Editorial Material
Cell Biology
Gayathri Anandappa, Michael J. Overman
Summary: In a recent study, Amodio and colleagues discovered a method to modulate immunosurveillance in colorectal tumors by manipulating DNA mismatch repair heterogeneity. They found that enriching the MMR deficient component using 6-thioguanine can improve tumor control in murine models.
CELL REPORTS MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Vitaly Shubin, Yury Shelygin, Sergey Achkasov, Oleg Sushkov, Ilya Nazarov, Alexey Ponomarenko, Iuliia Alimova, Anna Loginova, Aleksey Tsukanov
Summary: The aim of this study was to determine the characteristics of Russian patients with microsatellite instability (MSI) tumors. The results showed that patients with MSI tumors differed in the age of diagnosis, tumor localization, time of cancer recurrence, and stage of the disease. Patients whose tumors had MSI status had higher overall and disease-free survival rates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Cristian Perna, Antonia Navarro, Ignacio Ruz-Caracuel, Tamara Caniego-Casas, Eva Cristobal, Susanna Leskela, Federico Longo, Alejandra Caminoa, Almudena Santon, Reyes Ferreiro, David Pizarro, Maria Luisa Palacios-Berraquero, Jose Palacios
Summary: The study characterized the clinicopathological, immunohistochemical, and molecular features of high grade colorectal carcinomas (HG-CRCs), finding that mismatch repair deficiency (MMRd) was a major contributing factor to intertumor and intratumor molecular heterogeneity in HG-CRCs. MMR status conditioned the frequency and clonality of molecular alterations, with distinct molecular differences observed between MMR deficient and MMR proficient tumors.
Article
Biology
Paulina Rzasa, Sarah Whelan, Pooyeh Farahmand, Hong Cai, Inna Guterman, Raquel Palacios-Gallego, Shanthi S. Undru, Lauren Sandford, Caleb Green, Catherine Andreadi, Maria Mintseva, Emma Parrott, Hong Jin, Fiona Hey, Susan Giblett, Nicolas B. Sylvius, Natalie S. Allcock, Anna Straatman-Iwanowska, Roberto Feuda, Cristina Tufarelli, Karen Brown, Catrin Pritchard, Alessandro Rufini
Summary: BRAF mutations occur early in serrated colorectal cancers, but their long-term influence on tissue homeostasis is poorly characterized. Short-term and long-term expression of Braf(V600E) in the intestinal tissue perturbs the homeostasis of intestinal epithelial cells, impairs differentiation of enterocytes, and leads to persistent transcriptional reprogramming.
COMMUNICATIONS BIOLOGY
(2023)
Article
Oncology
Miao-Zhen Qiu, Cai-Yun He, Xin-Hua Yang, Li-Qiong Yang, Jun-Zhong Lin, Da-Lei Zhou, Ya-Kang Long, Wen-Long Guan, Ying Jin, Yu-Hong Li, Feng-Hua Wang, Da-Jun Yang, Rui-Hua Xu
Summary: The study found a high microsatellite instability-high (MSI-H) rate in HER2 mutated cases, but no MSI-H in HER2 amplification cases. Moreover, MSI-H patients with HER2 mutation had worse progression-free survival for programmed death-1 antibody than those without. Further research is needed to explore the internal relationship between HER2 alteration and MSI-H.
Article
Multidisciplinary Sciences
Inas Elsayed, Robert Geraghty, Salwa O. Mekki, Ahmed A. Mohamedani, Susan Ahern, Omer E. H. Salim, Balgis B. M. Khalil, Sawsan Abdelrahim, Suliman H. Suliman, Moawia M. A. Elhassan, Salah O. Salah, Mohamed E. Salih, Abubakr H. Widatalla, Osman S. Abdelhamed, Xiaosheng Wang, Eanna J. Ryan, Des Winter, Salih Bakhiet, Kieran Sheahan
Summary: There is a significant clinical need for molecular pathology services for colorectal cancer in Sudan. In this study, researchers aimed to introduce a molecular genetic service for colorectal cancer in Sudan and explore the molecular features and their relationship to patient survival and clinicopathological characteristics. They found that a subtype of mismatch repair deficient colorectal cancer was present in 16% of cases, and a presumptive diagnosis of Lynch Syndrome was made in 14% of patients. The study also revealed a high mortality rate in Sudanese colorectal cancer patients, which was correlated with advanced disease stage and mismatch repair status.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Kuo-Hsing Chen, Liang-In Lin, Chang-Tsu Yuan, Li-Hui Tseng, Yu-Liang Chao, Yi-Hsin Liang, Jin-Tung Liang, Been-Ren Lin, Ann-Lii Cheng, Kun-Huei Yeh
Summary: In Taiwan, distinct clinicopathological features were identified for CIMP-high CRC among different age groups. Our data suggest the association between BMI >= 27.5 kg/m(2) and CIMP-high CRC in patients younger than 50 years.
