Review
Biochemistry & Molecular Biology
Xin Liu, Jiayu Chen, Wenliang Chen, Yangtao Xu, Yang Shen, Ximing Xu
Summary: RNA-binding proteins play a crucial role in regulating various pathways by binding to RNAs. IGF2BP3, a component of m6A binding proteins, is involved in decoding m6A marks and performing diverse biological functions. Abnormal expression of IGF2BP3 is often associated with poor prognosis in human cancers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Tom R. Booker, Bret A. Payseur, Anna Tigano
Summary: Recombination rate evolution can affect genetic variation under BGS, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, evidence suggests that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Tommaso Grassi, Faye R. Harris, James B. Smadbeck, Stephen J. Murphy, Matthew S. Block, Francesco Multinu, Janet L. Schaefer Klein, Piyan Zhang, Giannoula Karagouga, Minetta C. Liu, Alyssa Larish, Maureen A. Lemens, Marla Kay S. Sommerfield, Serena Cappuccio, John C. Cheville, George Vasmatzis, Andrea Mariani
Summary: This pilot study demonstrates the feasibility of using personalized tumor-specific junction panels for detecting ctDNA in the plasma of endometrial cancer patients. Larger studies and longer follow-up are needed to validate the potential association between pre-surgical ctDNA detection and the presence of cancers with aggressive pathologic tumor characteristics or advanced stage observed in this study.
Review
Cell Biology
Salvador Alonso, Lukas E. Dow
Summary: The advancements and innovations in technology have made it easier and more accurate to model cancer-associated chromosomal rearrangements in the laboratory, aiding in a better understanding of the mechanisms that regulate cancer growth.
DISEASE MODELS & MECHANISMS
(2021)
Article
Genetics & Heredity
Kristina Keuper, Angela Wieland, Markus Raeschle, Zuzana Storchova
Summary: Cancer genome sequencing has revealed a complex landscape of chromosomal variants and alterations, providing insights into the molecular mechanisms underlying chromosomal aberrations formation.
Article
Oncology
Denis Eriksonovich Demin, Matvey Mikhailovich Murashko, Aksinya Nicolaevna Uvarova, Ekaterina Mikhailovna Stasevich, Elena Yurievna Shyrokova, Gennady Efimovich Gorlachev, Andrew Rostislavovich Zaretsky, Kirill Viktorovich Korneev, Alina Sergeevna Ustiugova, Elena Andreevna Tkachenko, Valentina Vitalevna Kostenko, Karina Aleksandrovna Tatosyan, Saveliy Andreevich Sheetikov, Pavel Vladimirovich Spirin, Dmitry Vladimirovich Kuprash, Anton Markovich Schwartz
Summary: The importance of long non-coding RNAs (lncRNAs) in various areas, including tumor biology, is unquestionable based on the flurry of publications dedicated to their functions in the last decade. However, their contribution to the early stages of oncogenesis is still poorly understood. In this study, we discovered a new role for lncRNAs in stimulating specific chromosomal rearrangements in response to DNA damage. Specifically, we demonstrated that lncRNA CASTL1 (ENSG00000269945) promotes the formation of the CCDC6-RET inversion (RET/PTC1) in human thyroid cells exposed to radiation or chemical DNA damage. The findings suggest a new avenue for studying early oncogenesis in various tumor types, particularly those associated with DNA damage.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Hematology
Evan J. Barnes, Christopher A. Eide, Andy Kaempf, Daniel Bottomly, Kyle A. Romine, Beth Wilmot, Dominick Saunders, Shannon K. McWeeney, Cristina E. Tognon, Brian J. Druker
Summary: Drug resistance in chronic myeloid leukaemia (CML) can be caused by mutations in the BCR::ABL1 fusion or BCR::ABL1-independent mechanisms. This study found that secondary fusion genes contribute to BCR::ABL1-independent resistance in CML patients. Specifically, the expression of RUNX1::MECOM leads to resistance to ABL1 tyrosine kinase inhibitors. These findings suggest that combined therapies could be effective in combating drug resistance.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Oncology
Qiang Ma, Feifei Yang, Bo Huang, Xiaojuan Pan, Wei Li, Ting Yu, Xiaolin Wang, Lingyu Ran, Kun Qian, Hui Li, Haiping Li, Yuying Liu, Ce Liang, Junwu Ren, Yuying Zhang, Shimin Wang, Bin Xiao
Summary: This study identified a novel circular RNA, circARID1A, that can bind to the IGF2BP3 protein. CircARID1A was significantly upregulated in gastric cancer tissues and positively correlated with tumor characteristics. Knocking down circARID1A inhibited the proliferation of gastric cancer cells. Mechanistically, circARID1A acted as a scaffold to facilitate the interaction between IGF2BP3 and SLC7A5 mRNA, thereby increasing the stability of SLC7A5 mRNA and promoting gastric cancer proliferation through the AKT/mTOR pathway.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Paul Banse, Juliette Luiselli, David P. Parsons, Theotime Grohens, Marco Foley, Leonardo Trujillo, Jonathan Rouzaud-Cornabas, Carole Knibbe, Guillaume Beslon
Summary: While little is known about the evolutionary significance of chromosomal rearrangements, the study using Aevol simulation platform shows that chromosomal rearrangements make decisive contributions to evolutionary dynamics by expanding the gene repertoire, reducing the effect of diminishing-returns epistasis, and regulating the size of the genome through indirect selection for reproductive robustness.
