Comparative genomics incorporating translocation renal cell carcinoma mouse model reveals molecular mechanisms of tumorigenesis
J Clin Invest. 2024 Feb 22:e170559. doi: 10.1172/JCI170559. Online ahead of print.ABSTRACTTranslocation Renal Cell Carcinoma (tRCC) most commonly involves an ASPSCR1-TFE3 fusion, but molecular mechanisms remain elusive and animal models are lacking. Here, we show that human ASPSCR1-TFE3 driven by Pax8-Cre (a credentialed ccRCC driver) disrupted nephrogenesis and glomerular development causing neonatal death, whilst the ccRCC failed driver, Sglt2-Cre, induced aggressive tRCC (as well as ASPS) with complete penetrance and short latency. However, in both contexts, ASPSCR1-TFE3 led to characteristic morphological cellular chan...
Source: Genomics Proteomics ... - February 22, 2024 Category: Genetics & Stem Cells Authors: Gopinath Prakasam Akhilesh Mishra Alana Christie Jeffrey Miyata Deyssy Carrillo Vanina T Tcheuyap Hui Ye Quyen N Do Yunguan Wang Oscar Reig Torras Ramesh Butti Hua Zhong Jeffrey Gagan Kevin B Jones Thomas J Carroll Zora Modrusan Steffen Durinck Mai-Carmen Source Type: research
Comparative genomics incorporating translocation renal cell carcinoma mouse model reveals molecular mechanisms of tumorigenesis
J Clin Invest. 2024 Feb 22:e170559. doi: 10.1172/JCI170559. Online ahead of print.ABSTRACTTranslocation Renal Cell Carcinoma (tRCC) most commonly involves an ASPSCR1-TFE3 fusion, but molecular mechanisms remain elusive and animal models are lacking. Here, we show that human ASPSCR1-TFE3 driven by Pax8-Cre (a credentialed ccRCC driver) disrupted nephrogenesis and glomerular development causing neonatal death, whilst the ccRCC failed driver, Sglt2-Cre, induced aggressive tRCC (as well as ASPS) with complete penetrance and short latency. However, in both contexts, ASPSCR1-TFE3 led to characteristic morphological cellular chan...
Source: Genomics Proteomics ... - February 22, 2024 Category: Genetics & Stem Cells Authors: Gopinath Prakasam Akhilesh Mishra Alana Christie Jeffrey Miyata Deyssy Carrillo Vanina T Tcheuyap Hui Ye Quyen N Do Yunguan Wang Oscar Reig Torras Ramesh Butti Hua Zhong Jeffrey Gagan Kevin B Jones Thomas J Carroll Zora Modrusan Steffen Durinck Mai-Carmen Source Type: research
Comparative genomics incorporating translocation renal cell carcinoma mouse model reveals molecular mechanisms of tumorigenesis
J Clin Invest. 2024 Feb 22:e170559. doi: 10.1172/JCI170559. Online ahead of print.ABSTRACTTranslocation Renal Cell Carcinoma (tRCC) most commonly involves an ASPSCR1-TFE3 fusion, but molecular mechanisms remain elusive and animal models are lacking. Here, we show that human ASPSCR1-TFE3 driven by Pax8-Cre (a credentialed ccRCC driver) disrupted nephrogenesis and glomerular development causing neonatal death, whilst the ccRCC failed driver, Sglt2-Cre, induced aggressive tRCC (as well as ASPS) with complete penetrance and short latency. However, in both contexts, ASPSCR1-TFE3 led to characteristic morphological cellular chan...
Source: Genomics Proteomics ... - February 22, 2024 Category: Genetics & Stem Cells Authors: Gopinath Prakasam Akhilesh Mishra Alana Christie Jeffrey Miyata Deyssy Carrillo Vanina T Tcheuyap Hui Ye Quyen N Do Yunguan Wang Oscar Reig Torras Ramesh Butti Hua Zhong Jeffrey Gagan Kevin B Jones Thomas J Carroll Zora Modrusan Steffen Durinck Mai-Carmen Source Type: research
Pan-cancer proteogenomics characterization of tumor immunity
Cell. 2024 Feb 12:S0092-8674(24)00064-3. doi: 10.1016/j.cell.2024.01.027. Online ahead of print.ABSTRACTDespite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten differ...