BRITISH JOURNAL OF CANCER
(2021)
Article
Oncology
Dung T. Le, Luis A. Diaz Jr, Tae Won Kim, Eric Van Cutsem, Ravit Geva, Dirk Jaeger, Hiroki Hara, Matthew Burge, Bert H. O'Neil, Petr Kavan, Takayuki Yoshino, Rosine Guimbaud, Hiroya Taniguchi, Elena Elez, Salah-Eddin Al-Batran, Patrick M. Boland, Yi Cui, Pierre Leconte, Patricia Marinello, Thierry Andre
Summary: The study demonstrated that Pembrolizumab had durable clinical benefit and manageable safety in previously treated MSI-H/dMMR colorectal cancer patients. It showed persistent antitumor activity, prolonged overall survival, and tolerable safety profile.
EUROPEAN JOURNAL OF CANCER
(2023)
Review
Immunology
Wei-Jian Mei, Mi Mi, Jing Qian, Nan Xiao, Ying Yuan, Pei-Rong Ding
Summary: Colorectal cancers with high microsatellite instability and deficient mismatch repair have different characteristics compared to normal CRC, but the testing rates for MSI and MMR remain low in clinical practice. Insufficient testing fails to identify patients with these types of CRC who could benefit from immunotherapy. Understanding the importance of MMR/MSI status in the clinical characteristics and prognosis of CRC may help improve testing rates and guide the development of more effective therapies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Daisuke Ohki, Nobutake Yamamichi, Yoshiki Sakaguchi, Yu Takahashi, Natsuko Kageyama-Yahara, Mitsue Yamamichi, Chihiro Takeuchi, Yosuke Tsuji, Yasuhiro Sakai, Kouhei Sakurai, Shuta Tomida, Kazuhiko Koike, Mitsuhiro Fujishiro
Summary: This study elucidates the gene expression characteristics of sessile serrated adenoma/polyp (SSA/P), showing a strong resemblance to microsatellite instability-high (MSI-H) colorectal cancer (CRC). The downregulation of CDX2 expression plays an essential molecular mechanism in the initial stage of SSA/P tumorigenesis.
Article
Oncology
Sophia J. Wagner, Daniel Reisenbuechler, Nicholas P. West, Jan Moritz Niehues, Jiefu Zhu, Sebastian Foersch, Gregory Patrick Veldhuizen, Philip Quirke, Heike I. Grabsch, Piet A. van den Brandt, Gordon G. A. Hutchins, Susan D. Richman, Tanwei Yuan, Rupert Langer, Josien C. A. Jenniskens, Kelly Offermans, Wolfram Mueller, Richard Gray, Stephen B. Gruber, Joel K. Greenson, Gad Rennert, Joseph D. Bonner, Daniel Schmolze, Jitendra Jonnagaddala, Nicholas J. Hawkins, Robyn L. Ward, Dion Morton, Matthew Seymour, Laura Magill, Marta Nowak, Jennifer Hay, Viktor H. Koelzer, David N. Church, Christian Matek, Carol Geppert, Chaolong Peng, Cheng Zhi, Xiaoming Ouyang, Jacqueline A. James, Maurice B. Loughrey, Manuel Salto-Tellez, Hermann Brenner, Michael Hoffmeister, Daniel Truhn, Julia A. Schnabel, Melanie Boxberg, Tingying Peng, Jakob Nikolas Kather
Summary: This study develops a new transformer-based pipeline for predicting prognostic biomarkers from colorectal cancer pathology slides. The results show that this approach significantly improves performance, generalizability, data efficiency, and interpretability compared to current algorithms. The method also solves a longstanding diagnostic problem by achieving clinical-grade performance on endoscopic biopsy tissue.
