Additional file 1 of Recognizing puzzling PD1 + infiltrates in marginal zone lymphoma by integrating clonal and mutational findings: pitfalls in both nodal and transformed splenic cases

Additional file 1. Supplementary Materials. Methods. Histology and Immunohistochemistry. Cases were collected from the Peking University Cancer Hospital and reviewed by an expert panel (YF.S., YM.L., and XH.L.), with a consensus diagnosis of MZL or tSMZL. The study was approved by the ethical committee of the institution and followed the 1964 Helsinki Declaration. Hematoxylin and eosin (H&E) and immunohistochemistry-stained slides from each case were evaluated. Immunohistochemistry was performed on FFPE sections on a Ventana Benchmark automated immunostainer using UltraView detection kits. The panel of antibodies can be seen in Table S2. The interpretation of the PD1 staining pattern included both the predominant location of the PD1-positive cells (follicular or extrafollicular) and was considered “normal” if most PD-1-positive cells were confined to intrafollicular areas and concentrated in the light zone. In situ hybridization to detect EBV-encoded RNA. EBV status was determined by in situ hybridization (ISH) to detect EBV-encoded RNA 1 and 2 (EBER1/2s) using peroxidase-labeled probes (ISH-7001UM, Beijing Zhongshan Golden Bridge Biotechnology). Tissue from a known EBV-positive nasopharyngeal carcinoma was used as a positive control. The EBV status was considered positive if at least one definitive cell expressed EBER. All H&E, IHC and ISH slides were independently and dual assessed. Immunoglobulin Gene and T-Cell Receptor Gene Rearrangement Studies. DNA was extracted from FFPE tissue sections using a QIAGEN QIAamp DNA FFPE Tissue Kit according to the manufacturer’s protocol (QIAGEN, Germantown, MD). Polymerase chain reaction (PCR) for immunoglobulin gene (IGH and IGK loci) and T-cell receptor (TCR locus) rearrangements was performed using commercially available BIOMED-2 multiplex PCR kits (Righton Gene, Shanghai). PCR products were separated by capillary electrophoresis and subjected to GeneScan analysis for confirmation of the monoclonal character of the IG or TCR gene rearrangements on an ABI 9700 Genetic Analyzer (Applied Biosystems, Foster City, CA), and electropherograms were analyzed using GeneMapper software, version 4.0. Targeted exome sequencing (TES) and sequence data analysis. Genomic DNA (gDNA) extraction from FFPE tissues, library preparation, and target gene enrichment were performed according to the manufacturer’s protocol. The gDNA libraries were subjected to high-throughput sequencing with 150-bp paired-end reads on the NovaSeq 60,000 Sequencing System (Illumina, San Diego, CA) supported by a commercial vendor (Geneplus-Beijing, China). The average sequencing depth of tissues was ~500×. Sequence reads were aligned using BWA version 0.5.9 (Broad Institute). Single nucleotide variants (SNVs) were called using MuTect (version 1.1.4) and NChot. Small insertions and deletions (Indels) were determined by GATK. All final candidate variants were manually reviewed by using the IGV browser as reported previously [13]

Media 1: <i>In vivo</i> photoacoustic imaging of transverse blood flow by using Doppler broadening of bandwidth

Originally published in Optics Letters on 01 May 2010 (ol-35-9-1419

Multibenzocyclobutene Functionalized Silane for Low‑<i>k</i> Polyarylsilane Thermosets with Low Coefficient of Thermal Expansion and High Thermostability

Highly cross-linked thermosets have been extensively studied for their good thermostability and low coefficient of thermal expansion (CTE). Herein, multibenzocyclobutene (multi-BCB) functionalized silane monomers and the related thermosets as polyarylsilane are reported. These silane monomers can be cured at a high temperature above 200 °C. After curing, the corresponding transparent thermosets showed good thermal property. The results indicated that more benzocyclobutene (BCB) groups on the corresponding silane monomer induced a higher cross-linked structure, which contributes to improve heat resistance, glass transition temperature (Tg), and dimensional stability. Particularly, the cured tetra­(benzocyclobutene-4-yl) silane (SiB4) showed extremely high Tg over 400 °C, high initial storage modulus, and good thermostability (Td5 = 532 °C). The cured SiB4 also showed excellent thermomechanical properties with a low CTE at 24 ppm/°C. These polymers also showed good dielectric properties with a low k below 2.70. The low-k material with a low CTE may be a good candidate for high-performance composite resin matrix and high-density substrates

Additional file 3: of The proto-oncogene Mer tyrosine kinase is a novel therapeutic target in mantle cell lymphoma

Figure S1. MerTK knockdown mediated by shMerTK 4 suppressed downstream signaling pathways and proliferation in MCL cells. Figure S2. MerTK inhibition by either shRNA or treatment with UNC2250 suppressed migration of MCL cells. Figure S3. The effects of UNC2250 on proliferation and apoptosis of MCL cells. Figure S4. Representative flow cytometry profiles for apoptosis assays in Z-138, Mino and JVM-2 cells. Figure S5. Representative flow cytometry profiles for cell cycle analysis in Z-138, Mino and JVM-2 cells. Figure S6. Proliferation of Z-138 and Mino cells was inhibited with increasing concentrations of vincristine or doxorubicin. Figure S7. Expression of microRNA-126, microRNA-335 and Gas6 in MCL cells. (DOCX 15 kb

