Article
Oncology
Karoline Andersen, Kasper Holm, Mette Tranberg, Cecilie Lebech Pedersen, Sara Bonlokke, Torben Steiniche, Berit Andersen, Magnus Stougaard
Summary: This study demonstrates the use of a targeted HPV next generation sequencing (NGS) panel for cervical cancer screening. The targeted panel shows similar sensitivity and specificity to commercial HPV assays, but also provides additional advantages such as specific detection of all relevant HPV types and identification of viral integration and variants.
Article
Pathology
J. Lippert, S. Bonlokke, A. Utke, B. R. Knudsen, B. S. Sorensen, T. Steiniche, M. Stougaard
Summary: The study demonstrates that targeted NGS is effective in detecting and genotyping HPV in both FFPE biopsies and plasma samples. This method provides early diagnosis and prognosis for cervical cancer progression, enhancing recovery and survival potential for patients.
EXPERIMENTAL AND MOLECULAR PATHOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Pasquale Tripodi
Summary: This review examines the application of genomic technologies in studying the diversity of tomatoes, with a focus on next-generation sequencing strategies and methods. It also discusses how genomics has provided insights into the domestication process of tomatoes and presents perspectives on utilizing natural variation for breeding purposes through pan-genome construction and graphical pan-genome development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Virology
Laila Sara Arroyo Muhr, Daniel Guerendiain, Kate Cuschieri, Karin Sundstrom
Summary: NGS technology provides powerful opportunities for HPV genomics research, but rigorous validation and quality assurance procedures are essential to ensure reliable interpretation of results. Recommendations for optimizing sequencing data yield and curated bioinformatical procedures are crucial for robust analysis of HPV genotypes and mutations. International standards for quality assurance in HPV NGS should be developed to enhance testing and diagnostics in global efforts.
Article
Virology
Sharonjit K. Dhillon, Pui Yan Jenny Chung, Elizaveta Padalko, Marleen Praet, Ana Rita Pereira, Nina Redzic, Davy Vanden Broeck, Marc Arbyn
Summary: The implementation of cervical screening based on HPV is rapidly progressing worldwide, and this study evaluates the reproducibility of the RIATOL-qPCR assay. The study found that this detection method demonstrates good reproducibility both within and between laboratories. The assay fulfills the reproducibility requirement for HPV testing in cervical cancer screening.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Medicine, General & Internal
Junqiu Xiang, Long Han, Yanfei Fan, Bin Feng, Haoqing Wu, Chunmin Hu, Manli Qi, Huiping Wang, Quanzhong Liu, Yuanjun Liu
Summary: HPV prevalence was high among both male and female patients at the STD clinic, with HPV6 being the most common genotype. Single HPV subtype infection was predominant in both sexes.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2021)
Article
Microbiology
Jane Shen-Gunther, Qingqing Xia, Hong Cai, Yufeng Wang
Summary: Through customization of a papillomavirus database and the CLC Microbial Genomics Module, automated workflows were developed for HPV taxonomic profiling and visualization, resulting in a fast method for virome profiling.
Article
Oncology
Ariana Rostami, Scott Bratman, Kathy Han
Summary: Liquid biopsy approaches for detecting viral DNA play a crucial role in diagnosing virally-associated cancers. The CaptHPV method based on next-generation sequencing is discussed for its potential in detecting plasma HPV DNA in HPV-associated cancers and its potential clinical utility.
CLINICAL CANCER RESEARCH
(2021)
Article
Pharmacology & Pharmacy
Samuel D. Chorlton, Gordon Ritchie, Tanya Lawson, Elizabeth McLachlan, Marc G. Romney, Nancy Matic, Christopher F. Lowe
Summary: A next-generation sequencing (NGS) assay was developed for CMV antiviral drug resistance (AVDR) testing, which using MinION technology detected additional mutations compared to traditional Sanger sequencing. Through the application of an online bioinformatics pipeline, barriers associated with MinION and NGS in clinical laboratories were eliminated.