Source: Genomics Proteomics ... - February 15, 2024 Category: Genetics & Stem Cells Authors: Francesca Petralia Weiping Ma Tomer M Yaron Francesca Pia Caruso Nicole Tignor Joshua M Wang Daniel Charytonowicz Jared L Johnson Emily M Huntsman Giacomo B Marino Anna Calinawan John Erol Evangelista Myvizhi Esai Selvan Shrabanti Chowdhury Dmitry Rykunov Source Type: research
Pan-cancer proteogenomics characterization of tumor immunity
Cell. 2024 Feb 12:S0092-8674(24)00064-3. doi: 10.1016/j.cell.2024.01.027. Online ahead of print.ABSTRACTDespite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten differ...
Source: Genomics Proteomics ... - February 15, 2024 Category: Genetics & Stem Cells Authors: Francesca Petralia Weiping Ma Tomer M Yaron Francesca Pia Caruso Nicole Tignor Joshua M Wang Daniel Charytonowicz Jared L Johnson Emily M Huntsman Giacomo B Marino Anna Calinawan John Erol Evangelista Myvizhi Esai Selvan Shrabanti Chowdhury Dmitry Rykunov Source Type: research
Pan-cancer proteogenomics characterization of tumor immunity
Cell. 2024 Feb 12:S0092-8674(24)00064-3. doi: 10.1016/j.cell.2024.01.027. Online ahead of print.ABSTRACTDespite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten differ...
Source: Genomics Proteomics ... - February 15, 2024 Category: Genetics & Stem Cells Authors: Francesca Petralia Weiping Ma Tomer M Yaron Francesca Pia Caruso Nicole Tignor Joshua M Wang Daniel Charytonowicz Jared L Johnson Emily M Huntsman Giacomo B Marino Anna Calinawan John Erol Evangelista Myvizhi Esai Selvan Shrabanti Chowdhury Dmitry Rykunov Source Type: research
Pan-cancer proteogenomics characterization of tumor immunity
Cell. 2024 Feb 12:S0092-8674(24)00064-3. doi: 10.1016/j.cell.2024.01.027. Online ahead of print.ABSTRACTDespite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten differ...
Source: Genomics Proteomics ... - February 15, 2024 Category: Genetics & Stem Cells Authors: Francesca Petralia Weiping Ma Tomer M Yaron Francesca Pia Caruso Nicole Tignor Joshua M Wang Daniel Charytonowicz Jared L Johnson Emily M Huntsman Giacomo B Marino Anna Calinawan John Erol Evangelista Myvizhi Esai Selvan Shrabanti Chowdhury Dmitry Rykunov Source Type: research
Pan-cancer proteogenomics characterization of tumor immunity
Cell. 2024 Feb 12:S0092-8674(24)00064-3. doi: 10.1016/j.cell.2024.01.027. Online ahead of print.ABSTRACTDespite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten differ...
Source: Genomics Proteomics ... - February 15, 2024 Category: Genetics & Stem Cells Authors: Francesca Petralia Weiping Ma Tomer M Yaron Francesca Pia Caruso Nicole Tignor Joshua M Wang Daniel Charytonowicz Jared L Johnson Emily M Huntsman Giacomo B Marino Anna Calinawan John Erol Evangelista Myvizhi Esai Selvan Shrabanti Chowdhury Dmitry Rykunov Source Type: research
Interpretable deep learning methods for multiview learning
CONCLUSION: iDeepViewLearn is an innovative deep learning model capable of capturing nonlinear relationships between data from multiple views while achieving feature selection. It is fully open source and is freely available at https://github.com/lasandrall/iDeepViewLearn .PMID:38350879 | DOI:10.1186/s12859-024-05679-9 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 13, 2024 Category: Genetics & Stem Cells Authors: Hengkang Wang Han Lu Ju Sun Sandra E Safo Source Type: research
Interpretable deep learning methods for multiview learning
CONCLUSION: iDeepViewLearn is an innovative deep learning model capable of capturing nonlinear relationships between data from multiple views while achieving feature selection. It is fully open source and is freely available at https://github.com/lasandrall/iDeepViewLearn .PMID:38350879 | DOI:10.1186/s12859-024-05679-9 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 13, 2024 Category: Genetics & Stem Cells Authors: Hengkang Wang Han Lu Ju Sun Sandra E Safo Source Type: research
Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities
Nat Cancer. 2024 Feb 12. doi: 10.1038/s43018-024-00725-0. Online ahead of print.ABSTRACTMolecular profiling guides precision treatment of breast cancer; however, Asian patients are underrepresented in publicly available large-scale studies. We established a comprehensive multiomics cohort of 773 Chinese patients with breast cancer and systematically analyzed their genomic, transcriptomic, proteomic, metabolomic, radiomic and digital pathology characteristics. Here we show that compared to breast cancers in white individuals, Asian individuals had more targetable AKT1 mutations. Integrated analysis revealed a higher proport...
