Integrated Transcriptome Analysis Reveals Novel Molecular Signatures for Schizophrenia Characterization by Tong Ni, Yu Sun, Zefeng Li, Tao Tan, Wei Han, Miao Li, Li Zhu, Jing Xiao, Huiying Wang, Wenpei Zhang, Yitian Ma, Biao Wang, Di Wen, Teng Chen, Justin Tubbs, Xiaofeng Zeng, Jiangwei Yan, Hongsheng Gui, Pak Sham, Fanglin Guan

“…The current study aimed to identify and evaluate disease‐responsive essential genes (DREGs) to enhance the molecular characterization of SCZ. RNA‐sequencing data from PsychENCODE (536 SCZ patients, 832 controls) and peripheral blood transcriptome data from 144 recruited subjects (59 SCZ patients, 6 non‐SCZ psychiatric patients, 79 controls) are analyzed. …”
Get full text

Sitravatinib in combination with nivolumab plus ipilimumab in patients with advanced clear cell renal cell carcinoma: a phase 1 trial by Pavlos Msaouel, Kai Yu, Ying Yuan, Jianfeng Chen, Xinmiao Yan, Menuka Karki, Fei Duan, Rahul A. Sheth, Priya Rao, Kanishka Sircar, Amishi Y. Shah, Amado J. Zurita, Giannicola Genovese, Min Li, Chih-Chen Yeh, Minghao Dang, Guangchun Han, Yanshuo Chu, Max Hallin, Peter Olson, Rui Yang, Daniela Slavin, Hirak Der-Torossian, Curtis D. Chin, Nizar M. Tannir, Linghua Wang, Jianjun Gao

“…Sitravatinib exposure increased dose-dependently. Single-cell RNA-seq of longitudinally collected tumor biopsies from 12 patients identified a tumor cell-specific epithelial-mesenchymal transition-like program associated with treatment resistance and poor outcomes. …”
Get full text

Predictive value of ENLIGHT-DP in patients with metastatic lung adenocarcinoma treated with immune checkpoint inhibitors and platinum chemotherapy directly from histopathology slid... by Eli Pikarsky, Anna Elia, Gal Dinstag, Omer Tirosh, Tuvik Beker, Ranit Aharonov, Hovav Nechushtan, Leon Gugel, Yaron Kinar, Michael Tabi, Tzivia Gottlieb, Aron Popovtzer, Johnathan Arnon, Yakir Rottenberg, Philip Blumenfeld

“…ENLIGHT-DP predicts response to ICI and targeted therapies given H&E slide scans in two steps: (1) predict individual messenger RNA expression directly from high-resolution H&E scanned slides using DeepPT, a digital-pathology-based algorithm. (2) Use these values as input to ENLIGHT, a transcriptome-based platform that predicts response to ICI and targeted therapies derived from drug-specific networks of gene expressions. …”
Get full text

Unraveling pathogenesis and potential biomarkers for autism spectrum disorder associated with HIF1A pathway based on machine learning and experiment validation by Jinru Cui, Heli Li, Cong Hu, Feiyan Zhang, Yunjie Li, Ying Weng, Liping Yang, Yingying Li, Minglan Yao, Hao Li, Xiaoping Luo, Yan Hao

“…Machine learning identified hub genes from intersection genes and PPI networks were constructed to explore relationships among hub and HIF1A. Single-cell RNA sequencing analyzed hub gene distribution across cell clusters. …”
Get full text

Effects of Mixing Ratio and Lactic Acid Bacteria Preparation on the Quality of Whole-Plant Quinoa and Whole-Plant Corn or Stevia Powder Mixed Silage by Chao He, Qian Li, Huaidong Xiao, Xuchun Sun, Zepeng Gao, Yuan Cai, Shengguo Zhao

“…Max and Mix significantly reduced the levels of mycotoxins, both of which were far below the range of feed safety testing, and 16S rRNA sequencing revealed that the silage microbiota varied with different mixing ratios and whether lactic acid bacteria preparations were used. …”
Get full text