Additional file 2: of The proto-oncogene Mer tyrosine kinase is a novel therapeutic target in mantle cell lymphoma

Supplementary Methods: Confocal immunofluorescence assays; RNA extraction, reverse transcription and Real-Time PCR. (DOCX 2252 kb

Additional file 1: of The proto-oncogene Mer tyrosine kinase is a novel therapeutic target in mantle cell lymphoma

Table S1. Baseline characteristics of MCL patients receiving R-CHOP like regimens and their correlations with MerTK. Table S2. Information of antibodies applied in immunohistochemistry and western blot assays. Table S3. Combination index values of UNC2250 and Vincristine or Doxorubicin in Z-138 and Mino cells. (DOCX 28 kb

Novel Citral-thiazolyl Hydrazine Derivatives as Promising Antifungal Agents against Phytopathogenic Fungi

To develop new antifungal agents against phytopathogenic fungi, a series of citral-thiazolyl hydrazine derivatives were designed, synthesized, and characterized by FT-IR, 1H NMR, 13C NMR, and HRMS. Antifungal activity results showed that most synthetic compounds exhibited broad-spectrum antifungal activities against six phytopathogenic fungi in vitro. Notably, compounds b and c15 exhibited remarkable antifungal activity against Colletotrichum gloeosprioides, Rhizoctonia solani, Phytophthora nicotianae var. nicotianae, Diplodia pinea, Colletotrichum acutatum, and Fusarium oxysporum f. sp. niveum, which were all superior to the positive control tricyclazole. Structure–activity relationship (SAR) studies demonstrated that introducing electron-withdrawing groups such as F on the benzene ring exhibited outstanding antifungal activities against all the tested fungi. Furthermore, compound b could effectively control rice sheath blight and showed higher curative activities against R. solani than validamycin·bacillus in vivo. In addition, the in vitro cytotoxicity results indicated that compound b possessed moderate cytotoxicity activity, and all citral-thiazolyl hydrazine derivatives exhibited lower or no cytotoxicity to the LO2 and HEK293 cell lines. In addition, the acute oral toxicity test showed that compound b had moderate toxicity (level II) with an LD50 value of 310 mg/kg bw (95% confidence limit: 175–550 mg/kg bw). Finally, a preliminary action mechanism study showed that causing obvious malformation of mycelium and increasing cell membrane permeability are two of the potential mechanisms by which compound b exerts antifungal activity. The present work indicates that some of these derivatives may serve as novel potential fungicides, and compound b is expected to be the leading structure for the development of new antifungal agents

MOESM2 of ITK inhibition induced in vitro and in vivo anti-tumor activity through downregulating TCR signaling pathway in malignant T cell lymphoma

Additional file 2: Table S1. Patients’ characteristics and correlations with the expression of p-ZAP70

Image_1_Various Subtypes of EGFR Mutations in Patients With NSCLC Define Genetic, Immunologic Diversity and Possess Different Prognostic Biomarkers.tif

Based on data analysis of 9649 Chinese primary NSCLC patients, we calculated the exact proportion of EGFR subtypes in NSCLC and evaluated the TMB level, PD-L1 expression level and tumor immune microenvironment among different EGFR mutation subtypes. Postoperative follow-up data for 98 patients were collected and analyzed. The results showed that several uncommon EGFR mutation subtypes have a higher proportion of TMB-high or strong positive PD-L1 expression than the total EGFR mutation group. In addition, different subtypes have different characteristics related to the immune microenvironment, such as G719 mutations being associated with more CD8+ T cell infiltration into tumors; except for EGFR 19del, CD8+ T cell infiltration into tumors of other EGFR mutation subtypes were similar to that of wildtype EGFR. Moreover, follow-up results revealed that components of the immune microenvironment have prognostic value for NSCLC patients, with different prognostic biomarkers for NSCLC patients with and without EGFR mutations. These results suggest that patients with different EGFR mutations need to be treated differently. The prognosis of NSCLC patients may be assessed through components of tumor immune microenvironment, and ICIs treatment may be considered for those with some uncommon EGFR mutation subtypes.</p

Table_1_Various Subtypes of EGFR Mutations in Patients With NSCLC Define Genetic, Immunologic Diversity and Possess Different Prognostic Biomarkers.docx

Based on data analysis of 9649 Chinese primary NSCLC patients, we calculated the exact proportion of EGFR subtypes in NSCLC and evaluated the TMB level, PD-L1 expression level and tumor immune microenvironment among different EGFR mutation subtypes. Postoperative follow-up data for 98 patients were collected and analyzed. The results showed that several uncommon EGFR mutation subtypes have a higher proportion of TMB-high or strong positive PD-L1 expression than the total EGFR mutation group. In addition, different subtypes have different characteristics related to the immune microenvironment, such as G719 mutations being associated with more CD8+ T cell infiltration into tumors; except for EGFR 19del, CD8+ T cell infiltration into tumors of other EGFR mutation subtypes were similar to that of wildtype EGFR. Moreover, follow-up results revealed that components of the immune microenvironment have prognostic value for NSCLC patients, with different prognostic biomarkers for NSCLC patients with and without EGFR mutations. These results suggest that patients with different EGFR mutations need to be treated differently. The prognosis of NSCLC patients may be assessed through components of tumor immune microenvironment, and ICIs treatment may be considered for those with some uncommon EGFR mutation subtypes.</p