhouse Braden J. , Coats Esther , Le Quesne Stabej Polona , Reeve Jane , Parker Kate , Lawrence Ben , Blenkiron Cherie , Print Cristin G.
Published: April 2023

Supplementary Figure S2: Breakpoints in 10x Loupe software linked-reads view.

Each bar represents a sequencing read, and those joined with a horizontal line share the same barcode.

Reads are grouped by haplotype (green and purple), with unphased reads in grey. Vertical orange lines
indicate putative breakpoints defined by the software. Given that the maximum region of the
chromosome phased was significantly shorter than the length of Chr 11 (as indicated in the ‘phase block
view’ plot), some breakpoints are assigned to different haplotypes, therefore haplotypes should not be
compared between regions (the breakpoint appears in purple in some regions and in green in others).

The copy number patterns are consistent with all breakpoints occurring on the same copy of the
chromosome.
Supplemental Figures/Tables S1 from Reprogramming the Canine Glioma Microenvironment with Tumor Vaccination plus Oral Losartan and Propranolol Induces Objective Responses
Authors: Ammons Dylan T. , Guth Amanda , Rozental Aaron J. , Kurihara Jade , Marolf Angela J. , Chow Lyndah , Griffin John F. , Makii Rebecca , MacQuiddy Brittany , Boss Mary-Keara , Regan Daniel P. , Frank Chad , McGrath Stephanie , Packer Rebecca A. , Dow Steven
Published: April 2023

Supplemental Table 1. Breakdown of study dog demographics.

Supplemental Figure 1. Spheroid culture enriches for CD44 on three canine cancer cell lines.

Supplemental Figure 2. Patient serum has minimal reactivity to parental J3T.

Supplemental Figure 3. Additional western blots from vaccinated study dogs.

Supplemental Figure 4. Additional images of spheroid ICC antibody binding.

Supplemental Figure 5. Responders exhibit durable antibody responses.

Supplemental Figure 6. Comparison of maximal response between humoral responders and non-responders.

Supplemental Table 2. Univariate analysis of key strata indicate humoral status is the only predictor of survival.

Supplemental Figure 7. Differential gene expression analysis reveals enhanced immunoreactivity in high-grade canine gliomas relative to low-grade.

Supplemental Figure 8. Tumor grade does not impact abundance of tumor infiltrating immune cells at the time of necropsy.
Figure S5 from Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma
Authors: Wong Derek , Luo Ping , Znassi Nadia , Arteaga Diana P. , Gray Diana , Danesh Arnavaz , Han Ming , Zhao Eric Y. , Pedersen Stephanie , Prokopec Stephenie , Sundaravadanam Yogi , Torti Dax , Marsh Kayla , Keshavarzi Sareh , Xu Wei , Krema Hatem , Joshua Anthony M. , Butler Marcus O. , Pugh Trevor J.
Published: April 2023

Supplemental Figure 5
Supplementary Figures S1-S6 and Tables from Regulation of Prostate Androgens by Megalin and 25-hydroxyvitamin D Status: Mechanism for High Prostate Androgens in African American Men
Authors: Garcia Jason , Krieger Kirsten D. , Loitz Candice , Perez Lillian M. , Richards Zachary A. , Helou Yves , Kregel Steve , Celada Sasha , Mesaros Clementina A. , Bosland Maarten , Gann Peter H. , Willnow Thomas E. , Vander Griend Donald , Kittles Rick , Prins Gail S. , Penning Trevor , Nonn Larisa
Published: April 2023

S1. Accompanies Figure 1 and 2.

S2. Accompanies Figure 2. No differences in bitransgenic mouse prostate histology, weights and fertility.

S3. Relates to Figure 3. Vitamin D receptor and androgen receptor response elements in LRP2 promoter.

S4. Relates to Figure 3. Prostate slices express hormone response components and respond to 25D and T.

S5. Relates to Figure 4. Androgen levels by Gleason and Age.

S6. Relates to Figure 6. Expression of LRP2 by age and BCR in DFKZ and TCGA cohorts.

Table S1. Cell and tissue characteristics

Table S2. Primer sequences
Figure S6 from Loss of Dok-3 in Non-tumor Cells Induces Malignant Transformation of Benign Epithelial Tumor Cells of the Intestine
Authors: Arimura Sumimasa , Inoue-Yamauchi Akane , Katayama Kotoe , Kanno Tatsuo , Jozawa Hiroki , Imoto Seiya , Yamanashi Yuji
Published: April 2023

Dok-3 deficiency causes malignant progression of colorectal tumors of Apc mice.
Figure S5 from Loss of Dok-3 in Non-tumor Cells Induces Malignant Transformation of Benign Epithelial Tumor Cells of the Intestine
Authors: Arimura Sumimasa , Inoue-Yamauchi Akane , Katayama Kotoe , Kanno Tatsuo , Jozawa Hiroki , Imoto Seiya , Yamanashi Yuji
Published: April 2023