Source: Genomics Proteomics ... - February 12, 2024 Category: Genetics & Stem Cells Authors: Yi-Zhou Jiang Ding Ma Xi Jin Yi Xiao Ying Yu Jinxiu Shi Yi-Fan Zhou Tong Fu Cai-Jin Lin Lei-Jie Dai Cheng-Lin Liu Shen Zhao Guan-Hua Su Wanwan Hou Yaqing Liu Qingwang Chen Jingcheng Yang Naixin Zhang Wen-Juan Zhang Wei Liu Weigang Ge Wen-Tao Yang Chao You Source Type: research
Faecal microbial transfer and complex carbohydrates mediate protection against COPD
CONCLUSION: The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.PMID:38331563 | DOI:10.1136/gutjnl-2023-330521 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 8, 2024 Category: Genetics & Stem Cells Authors: Kurtis F Budden Shakti D Shukla Kate L Bowerman Annalicia Vaughan Shaan L Gellatly David L A Wood Nancy Lachner Sobia Idrees Saima Firdous Rehman Alen Faiz Vyoma K Patel Chantal Donovan Charlotte A Alemao Sj Shen Nadia Amorim Rajib Majumder Kanth S Vanka Source Type: research
Spatial transcriptomics reveals heterogeneity of histological subtypes between lepidic and acinar lung adenocarcinoma
CONCLUSIONS: These findings illustrate that assessing patient histological subtypes at the single-cell level is feasible. Additionally, tumour endothelial cells that express PD-L1 in stage IA LUAD suppress immune-responsive CD8+ T cells.PMID:38318637 | PMC:PMC10844893 | DOI:10.1002/ctm2.1573 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 6, 2024 Category: Genetics & Stem Cells Authors: Linshan Xie Hui Kong Jinjie Yu Mengting Sun Shaohua Lu Yong Zhang Jie Hu Fang Du Qiuyu Lian Hongyi Xin Jian Zhou Xiangdong Wang Charles A Powell Fred R Hirsch Chunxue Bai Yuanlin Song Jun Yin Dawei Yang Source Type: research
A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1
Nat Commun. 2024 Feb 6;15(1):968. doi: 10.1038/s41467-024-45067-8.ABSTRACTTumor microtubes (TMs) connect glioma cells to a network with considerable relevance for tumor progression and therapy resistance. However, the determination of TM-interconnectivity in individual tumors is challenging and the impact on patient survival unresolved. Here, we establish a connectivity signature from single-cell RNA-sequenced (scRNA-Seq) xenografted primary glioblastoma (GB) cells using a dye uptake methodology, and validate it with recording of cellular calcium epochs and clinical correlations. Astrocyte-like and mesenchymal-like GB cell...
Source: Genomics Proteomics ... - February 6, 2024 Category: Genetics & Stem Cells Authors: Ling Hai Dirk C Hoffmann Robin J Wagener Daniel D Azorin David Hausmann Ruifan Xie Magnus-Carsten Huppertz Julien Hiblot Philipp Sievers Sophie Heuer Jakob Ito Gina Cebulla Alexandros Kourtesakis Leon D Kaulen Miriam Ratliff Henriette Mandelbaum Erik Jung Source Type: research
A Novel Multi-Strain E3 Probiotic Formula Improved the Gastrointestinal Symptoms and Quality of Life in Chinese Psoriasis Patients
Microorganisms. 2024 Jan 19;12(1):208. doi: 10.3390/microorganisms12010208.ABSTRACTPsoriasis is a chronic immune-mediated inflammatory disease affecting the skin and other systems. Gastrointestinal disease was found to be correlated with psoriasis in previous studies and it can significantly affect the quality of life of psoriasis patients. Despite the importance of the gut microbiome in gut and skin health having already been demonstrated in many research studies, the potential effect of probiotics on GI comorbidities in psoriasis patients is unclear. To investigate the effects of probiotics on functional GI comorbidities...
Source: Genomics Proteomics ... - January 26, 2024 Category: Genetics & Stem Cells Authors: Pui Ling Kella Siu Chi Tung Choy Helen Hoi Yin Chan Ross Ka Kit Leung Un Kei Chan Junwei Zhou Chi Ho Wong Yuk Wai Lee Ho Wang Chan Claudia Jun Yi Lo Joseph Chi Ching Tsui Steven King Fan Loo Stephen Kwok Wing Tsui Source Type: research