ANTIVIRAL RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati, Bruna Scaggiante
Summary: The poor survival of triple-negative breast cancer (TNBC) is attributed to its aggressive behavior, large heterogeneity, and high risk of recurrence. Next-generation sequencing (NGS) has been used to investigate the molecular characteristics of TNBC, revealing recurrent pathogenic alterations in TP53, immunocheckpoint response genes, and PIK3CA and DNA repair pathways. NGS has also identified potential personalized treatments and novel biomarkers such as AURKA, MYC, and JARID2 mutations. Additionally, NGS studies have identified ethnicity-specific alterations in African and African American TNBC, including EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation. The development of long-read sequencing methods and their combination with optimized short-read techniques hold promise for improving the efficiency of NGS approaches in future clinical use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Mark H. Stoler, Thomas C. Wright Jr, Valentin Parvu, Karen Yanson, Charles K. Cooper, Jeffrey A. Andrews
Summary: The Onclarity cervical cancer screening trial aims to establish the clinical efficacy of the Onclarity HPV assay for extended genotyping. Three-year follow-up data shows that this screening strategy has better sensitivity and a lower colposcopy/lesion ratio compared to baseline data.
GYNECOLOGIC ONCOLOGY
(2023)
Article
Virology
Fernanda L. S. G. Santos, Maria C. V. Invencao, Edilaine D. Araujo, Gerlane S. Barros, Marcus V. A. Batista
Summary: This study evaluated the effectiveness of three different PCR-based strategies for HPV detection and genotyping from cervical samples. The results showed that different primer design strategies influenced the sensitivity and specificity of detecting different HPV types. EntroA primers were able to detect HPV in more samples compared to MY09/MY11, while multiplex PCR had higher sensitivity despite targeting a limited number of HPV types.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Immunology
Ferhat Guzel, Micol Romano, Erdi Keles, David Piskin, Seza Ozen, Hakan Poyrazoglu, Ozgur Kasapcopur, Erkan Demirkaya
Summary: This study describes the development and validation of an NGS-based multiplex array for targeted sequencing of nine genes associated with common AIDs, offering a cost-effective, comprehensive, and informative screening tool compared to other methods.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Medicine, Research & Experimental
Alice Avian, Nicolo Clemente, Elisabetta Mauro, Erica Isidoro, Michela Di Napoli, Sandra Dudine, Anna Del Fabro, Stefano Morini, Tiziana Perin, Fabiola Giudici, Tamara Cammisuli, Nicola Foschi, Marco Mocenigo, Michele Montrone, Chiara Modena, Martina Polenghi, Luca Puzzi, Vjekoslav Tomaic, Giulio Valenti, Riccardo Sola, Shivani Zanolla, Enea Vogrig, Elisabetta Riva, Silvia Angeletti, Massimo Ciccozzi, Santina Castriciano, Maria Pachetti, Matteo Petti, Sandro Centonze, Daniela Gerin, Lawrence Banks, Bruna Marini, Vincenzo Canzonieri, Francesco Sopracordevole, Fabrizio Zanconati, Rudy Ippodrino
Summary: According to the study, HPV Selfy, a full-genotyping HPV DNA test, meets the criteria for primary cervical cancer screening described in international guidelines and shows good performance on both clinician-collected and self-collected samples.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Medicine, Research & Experimental
Fabiola Hernandez-Rosas, Erika Orozco-Hernandez, Liliana Maza-Sanchez, Pamela Citlalli Salgado-Garcia, Enrique Navarro-Vidal, Mercedes Piedad de Leon-Bautista
Summary: The study found a high prevalence of HPV infection in Mexican women, with risk factors such as lifetime sexual partners and smoking. Common HPV genotypes in healthy women included 6, 31, and HR-HPV was associated with a low frequency of cytological abnormalities and CIN1-3 occurrences.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2021)
Article
Oncology
Carlos A. Barron-Gallardo, Mariel Garcia-Chagollan, Andres J. Moran-Mendoza, Raul Delgadillo-Cristerna, Maria G. Martinez-Silva, Adriana Aguilar-Lemarroy, Luis F. Jave-Suarez
Summary: Breast cancer is a complex disease with distinct molecular profiles. This study analyzed the gene expression of breast cancer patients who received neoadjuvant chemotherapy and identified differentially expressed genes associated with chemotherapy response and overall survival.