Review
Gastroenterology & Hepatology
An Huang, Yong Yang, Jing-Yi Shi, Yu-Kun Li, Jing-Xuan Xu, Yu Cheng, Jin Gu
Summary: Mucinous adenocarcinoma (MAC) is a unique subtype of colorectal cancer characterized by distinct clinical and molecular features compared to non-MAC (NMAC). MAC is more frequently located in the proximal colon and associated with a poorer prognosis.
WORLD JOURNAL OF GASTROINTESTINAL SURGERY
(2021)
Article
Multidisciplinary Sciences
Olusegun Isaac Alatise, Gregory C. Knapp, Avinash Sharma, Walid K. Chatila, Olukayode A. Arowolo, Olalekan Olasehinde, Olusola C. Famurewa, Adeleye D. Omisore, Akinwumi O. Komolafe, Olaejinrinde O. Olaofe, Aba I. Katung, David E. Ibikunle, Adedeji A. Egberongbe, Samuel A. Olatoke, Sulaiman O. Agodirin, Olusola A. Adesiyun, Ademola Adeyeye, Oladapo A. Kolawole, Akinwumi O. Olakanmi, Kanika Arora, Jeremy Constable, Ronak Shah, Azfar Basunia, Brooke Sylvester, Chao Wu, Martin R. Weiser, Ken Seier, Mithat Gonen, Zsofia K. Stadler, Yelena Kemel, Efsevia Vakiani, Michael F. Berger, Timothy A. Chan, David B. Solit, Jinru Shia, Francisco Sanchez-Vega, Nikolaus Schultz, Murray Brennan, J. Joshua Smith, T. Peter Kingham
Summary: Understanding the molecular and phenotypic profile of colorectal cancer (CRC) in West Africa is crucial for addressing the rising burden of disease, as shown by a study comparing Nigerian CRC patients to those from TCGA and MSKCC. High microsatellite instability, differences in genetic mutations, and presentation characteristics suggest a unique biology of CRC in Nigeria that requires tailored diagnostic and treatment approaches.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Satoshi Fujii, Daisuke Kotani, Masahiro Hattori, Masato Nishihara, Toshihide Shikanai, Junji Hashimoto, Yuki Hama, Takuya Nishino, Mizuto Suzuki, Ayatoshi Yoshidumi, Makoto Ueno, Yoshito Komatsu, Toshiki Masuishi, Hiroki Hara, Taito Esaki, Yoshiaki Nakamura, Hideaki Bando, Tomoyuki Yamada, Takayuki Yoshino
Summary: This study utilized deep learning techniques to extract pathomorphologic features from tissue section images, enabling the accurate prediction of genetic abnormalities in cancer. The results demonstrated high accuracy of this method and its potential for predicting genetic abnormalities without the need for gene tests.
CLINICAL CANCER RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Martino Mezzapesa, Giuseppe Losurdo, Francesca Celiberto, Salvatore Rizzi, Antonio d'Amati, Domenico Piscitelli, Enzo Ierardi, Alfredo Di Leo
Summary: Until 2010, colorectal serrated lesions were generally considered harmless, but recent evidence shows they may develop into colorectal carcinoma. The World Health Organization has classified serrated lesions into four categories and identified SSLs and TSAs as the most common precursors of CRC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Manuel Ugidos, Maria Jose Nueda, Jose M. Prats-Montalban, Alberto Ferrer, Ana Conesa, Sonia Tarazona
Summary: This article introduces the MultiBaC R package, a tool for batch effect removal in multi-omics and hidden batch effect scenarios. It includes various graphical outputs for model validation and assessment of batch effect correction.