Article
Biochemistry & Molecular Biology
Tim Connallon, Colin Olito
Summary: Chromosomal inversions play a substantial role in genome evolution, with the length of inversions affecting their evolutionary fates across different types. Small rearrangements contribute the most to genome evolution under neutral and underdominant scenarios, while directly beneficial inversions prefer small rearrangements for fixation and maintain intermediate-to-large inversions as balanced polymorphisms.
Review
Oncology
Concetta Federico, Francesca Bruno, Denise Ragusa, Craig S. Clements, Desiree Brancato, Marianne P. Henry, Joanna M. Bridger, Sabrina Tosi, Salvatore Saccone
Summary: Recent research has made significant progress in understanding the spatial organization of the genome within the cell nucleus and its implications for diseases like cancer. The spatial positioning of genes within the nucleus is closely related to gene expression, with disruptions in genome organization potentially leading to diseases like cancer. Further studies on radial gene positioning and its correlation to gene expression in cancer are needed to enhance our understanding of the biological mechanisms underlying cancer initiation and progression.
Review
Oncology
Elisabetta Macerola, Anello Marcello Poma, Paola Vignali, Alessio Basolo, Clara Ugolini, Liborio Torregrossa, Ferruccio Santini, Fulvio Basolo
Summary: Thyroid tumors derived from follicular cells are heterogeneous in nature, with variable morphological appearance and differentiation levels. Molecular markers play a significant role in both diagnostic and prognostic stratification, especially in the presurgical setting and for identifying genetic alterations related to prognosis. The advent of targeted drugs has further emphasized the importance of molecular characterization in guiding therapeutic strategies for patients with advanced tumors.
Article
Endocrinology & Metabolism
Antonio Di Cristofano
Summary: Over the past two years, there have been significant developments in basic and translational thyroid cancer research, covering areas such as genetics, genomics, molecular biology, and signaling. These studies have not only shed new light on long-standing scientific questions but have also highlighted the major challenges and unanswered questions that will need to be addressed in the future.
Review
Cell Biology
Kornsorn Srikulnath, Syed Farhan Ahmad, Worapong Singchat, Thitipong Panthum
Summary: Vertebrates, with over 70,000 living species, play a significant role in biology and research, especially in the study of karyotype evolution. The mysterious presence of microchromosomes in many vertebrate karyotypes raises questions about their evolutionary origins and unique genome structure characteristics. Recent studies have shed light on the high gene densities, low heterochromatin levels, and high recombination rates of microchromosomes, expanding our understanding of karyotype evolution dynamics.
Article
Genetics & Heredity
Jesper Eisfeldt, Maria Pettersson, Anna Petri, Daniel Nilsson, Lars Feuk, Anna Lindstrand
Summary: This study reported a healthy female carrying two novel CCRs and characterized these complex rearrangements. The results were validated using multiple cytogenetic methods, revealing the highest number of breakpoint junctions (137) and indicating an association between CCR formation and active gene transcription.
Letter
Medical Laboratory Technology
William E. Gooding, Simion I. Chiosea
DIAGNOSTIC CYTOPATHOLOGY
(2021)
Article
Oncology
Michael S. Landau, Yuri E. Nikiforov, N. Paul Ohori, Simion I. Chiosea
Summary: Some FNHCT nodules are AFTNs and oncocytic metaplasias, detectable based on characteristic mutations or lack of alterations on molecular testing. GH-CNAs characterize approximately half of histologically confirmed follicular oncocytic neoplasms among resected FNHCTs.