Characterization of invasive tumors in Apc/Dok3 mice.
Supplementary Movie 2 from Three-dimensional Imaging Reveals Immune-driven Tumor-associated High Endothelial Venules as a Key Correlate of Tumor Rejection Following Depletion of Regulatory T Cells
Authors: Milutinovic Stefan , Abe Jun , Jones Emma , Kelch Inken , Smart Kathryn , Lauder Sarah N. , Somerville Michelle , Ware Carl , Godkin Andrew , Stein Jens V. , Bogle Gib , Gallimore Awen
Published: April 2023

Global overview of intra-tumoral HEVs in a 4T1 regressor tumour following PI-3065 treatment.
Table S1 from Elevated Dietary Carbohydrate and Glycemic Intake Associate with an Altered Oral Microbial Ecosystem in Two Large U.S. Cohorts
Authors: Monson Kelsey R. , Peters Brandilyn A. , Usyk Mykhaylo , Um Caroline Y. , Oberstein Paul E. , McCullough Marjorie L. , Purdue Mark P. , Freedman Neal D. , Hayes Richard B. , Ahn Jiyoung
Published: April 2023

Carbohydrate and GI Alpha diversity
Supplementary Table TS4 from Targeting NEDDylation is a Novel Strategy to Attenuate Cisplatin-induced Nephrotoxicity
Authors: Jones Trace M. , Espitia Claudia M. , Chipollini Juan , Lee Benjamin R. , Wertheim Jason A. , Carew Jennifer S. , Nawrocki Steffan T.
Published: April 2023

Median survival time of FaDu tumor bearing mice.
Data from Systemic LRG1 expression in melanoma is associated with disease progression and recurrence
Authors: Hoefsmit Esmee P. , Völlmy Franziska , Rozeman Elisa A. , Reijers Irene L. M. , Versluis Judith M. , Hoekman Liesbeth , van Akkooi Alexander C. J. , Long Georgina V. , Schadendorf Dirk , Dummer Reinhard , Altelaar Maarten , Blank Christian U.
Published: April 2023

Abstract
The response rates upon neoadjuvant immune checkpoint blockade (ICB) in stage III melanoma are higher as compared to stage IV disease. Given that successful ICB depends on systemic immune response, we hypothesized that systemic immune suppression might be a mechanism responsible for lower response rates in late-stage disease, and also potentially with disease recurrence in early-stage disease. Plasma and serum samples of cohorts of melanoma patients were analyzed for circulating proteins using mass spectrometry proteomic profiling and Olink proteomic assay. A cohort of paired samples of patients with stage III that progressed to stage IV disease (n=64) was used to identify markers associated with higher tumor burden. Baseline patient samples from the OpACIN-neo study (n=83) and PRADO study (n=49; NCT02977052) were used as two independent cohorts to analyze whether the potential identified markers are also associated with disease recurrence after neoadjuvant ICB therapy. When comparing baseline proteins overlapping between patients with progressive disease and patients with recurrent disease, we found leucine-rich alpha-2-glycoprotein 1 (LRG1) to be associated with worse prognosis. Especially non-responder patients to neoadjuvant ICB (OpACIN-neo) with high LRG1 expression had a poor outcome with an estimated 36-month event-free survival of 14% as compared to 83% for non-responders with a low LRG1 expression (P = 0.014). This finding was validated in an independent cohort (P = 0.0021). LRG1 can be used as a biomarker to identify patients with high risk for disease progression and recurrence, and might be a target to be combined with neoadjuvant ICB.
A Political Time Rewritten: Revisiting the Founding Year of the Khitan Empire
Authors: Miao Runbo
Published: April 2023

Materials dating from the Liao dynasty usually record the founding year of the Khitan Empire as 907; this was done deliberately, rather than it being caused by the negligence of historians. The official history records of the Khitan Empire contain two completely different narratives of the founding year: the account of “Junji Taiyi deity Repeatedly Appearing” from the “Biography of Taizu” in Liaoshi reflects the original appearance of the history of the empire foundation period in the first year of the Shence era (916). Other records were reworded by later historians, which caused the contents of these originally clear records to become completely blurred and concealed. This rewriting process may have been completed in the thirteenth year of the Zhongxi era (1044) during Emperor Xingzong’s reign; the records advance Emperor Taizu’s rise to the throne to the year that the Tang dynasty was destroyed. That year was essential in reconstructing the founding history of the Khitan Empire and a narrative showed a strong tendency to orthodoxy in the late Liao dynasty. This article offers further reflection on the portrayal of a political epoch in historical records from a dynamic and productive angle.
Two new species of Oricymba (Bacillariophyta) from China, described with reference to the structure of the apical pore field
Authors: YUAN LI , LIU BING , RIOUAL PATRICK , YI MAN-QI , ZHENG YAN
Published: April 2023