Article
Biochemistry & Molecular Biology
Tianyuan Liu, Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Ziva Ramsak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa
Summary: PaintOmics is a web server for integrative analysis of multi-omics data, offering various new analysis features and comprehensive pathway knowledge, providing novel insights into regulatory biology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Neurosciences
Jose Francisco Catala-Senent, Zoraida Andreu, Marta R. Hidalgo, Irene Soler-Saez, Francisco Jose Roig, Natalia Yanguas-Casas, Almudena Neva-Alejo, Adolfo Lopez-Cerdan, Maria de la Iglesia-Vaya, Barbara E. Stranger, Francisco Garcia-Garcia
Summary: This study provides insights into the molecular mechanisms underlying gender differences in multiple sclerosis (MS) by conducting a systematic review and analysis of genome-wide transcriptome studies. The results reveal differential gene expression patterns between male and female patients in various brain and blood tissues, guiding potential personalized treatments for MS based on gender.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Microbiology
Salvador Meseguer, Mari-Paz Rubio, Begona Lainez, Beatriz Perez-Benavente, Raul Perez-Moraga, Sergio Romera-Giner, Francisco Garcia-Garcia, Olalla Martinez-Macias, Antonio Cremades, Francisco J. Iborra, Oscar Candelas-Rivera, Fernando Almazan, Enric Esplugues
Summary: It has been found that levels of SERINC5 are reduced in COVID-19 patients, and the repression of SERINC5 expression may be caused by viral non-coding small RNAs (svRNAs).
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Endocrinology & Metabolism
Maria Guaita-Cespedes, Ruben Grillo-Risco, Marta R. Hidalgo, Sonia Fernandez-Veledo, Deborah Jane Burks, Maria de la Iglesia-Vaya, Amparo Galan, Francisco Garcia-Garcia
Summary: The expression stability of classical housekeeping genes in human adipose tissue varies by sex, indicating that they are not suitable as internal controls. Some new potential housekeeping genes that are not affected by sex bias are proposed.
BIOLOGY OF SEX DIFFERENCES
(2023)
Article
Endocrinology & Metabolism
Carla Perpina-Clerigues, Susana Mellado, Jose F. Catala-Senent, Francesc Ibanez, Pilar Costa, Miguel Marcos, Consuelo Guerri, Francisco Garcia-Garcia, Maria Pascual
Summary: The study shows that drinking alcohol leads to the enrichment of plasma EV lipid species in female adolescents, which is associated with the propagation of neuroinflammatory responses. Gender differences in lipid abundance were also observed in wild-type mice and Toll-like receptor 4 deficient mice. These findings support the potential use of EV-enriched lipids as biomarkers of ethanol-induced neuroinflammation.
BIOLOGY OF SEX DIFFERENCES
(2023)
Review
Oncology
Irene Perez-Diez, Zoraida Andreu, Marta R. Hidalgo, Carla Perpina-Clerigues, Lucia Fantin, Antonio Fernandez-Serra, Maria de la Iglesia-Vaya, Jose A. Lopez-Guerrero, Francisco Garcia-Garcia
Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease with limited treatment options. The desmoplastic stroma and immune system evasion in PDAC pose challenges to therapeutic strategies. Characterizing the PDAC microenvironment is crucial for developing effective therapies. A meta-analysis identified 1153 dysregulated genes involved in extracellular matrix remodeling and the immune system. The study also identified immune gene signatures and stromal gene signatures associated with PDAC patients' survival, and discovered new immune genes associated with PDAC prognosis.
Article
Biophysics
Maria del Mar Alvarez-Torres, Adolfo Lopez-Cerdan, Zoraida Andreu, Maria de la Iglesia Vaya, Elies Fuster-Garcia, Francisco Garcia-Garcia, Juan M. Garcia-Gomez
Summary: Global agreement in CNS tumor classification is crucial for patient prognosis, treatment decisions, and international clinical trials. The latest update by the World Health Organization recognized IDH-wildtype glioblastoma and astrocytoma IDH-mutant grade 4 as distinct tumors. IDH mutations contribute to gliomagenesis by affecting tumor cell metabolism and hypoxia processes. Alternative biomarkers, such as MRI-perfusion biomarkers, could provide a reliable and cost-effective classification for CNS tumors.