CANCER CYTOPATHOLOGY
(2021)
Article
Biochemical Research Methods
Cemal Erdem, Adrian V. Lee, D. Lansing Taylor, Timothy R. Lezon
Summary: Insulin and insulin-like growth factor I (IGF1) receptors play a crucial role in the risk and advancement of various cancer types by activating cell survival cascades. A dual receptor computational model identified the role of ribosomal protein S6 kinase in regulating MAPK and Akt activation levels in response to Ins and IGF1 stimulation. The study suggests potential new targets for anti-IGF1R cancer therapy.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biology
Sara Sannino, Megan E. Yates, Mark E. Schurdak, Steffi Oesterreich, Adrian Lee, Peter Wipf, Jeffrey L. Brodsky
Summary: Breast cancer cells exhibit varying levels of resistance to Hsp70 inhibition, with highly resistant cells showing increased levels of autophagy. Resistance to compromised Hsp70 function depends on the integrated stress response transducer GCN2, while sensitive cells activate PERK in response to Hsp70 inhibition.
Article
Oncology
Zheqi Li, Yang Wu, Megan E. Yates, Nilgun Tasdemir, Amir Bahreini, Jian Chen, Kevin M. Levine, Nolan M. Priedigkeit, Azadeh Nasrazadani, Simak Ali, Laki Buluwela, Spencer Arnesen, Jason Gertz, Jennifer K. Richer, Benjamin Troness, Dorraya El-Ashry, Qiang Zhang, Lorenzo Gerratana, Youbin Zhang, Massimo Cristofanilli, Maritza A. Montanez, Prithu Sundd, Callen T. Wallace, Simon C. Watkins, Caterina Fumagalli, Elena Guerini-Rocco, Li Zhu, George C. Tseng, Nikhil Wagle, Jason S. Carroll, Paul Jank, Carsten Denkert, Maria M. Karsten, Jens-Uwe Blohmer, Ben H. Park, Peter C. Lucas, Jennifer M. Atkinson, Adrian Lee, Steffi Oesterreich
Summary: This study demonstrated the potential role of ESR1 mutations in distant recurrence of breast cancer. Through transcriptomic profiling and functional experiments, it was shown that ESR1 mutations altered the cell adhesive gene network, leading to enhanced cell-cell contacts and decreased cell-extracellular matrix adhesion. Additionally, ESR1-mutant cells formed larger and more compact multicellular circulating tumor cell clusters in vivo, and ESR1 mutations were associated with enrichment of circulating tumor cell clusters in metastatic breast cancer patients.
Article
Oncology
Mattia Marinucci, Caner Ercan, Stephanie Taha-Mehlitz, Lana Fourie, Federica Panebianco, Gaia Bianco, John Gallon, Sebastian Staubli, Savas D. Soysal, Andreas Zettl, Stephan Rauthe, Juerg Vosbeck, Raoul A. Droeser, Martin Bolli, Ralph Peterli, Markus von Fluee, Charlotte K. Y. Ng, Otto Kollmar, Mairene Coto-Llerena, Salvatore Piscuoglio
Summary: The use of patient-derived organoids (PDO) has become increasingly important in cancer research. In this study, we tested different washing solutions to prevent contamination in organoid cultures and found that phosphate-buffered saline (PBS) and PBS with penicillin/streptomycin reduced the contamination rate, while PBS with Primocin completely eliminated contamination. Interestingly, the addition of penicillin/streptomycin negatively impacted organoid growth.
FRONTIERS IN ONCOLOGY
(2022)
Review
Ethics
Margaret Rosenzweig, Lori A. Miller, Adrian Lee, Steffi Oesterreich, Humberto E. Trejo Bittar, Jennifer M. Atkinson, Ann Welsh
Summary: Establishing an autopsy/tissue donation programme for breast cancer research requires considerations such as patient engagement, family recruitment, the role of a clinical coordinator, regulatory issues, and coordination with pathology and research teams. The successful development and implementation of such a programme are feasible.