TECHNOLOGY IN CANCER RESEARCH & TREATMENT
(2022)
Editorial Material
Oncology
Natalia Garcia-Becerra, Adriana Aguilar-Lemarroy, Luis F. Jave-Suarez
Summary: Cervical cancer is a prevalent pathology in females and is the second leading cause of cancer-related deaths in developing countries. The development of cervical cancer is primarily caused by persistent infection with high-risk human papillomavirus. NF-kappa B signaling pathway plays a critical role in the development of cervical cancer.
ANTI-CANCER AGENTS IN MEDICINAL CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
Miguel Angel Garcia-Gonzalez, Veronica Vallejo-Ruiz, Fausto Atonal-Flores, Jorge Flores-Hernandez, Oswaldo Torres-Ramirez, Alfonso Diaz-Fonsecae, Francisco Perez Vizcaino, Jose Gustavo Lopez-Lopez
Summary: Chronic treatment with sildenafil has beneficial effects on pulmonary arterial pressure, right ventricular hypertrophy, and heart rate variability in rats with secondary pulmonary hypertension caused by type 1 diabetes.
CLINICAL AND EXPERIMENTAL HYPERTENSION
(2022)
Article
Oncology
Aribert Maryosly Castro-Amaya, Leonardo Fernandez-Avila, Carlos Alfredo Barron-Gallardo, Carlos Eliu Moreno-Rios, Sarah Naomi Guevara-Hernandez, Maria Teresa Magana-Torres, Clarisa Jazmin Pelayo-Aguirre, Luis Felipe Jave-Suarez, Adriana Aguilar-Lemarroy
Summary: This study reveals the transformative potential of Beta-2 Human papillomaviruses, especially HPV122, in cervical cancer samples from western Mexico. These viruses can modulate genes regulated by Alpha-HPVs and utilize alternative strategies to modulate diverse signaling pathways, potentially playing an important role in co-infections during carcinogenesis.
EXPERIMENTAL CELL RESEARCH
(2022)
Article
Oncology
Natalia Garcia-Becerra, Marco Ulises Aguila-Estrada, Luis Arturo Palafox-Mariscal, Georgina Hernandez-Flores, Adriana Aguilar-Lemarroy, Luis Felipe Jave-Suarez
Summary: FOXP3 is a critical transcription factor that plays a key role in the regulation of the lymphoid lineage. It has been found to be highly expressed in cervical cancer cells, and its isoform FOXP3 delta,2 delta,7 promotes proliferation, cell division, and migration in non-tumorigenic keratinocytes. RNAseq analysis revealed that FOXP3 delta,2 delta,7 induces the expression of protooncogenes and modulates essential pathways related to immune response and tumorigenic process.
Article
Medicine, General & Internal
Jessica Alejandra Zapata-Garcia, Alma Rocio Riveros-Magana, Pablo Cesar Ortiz-Lazareno, Georgina Hernandez-Flores, Luis Felipe Jave-Suarez, Adriana Aguilar-Lemarroy
Summary: This study identified genes present in chromosomal gain regions more frequently found in patients with acute lymphoblastic leukemia (ALL) using comparative genomic hybridization (CGH) and RNAseq. Several genes were found to be overexpressed in ALL cell lines and patients, including SALL2 in T-ALL and JUP in B-ALL, which correlated with worse patient prognosis.
Article
Biochemistry & Molecular Biology
Maryam Nasiri-Aghdam, Mariel Garcia-Chagollan, Ana Laura Pereira-Suarez, Adriana Aguilar-Lemarroy, Luis Felipe Jave-Suarez
Summary: Infection of epithelial cells with high-risk HPV types and expression of virus oncogenic proteins can lead to genomic imbalance, suppression of tumor inhibitors, and induction of oncogenes. Co-infection with low-risk HPV may decrease the risk of future invasive cancer. By comparing the functional differences between LR-HPV and HR-HPV, we can distinguish cancer-progressing changes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Brenda-Eugenia Martinez-Herrera, Leonardo-Xicotencatl Gutierrez-Rodriguez, Benjamin Trujillo-Hernandez, Michelle-Guadalupe Munoz-Garcia, Luz-Maria Cervantes-Gonzalez, Laura-Liliana Jose Ochoa, Javier-Andres Gonzalez-Rodriguez, Alejandro Solorzano-Melendez, Eduardo Gomez-Sanchez, Gabriela-Guadalupe Carrillo-Nunez, Mario Salazar-Paramo, Arnulfo-Hernan Nava-Zavala, Martha-Cecilia Velazquez-Flores, Carlos-M. Nuno-Guzman, Mario-Alberto Mireles-Ramirez, Luz-Ma. -Adriana Balderas-Pena, Daniel Sat-Munoz
Summary: This study focuses on the differences in phase angle as a predictor of prognosis, quality of life, and mortality in head and neck cancer patients. The results show that patients with low phase angle have worse nutritional and biochemical indicators, as well as lower quality of life scores. There are significant disparities between sexes, with malnourishment and tumor cachexia being more evident in women.