NMR IN BIOMEDICINE
(2023)
Review
Oncology
Benjamin Perez-Aguilar, Jens U. Marquardt, Encarnacion Munoz-Delgado, Rosa Maria Lopez-Duran, Maria Concepcion Gutierrez-Ruiz, Luis E. Gomez-Quiroz, Jose Luis Gomez-Olivares
Summary: The cholinergic system, specifically acetylcholine receptors (AChR) and acetylcholine (ACh), has been found to play a role in cancer development. Acetylcholinesterase (AChE), which regulates AChR by hydrolyzing ACh, has been observed to have a relevant role in cancer. However, there is controversy regarding AChE's participation in cancer, as its enzymatic activity can either increase or decrease in different tumors. This review focuses on analyzing the involvement of AChE in cancer progression and proposes AChE as a central regulator in the initiation and progression of cancer via the cholinergic system. Modulating ACh levels with AChE can regulate AChRs differentially, leading to diverse cancer events.
Article
Cell Biology
Marian Leon, Javier Prieto, Maria Micaela Molina-Navarro, Francisco Garcia-Garcia, Manuela Barneo-Munoz, Xavier Ponsoda, Rosana Saez, Francesc Palau, Joaquin Dopazo, Juan Carlos Izpisua Belmonte, Josema Torres
Summary: Charcot-Marie-Tooth disease is a chronic hereditary motor and sensory polyneuropathy affecting Schwann cells and motor neurons. The loss of function of the GDAP1 gene leads to altered mitochondrial morphology, activation of autophagy, abnormal metabolism, increased reactive oxygen species, and an elevated innate immune response. Understanding these cellular and molecular phenotypes could lead to the development of therapies for this disease.
CELL DEATH DISCOVERY
(2023)
Article
Art
Francisco Jose Gil-Ruiz, Francisco Garcia-Garcia
Summary: The article examines the representation of scientific communicators in the film Don't Look Up (Adam McKay, 2021). It analyzes the relationships between cinema, science, and pragmatics, and focuses on the roles of scientists, technological producers, communicators, politicians, and citizens. The study uses a model of pragmatic obligations to analyze the interactions between these agents and presents the findings in a relationship map. The results suggest that scientists are more likely to fulfill their obligations to the truth, while political power and producer-technology have a weaker connection to it. Communicators and citizens generally only partially fulfill their respective obligations. Furthermore, except for two scientists, all roles face challenges in effectively communicating the truth, and the influence of political power on truth administration is highlighted.
FOTOCINEMA-REVISTA CIENTIFICA DE CINE Y FOTOGRAFIA
(2023)
Letter
Biochemistry & Molecular Biology
Francisco J. Iborra, Cristina Marti, Virtu Calabuig-Navarro, Petros Papadopoulos, Salvador Meseguer, Pedro M. Iborra, Francisco Garcia, Antonio Martinez-Lorente, Fernando Almazan, Juana Calabuig
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Article
Biotechnology & Applied Microbiology
Jorge Mestre-Tomas, Tianyuan Liu, Francisco Pardo-Palacios, Ana Conesa
Summary: SQANTI-SIM is a versatile tool that wraps around popular long-read simulators, allowing precise management of transcript novelty based on the structural categories defined by SQANTI3. It effectively emulates scenarios involving unannotated transcripts and supports the simulation of additional types of data, making it the first multi-omics simulation tool for the lrRNA-seq field.
Article
Computer Science, Information Systems
Jesus Alejandro Alzate-Grisales, Alejandro Mora-Rubio, Francisco Garcia-Garcia, Reinel Tabares-Soto, Maria de la Iglesia-Vaya
Summary: This study presents a novel model, SAM-UNETR, for segmenting clinically significant prostate cancer regions from MRI images. SAM-UNETR combines the features of Segment Anything Model and UNETR, and uses multiple image modalities and preprocessing steps to improve accuracy. Compared with three other models, SAM-UNETR achieves higher reliability and accuracy in csPCa segmentation.
Article
Biotechnology & Applied Microbiology
Rachel M. Miller, Ben T. Jordan, Madison M. Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou, Simi Kaur, Robert J. Millikin, Yunxiang Dai, Simone Tiberi, Peter J. Castaldi, Michael R. Shortreed, Chance John Luckey, Ana Conesa, Lloyd M. Smith, Anne Deslattes Mays, Gloria M. Sheynkman
Summary: We describe a long-read proteogenomics approach that integrates long-read RNA-seq and MS-based proteomics data, enhancing the characterization of protein isoforms. The incorporation of long-read sequencing and proteomic data facilitates improved understanding of human protein isoform diversity.