Utilization of donor CLL-1 CAR-T cells for the treatment of relapsed of acute myeloid leukemia following allogeneic hematopoietic stem cell transplantation by Meng Zhang, Meng Zhang, Xiaomei Zhang, Xiaomei Zhang, Jiaxi Wang, Wenyi Lu, Xia Xiao, Hairong Lyu, Xiaoyuan He, Yedi Pu, Juanxia Meng, Cuicui Lyu, Xinping Cao, Mingfeng Zhao, Mingfeng Zhao

“…However, 2 patients withdrew from the study due to rapid disease progression. 12 participants received donor-derived CLL-1 CAR-T cells and were categorized into 3 groups based on the dosage of infused CAR-T cells dose (Group A:0.5×106/kg, Group B:1×106/kg, Group C:1.5×106/kg). And scRNA-seq was used to reveal CLL-1 CAR-T cells dynamics in a CAR-T cells infusion products and PBMCs at the peak of expansion for patient 4.ResultsCLL-1 CAR-T cells were well tolerated by all 12 patients. …”
Get full text

Dissection of the genetic basis and molecular mechanism of ovule number per ovary in oilseed rape (Brassica napus L.) by Muslim Qadir, Muslim Qadir, Muslim Qadir, Xinyi Lin, Farhan Nabi, Kishore Kumar Ashok, Xue-Rong Zhou, Qingbin Sun, Peiman Shi, Xinfa Wang, Jiaqin Shi, Hanzhong Wang

“…Transcriptomic analysis identified 7689 differentially expressed genes (DEGs) between the two pools, of which nearly half were enriched into functional categories of reported genes regulating ONPO, including protein, RNA, signalling, miscellaneous, development, hormone metabolism, and tetrapyrrole synthesis. …”
Get full text

S100A13-driven interaction between pancreatic adenocarcinoma cells and cancer-associated fibroblasts promotes tumor progression through calcium signaling by Liuyuan Xia, Xin Guo, Dong Lu, Yixin Jiang, Xiaohui Liang, Yiwen Shen, Jiayi Lin, Lijun Zhang, Hongzhuan Chen, Jinmei Jin, Xin Luan, Weidong Zhang

“…Stable S100A13 knockdown CAFs were generated using a short hairpin RNA system. Cellular viability and apoptosis rates were evaluated through CCK-8 and flow cytometry tests, respectively. …”
Get full text

Interrelationship between altered metabolites and the gut microbiota in people living with HIV with different immune responses to antiretroviral therapy by Xuebin Tian, Zhongyao Gao, Yiwen Xie, Xiangyun Lu, Yulong Zhao, Peng Yao, Mingqing Dong, Lifeng Yu, Nanping Wu

“…Further experiments showed that Indole-3-acetyl-beta-1-D-glucoside significantly decreased the proportions of CD4+CD57+, effector CD4+, CD4+PD1+, CD8+CD57+, effector CD8+, and CD8+HLA-DR+ T cells. Moreover, mRNA expression analysis showed that Indole-3-acetyl-beta-1-D-glucoside treatment led to a suppression of pro-inflammatory cytokines. …”
Get full text

Cultivating crayfish (Procambarus clarkii) significantly enhances the quantity and diversity of soil microorganisms: evidence from the comparison of rice-wheat and rice-crayfish ro... by Hui Xu, Hui Xu, Dan Wang, Dan Wang, Dan Wang, Xuguang Li, Xuguang Li, Jiajia Li, Jiajia Li, Yu Xu, Yu Xu, Zhiqiang Xu, Zhiqiang Xu

“…In this study, we compared the differences in soil microbial communities and predicted their functions in these two IFA models by sequencing the 16s rRNA and analyzing the bioinformation. The results showed that crayfish farming effectively increased the abundance and diversity of soil microorganisms. …”
Get full text