NEW BIOETHICS-A MULTIDISCIPLINARY JOURNAL OF BIOTECHNOLOGY AND THE BODY
(2021)
Article
Biology
Gaia Bianco, Mairene Coto-Llerena, John Gallon, Venkatesh Kancherla, Stephanie Taha-Mehlitz, Mattia Marinucci, Martina Konantz, Sumana Srivatsa, Hesam Montazeri, Federica Panebianco, Vijaya G. Tirunagaru, Marta De Menna, Viola Paradiso, Caner Ercan, Ahmed Dahmani, Elodie Montaudon, Niko Beerenwinkel, Marianna Kruithof-de Julio, Luigi M. Terracciano, Claudia Lengerke, Rinath M. Jeselsohn, Robert C. Doebele, Francois-Clement Bidard, Elisabetta Marangoni, Charlotte K. Y. Ng, Salvatore Piscuoglio
Summary: This study reveals the synthetic lethal interaction between GATA3 and MDM2 in ER-positive breast cancer, suggesting MDM2 inhibition as a potential therapeutic target for this subgroup of patients.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alexandra Gyurdieva, Stefan Zajic, Ya-Fang Chang, E. Andres Houseman, Shan Zhong, Jaegil Kim, Michael Nathenson, Thomas Faitg, Mary Woessner, David C. Turner, Aisha N. Hasan, John Glod, Rosandra N. Kaplan, Sandra P. D'Angelo, Dejka M. Araujo, Warren A. Chow, Mihaela Druta, George D. Demetri, Brian A. Van Tine, Stephan A. Grupp, Gregg D. Fine, Ioanna Eleftheriadou
Summary: This study identifies potential predictive and pharmacodynamic markers of response to NY-ESO-1 T-cell therapy in a solid tumor, which may inform lymphodepletion, cell dose, and strategies to enhance anticancer efficacy.
NATURE COMMUNICATIONS
(2022)
Article
Endocrinology & Metabolism
Simion Chiosea, Steven P. Hodak, Linwah Yip, Devaprabu Abraham, Chelsey Baldwin, Zubair Baloch, Seza A. Gulec, Zeina C. Hannoush, Bryan R. Haugen, Lija Joseph, Atil Y. Kargi, Elham Khanafshar, Masha J. Livhits, Bryan McIver, Kepal Patel, Snehal G. Patel, Gregory W. Randolph, Ashok R. Shaha, Jyotirmay Sharma, Nikolaos Stathatos, Annemieke van Zante, Sally E. Carty, Yuri E. Nikiforov, Marina N. Nikiforova
Summary: This study analyzed 50,734 thyroid nodule samples from 48,225 patients with Bethesda III-VI classification and found clinically relevant molecular alterations, including diagnostic, prognostic, and targetable genetic alterations. The study also demonstrated a 68% negative call rate in BCIII-IV nodules, indicating the potential for reducing unnecessary surgeries. Additionally, the study identified common genetic alterations in BCV-VI nodules, such as BRAF and TERT mutations, and targetable gene fusions.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Meeting Abstract
Oncology
Yang Wu, Zheqi Li, Amir Bahreini, Jian Chen, Ye Qin, Kevin M. Levine, Nilgun Tasdemir, Nolan M. Priedigkeit, Li Zhu, George C. Tseng, Yu Jiang, Benjamin Troness, Laki Buluwela, Simak Ali, Spencer Arnesen, Jason Gertz, Ben Ho Park, Jennifer M. Atkinson, Dorraya El-Ashry, Adrian V. Lee, Steffi Oesterreich
Meeting Abstract
Oncology
Simeng Liu, Geoffrey Pecar, Jagmohan Hooda, Jennifer M. Atkinson, Fangyuan Chen, Adrian V. Lee, Steffi Oesterreich
Meeting Abstract
Oncology
Xuxu Gou, Meenakshi Anurag, Jonathan T. Lei, Sinem Seker, Adrian V. Lee, Dan R. Robinson, Matthew J. Ellis
Article
Pathology
Jeremie Berdugo, Lisa M. Rooper, Simion I. Chiosea
Summary: RB1 loss is associated with a better disease free survival in p16-positive/HPV-negative oropharyngeal squamous cell carcinoma, while RB1 IHC does not provide additional prognostic information. RB1 inactivation rarely leads to false positive p16 IHC results. RB1 loss caused by the high-risk HPV E7 oncoprotein may coexist with RB1 deletion.
HEAD & NECK PATHOLOGY
(2021)
Meeting Abstract
Oncology
Kai Ding, Fangyuan Chen, Nolan Priedigkeit, Daniel D. Brown, Tanya Heim, Rebecca Watters, Kurt Weiss, Jennifer Atkinson, Steffi Oesterreich, Adrian Lee