Article
Medicine, General & Internal
Maria-Fatima Chilaca-Rosas, Manuel-Tadeo Contreras-Aguilar, Melissa Garcia-Lezama, David-Rafael Salazar-Calderon, Raul-Gabriel Vargas-Del-Angel, Sergio Moreno-Jimenez, Patricia Pina-Sanchez, Raul-Rogelio Trejo-Rosales, Felipe-Alfredo Delgado-Martinez, Ernesto Roldan-Valadez
Summary: This study aimed to identify the radiomic features that can distinguish between tumor regions (viable tumor and peritumoral edema) of diffuse midline gliomas (DMG) in patients with the H3.F3K27M mutation and equivalent midline normal tissue (EMNT). The results showed that only a small number of radiomic features could identify tumor regions in both the T1 and T2 sequences of conventional magnetic resonance imaging, providing important support for diagnosis, patient classification, and multimodality cancer treatment planning.
Article
Biochemistry & Molecular Biology
Leonardo Fernandez-Avila, Aribert Maryosly Castro-Amaya, Andrea Molina-Pineda, Rodolfo Hernandez-Gutierrez, Luis Felipe Jave-Suarez, Adriana Aguilar-Lemarroy
Summary: Cervical cancer is a major global health issue, and this study reveals that HPV16 and 18 oncoproteins, E6/E7, can regulate the expression of various chemokines, which are overexpressed in cervical cancer tissues and associated with poorer survival prognosis.
Article
Health Care Sciences & Services
Faviola Gonzalez-Barba, Luz-Ma. -Adriana Balderas-Pena, Benjamin Trujillo-Hernandez, Luz-Maria Cervantes-Gonzalez, Javier-Andres Gonzalez-Rodriguez, Leonardo-Xicotencatl Gutierrez-Rodriguez, Adriana Alvarado-Zermeno, Aldo-Antonio Alcaraz-Wong, Eduardo Gomez-Sanchez, Gabriela-Guadalupe Carrillo-Nunez, Mario Salazar-Paramo, Arnulfo-Hernan Nava-Zavala, Benjamin Rubio-Jurado, Mario-Alberto Mireles-Ramirez, Brenda-Eugenia Martinez-Herrera, Daniel Sat-Munoz
Summary: The phase angle, an indicator of muscle mass status and membrane cell integrity, has been found to be associated with negative outcomes in women with uterine cervical cancer. In a study with 65 participants, the low phase angle group exhibited higher levels of inflammation and poorer quality of life compared to the normal phase angle group. Additionally, the interaction between phase angle and obesity was found to be an important factor in different histologic subtypes of uterine cervical cancer.
Article
Engineering, Biomedical
L. G. De la Torre-Gutierrez, B. E. Martinez-Zerega, D. O. Oseguera-Galindo, A. Aguilar-Lemarroy, L. F. Jave-Suarez, L. A. Torres-Gonzalez, J. L. Gonzalez-Solis
Summary: This study monitored breast cancer patients undergoing chemotherapy using blood serum sample Raman spectroscopy and multivariate analysis. The results showed good discrimination between healthy individuals and clinically diagnosed breast cancer patients, with sensitivity and specificity rates of 87.14% and 90.55% respectively. Although no shifts in peak positions were found, differences in intensity were observed in certain peaks associated with amino acids, phospholipids, and glutathione. Monitoring six breast cancer patients during their chemotherapy treatments confirmed the potential correlation between the intensity of the 450 cm(- 1) Raman peak and the cancer progression. Overall, Raman spectroscopy and multivariate analysis were found to be effective in breast cancer detection and monitoring, providing less invasive alternatives to other methods.
LASERS IN MEDICAL SCIENCE
(2022)