Knockout of the inhibitory receptor TIGIT enhances the antitumor response of ex vivo expanded NK cells and prevents fratricide with therapeutic Fc-active TIGIT antibodies by Dean A Lee, Jeremiah L Oyer, Md Faqrul Hasan, Tayler J Croom-Perez, Liza D Robles-Carrillo, Sanjana Kumar, Brendan W Andersen, Brian P Tullius, Alicja J Copik, Amanda R Campbell, Thomas A Dieffenthaller, Catherine A Cash, Jonathan E Eloriaga, Meisam Naeimi Kararoudi

“…Phenotypic and transcriptomic properties of TIGIT KO and wild-type (WT) NK cells were compared with flow cytometry, CyTOF, and RNA sequencing. The effect of TIGIT KO on NK-cell cytotoxicity was determined by calcein-AM release and live cell imaging-based cytotoxicity assays. …”
Get full text

Ginsenoside Rd protects against acute liver injury by regulating the autophagy NLRP3 inflammasome pathway by Xiaomei Zhong, Yibin Sun, Yanxiang Lin, Shan Deng, Huan Wang, Xian Zhou, Jinjian Lu, Yanfang Zheng, Ruoyin Luo, Mingqing Huang, Jianyuan Song

“…It exhibited strong anti-inflammatory effect by reducing inflammation associated protein, such as cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), nod-like receptor protein 3 (NLRP3), associated speck-like protein containing a CARD (ASC), interleukin-18 (IL-18) and interleukin-1β(IL-1β) proteins and the mRNA expression levels of COX-2, Tumor Necrosis Factor α (TNF α), interleukin-6 (IL-6) and iNOS were decreased in liver tissue. …”
Get full text

Lower respiratory tract microbiome dysbiosis impairs clinical responses to immune checkpoint blockade in advanced non‐small‐cell lung cancer by Yong Zhang, Xiang‐Xiang Chen, Ruo Chen, Ling Li, Qing Ju, Dan Qiu, Yuan Wang, Peng‐Yu Jing, Ning Chang, Min Wang, Jian Zhang, Zhi‐Nan Chen, Ke Wang

“…Methods During this study, 26 bronchoalveolar lavage fluids (BALF) from advanced NSCLC participants who received immune checkpoint inhibitor monotherapy were performed 16S rRNA sequencing and untargeted metabolome sequencing to identify differentially abundant microbes and metabolic characteristics. …”
Get full text

T-cell receptor beta variable gene polymorphism predicts immune-related adverse events during checkpoint blockade immunotherapy by Linghua Wang, Siqing Fu, Aung Naing, Funda Meric-Bernstam, Carl Morrison, Joud Hajjar, Mingxuan Xu, Anas Alshawa, Bettzy Stephen, Ying Yuan, Jordi Rodon Ahnert, Abdulrazzak Zarifa, Shrutii Sarda, Timothy Looney, Sapna P Patel, Geoffrey M Lowman, Dzifa Yawa Duose, Jeffrey M Conroy, Evan Kwiatkowski

“…However, the repetitive nature of the TCRB locus and incomplete genome assembly has hampered the evaluation of TRBV polymorphisms in the past.Patients and methods We used a novel method for long-amplicon next generation sequencing of rearranged TCRB chains from peripheral blood total RNA to evaluate the link between TRBV polymorphisms and irAEs in patients treated with immunotherapy for cancer. …”
Get full text

Five-Year Prospective Follow-Up of Patients with Hepatitis C Virus Infection Treated with Direct-Acting Antiviral Agents by Zhang Y, Xia H, Fan L, Jiang L, Yang B, Wang F

“…The proportion of all participants with undetectable HCV-RNA exceeded 98% at all follow-up time points. Patients experienced virological relapse, HCC, death and disease progression with a cumulative AIRs of 1.03% (95% confidence interval [CI] 0.6– 1.5), 1.76% (95% CI 1.2– 2.3), 1.51% (95% CI 1.0– 2.0), and 5.81% (95% CI 4.8– 6.8), respectively. …”
Get full text