Epilithic diatoms form an important component of the benthos in freshwater rivers. As part of a study on the epilithic diatoms in rivers from Hunan and Guizhou Provinces, central China, two new Oricymba species, O. sinensis sp. nov. and O. fanjingensis sp. nov., were observed using light and scanning electron microscopy. Oricymba sinensis possesses a conspicuous dorsiventrality, which differs from other Oricymba species. Moreover, O. sinensis has very shallow grooves along either side of each marginal ridge and higher areola density than other Oricymba species. Oricymba fanjingensis has a unique combination of characters that includes apiculate apices of the valve, distinct grooves along either side of the marginal ridge, and a valve surface ridge parallel to its adjacent marginal ridge. This surface ridge is observed for the first time in Oricymba. The valve external and internal ultrastructure is clearly established for these two new species. In particular, their apical pore fields possess internal apertures of each pervalvar row of foramina that are covered by an undulate flap-like silica strip, which does not completely occlude the internal apertures. Some species of the genera Cymbella and Delicatophycus have a similar internal structure in the apical pore field. Thus, the ultrastructure of the apical pore fields should be considered an important distinguishing feature for Cymbelloid diatoms and is worth investigating systematically.
Modulation of the Oceanic Mesoscale Activity by the Mesoscale Thermal Feedback to the Atmosphere
Authors: Renault Lionel , Masson S. , Oerder V. , Colas F. , McWilliams J. C.
Published: April 2023

Ocean mesoscale thermal feedback (TFB) is the influence of mesoscale sea surface temperature (SST) anomalies on the overlying atmosphere and its feedback to the ocean. Over the past few decades, TFB has been shown to affect the atmosphere by inducing low-level wind and surface stress anomalies and modulating ocean–atmosphere heat fluxes ubiquitously over the global oceans. These anomalies can alter the climate variability. However, it is not clear yet to what extent heat and momentum flux anomalies modulate the mesoscale ocean activity. Here, using coupled ocean–atmosphere mesoscale simulations over a realistic subtropical channel centered on the equator in which the TFB can be turned off by spatially smoothing the SST as seen by the atmosphere, we show that TFB can damp the mesoscale activity, with a more pronounced effect near the surface. This damping appears to be sensitive to the cutoff filter used: on average, the surface mesoscale activity is attenuated by 9% when smoothing the SST using an ∼1000-km cutoff but by only 2% when using an ∼350-km cutoff. We demonstrate that the mesoscale activity damping is primarily caused by a sink of available eddy potential energy that is controlled by the induced-anomalous heat fluxes, the surface stress anomalies having a negligible role. When TFB is neglected, the absence of sink of potential energy is partly compensated by a more negative eddy wind work. We illustrate that TFB filtering in a coupled model must be done carefully because it can also impact the large-scale meridional SST gradients and subsequently the mean large-scale wind stress curl and ocean dynamics.
Photothermal therapy of papillary thyroid cancer tumor xenografts with targeted thyroid stimulating hormone receptor antibody functionalized multiwalled carbon nanotubes
Authors: Lee Seung Soo , Oudjedi Fatma , Kirk Andrew G. , Paliouras Miltiadis , Trifiro Mark A.
Published: April 2023

Multiwalled carbon nanotubes (MWCNTs) are being widely investigated in multiple biomedical applications including, and not limited to, drug delivery, gene therapy, imaging, biosensing, and tissue engineering. Their large surface area and aspect ratio in addition to their unique structural, optical properties, and thermal conductivity also make them potent candidates for novel hyperthermia therapy. Here we introduce thyroid hormone stimulating receptor (TSHR) antibody–conjugate–MWCNT formulation as an enhanced tumor targeting and light-absorbing device for the photoablation of xenografted BCPAP papillary thyroid cancer tumors. To ensure successful photothermal tumor ablation, we determined three key criteria that needed to be addressed: (1) predictive pre-operational modeling; (2) real-time monitoring of the tumor ablation process; and (3) post-operational follow-up to assess the efficacy and ensure complete response with minimal side effects. A COMSOL-based model of spatial temperature distributions of MWCNTs upon selected laser irradiation of the tumor was prepared to accurately predict the internal tumor temperature. This modeling ensured that 4.5W of total laser power delivered over 2 min, would cause an increase of tumor temperature above 45 ℃, and be needed to completely ablate the tumor while minimizing the damage to neighboring tissues. Experimentally, our temperature monitoring results were in line with our predictive modeling, with effective tumor photoablation leading to a significantly reduced post 5-week tumor recurrence using the TSHR-targeted MWCNTs. Ultimately, the results from this study support a utility for photosensitive biologically modified MWCNTs as a cancer therapeutic modality. Further studies will assist with the transition of photothermal therapy from preclinical studies to clinical evaluations.
De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments
Authors: Cui Jipeng , Qiu Tianhang , Li Li , Cui Suxia
Published: April 2023

Background

The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies.

Results

In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments.

Conclusions

Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.