Serum and tear autoantibodies from NOD and NOR mice as potential diagnostic indicators of local and systemic inflammation in Sjögren’s disease by Shruti Singh Kakan, Sara Abdelhamid, Sara Abdelhamid, Yaping Ju, Yaping Ju, J. Andrew MacKay, J. Andrew MacKay, J. Andrew MacKay, Maria C. Edman, Indu Raman, Chengsong Zhu, Prithvi Raj, Sarah F. Hamm-Alvarez, Sarah F. Hamm-Alvarez

“…Sources of Ig in tears were investigated using scRNA-Seq of the LG (GSE132420). Data were analyzed by R package Limma and Seurat.ResultsAnalysis of immunofluorescence in LG sections from both SjD models showed TLS. …”
Get full text

Time to HIV viral rebound and frequency of post-treatment control after analytical interruption of antiretroviral therapy: an individual data-based meta-analysis of 24 prospective... by Jesper D. Gunst, Jesal Gohil, Johanthan Z. Li, Ronald J. Bosch, Andrea White, Catherine Seamon, Tae-Wook Chun, Beatriz Mothe, Kathleen Gittens, Lauren Praiss, Marie-Angélique De Scheerder, Linos Vandekerckhove, Kevin Escandón, Ann Thorkelson, Timothy Schacker, Devi SenGupta, Christian Brander, Emmanouil Papasavvas, Luis J. Montaner, Javier Martinez-Picado, Ruxandra Calin, Antonella Castagna, Camilla Muccini, Wesley de Jong, Lorna Leal, Felipe Garcia, Rob A. Gruters, Timothy Tipoe, John Frater, Ole S. Søgaard, Sarah Fidler

“…In total, 24 eligible prospective studies with 382 individuals with ≥5 plasma HIV RNA viral loads (pVLs) within the first 84 days post-ATI were included. …”
Get full text

Treating drug-resistant tuberculosis in an era of shorter regimens: Insights from rural South Africa by J-D K Lotz, J Porter, H Conradie, T Boyles, B Gaunt, S Dimanda, D Cort

“…Injectables (adjusted odds ratio (aOR) 3.00, 95% confidence interval (CI) 1.48 - 6.09), bedaquiline (aOR 3.16, 95% CI 1.36 - 7.35), increasing age (aOR 0.97, 95% CI 0.95 - 0.99) and HIV viraemia defined as final HIV-RNA viral load >1 000 copies/mL (aOR 0.16, 95% CI 0.07 - 0.37) were all significantly and independently associated with treatment success. …”
Get full text

Specifically blocking αvβ8-mediated TGF-β signaling to reverse immunosuppression by modulating macrophage polarization by Cuicui Guo, Hui Sun, Yulei Du, Xiaodong Dai, Yu Pang, Zhen Han, Xinhui Xiong, Shaowei Li, Junhua Zhang, Qingbing Zheng, Xun Gui

“…Methods We utilized single-cell RNA sequencing to assess αvβ8 expression across various human tumors. …”
Get full text

Microbial community variations in adult Hyalomma dromedarii ticks from single locations in Saudi Arabia and Tunisia by Myriam Kratou, Apolline Maitre, Apolline Maitre, Apolline Maitre, Lianet Abuin-Denis, Lianet Abuin-Denis, Rachid Selmi, Hanène Belkahia, Abdullah D. Alanazi, Hattan Gattan, Hattan Gattan, Bassam M. Al-Ahmadi, Abdullah F. Shater, Lourdes Mateos-Hernández, Dasiel Obregón, Lilia Messadi, Alejandro Cabezas-Cruz, Mourad Ben Said, Mourad Ben Said

“…Despite prior studies on its microbiota, the effects of geographic origin and sex on microbial community structure and functional stability remain poorly understood.MethodsTo address this, we characterized the bacterial microbiota of H. dromedarii ticks collected from camels in Tunisia (TUN) and Saudi Arabia (SA) using 16S rRNA gene sequencing, microbial network analysis, and metabolic pathway prediction.ResultsOur findings indicate a dominant presence of Francisella endosymbionts in Tunisian ticks, suggesting adaptive roles of H. dromedarii ticks in arid ecosystems. …”
Get full text