Article
Biotechnology & Applied Microbiology
Kerstin U. Ludwig, Ricarda M. Schmithausen, David Li, Max L. Jacobs, Ronja Hollstein, Katja Blumenstock, Jana Liebing, Mikolaj Slabicki, Amir Ben-Shmuel, Ofir Israeli, Shay Weiss, Thomas S. Ebert, Nir Paran, Wibke Ruediger, Gero Wilbring, David Feldman, Barbel Lippke, Nina Ishorst, Lara M. Hochfeld, Eva C. Beins, Ines H. Kaltheuner, Maximilian Schmitz, Aliona Woehler, Manuel Doehla, Esther Sib, Marius Jentzsch, Jacob D. Borrajo, Jonathan Strecker, Julia Reinhardt, Brian Cleary, Matthias Geyer, Michael Holzel, Rhiannon Macrae, Markus M. Noethen, Per Hoffmann, Martin Exner, Aviv Regev, Feng Zhang, Jonathan L. Schmid-Burgk
Summary: Frequent and fast testing with high sensitivity and specificity, low cost, and easy deployment make LAMP-Seq a promising tool for integrated public health surveillance programs in containing COVID-19 outbreaks.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Kilian Vogele, Elisabeth Falgenhauer, Sophie von Schonberg, Friedrich C. Simmel, Tobias Pirzer
Summary: Cell-free systems allow interference with gene expression processes using small DNA molecules complementary to the mRNA, achieving significant reduction in gene expression. This technique was successfully applied to modulate gene expression from the native T7 phage genome, leading to improved gene replication and amplification in droplet-based experiments.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Oncology
Lea Jessica Albrecht, Anna Hoewner, Klaus Griewank, Smiths S. Lueong, Nils von Neuhoff, Peter A. Horn, Antje Sucker, Annette Paschen, Elisabeth Livingstone, Selma Ugurel, Lisa Zimmer, Susanne Horn, Jens T. Siveke, Dirk Schadendorf, Renata Varaljai, Alexander Roesch
Summary: This study identified a new liquid biopsy approach for melanoma diagnosis using circulating cell-free RNA (cfRNA). The cfRNA panel showed high diagnostic accuracy in distinguishing melanoma patients from healthy individuals. Additionally, cfRNA levels could predict patients' survival and therapeutic response.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Nanoscience & Nanotechnology
Jin Tao, Zhongzhu Liang, Guang Zeng, Dejia Meng, David R. Smith, Qing Huo Liu, Qingrui Yang, Menglun Zhang, Wei Pang, Jingqiu Liang, Tarik Bourouina
Summary: By integrating a perfect metamaterial absorber (PMA) with a film bulk acoustic wave resonator (FBAR) in a monolithic fashion, ultracompact uncooled infrared sensors of high sensitivity were produced. The resonance frequency of FBAR can be efficiently used as a sensor output, and the resulting sensor achieves a high absorption of 88% for an infrared spectrum centered at a wavelength of 8.2 μm.
Article
Multidisciplinary Sciences
Merve Sahin, Wilfred Wong, Yingqian Zhan, Kinsey Van Deynze, Richard Koche, Christina S. Leslie
Summary: Recent genome-wide chromosome conformation capture assays have greatly enhanced the resolution of studying 3D genomic architecture and function. HiC-DC+ is a software tool that integrates statistical framework for Hi-C/HiChIP interaction calling and differential analysis, providing a principled statistical analysis tool for genome-wide studies. HiC-DC+ accurately identifies enhancer-promoter interactions and recovers biological findings across conditions, enabling insights into global gene expression control.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Hua Bao, Zheng Wang, Xiaoji Ma, Wei Guo, Xiangyu Zhang, Wanxiangfu Tang, Xin Chen, Xinyu Wang, Yikuan Chen, Shaobo Mo, Naixin Liang, Qianli Ma, Shuyu Wu, Xiuxiu Xu, Shuang Chang, Yulin Wei, Xian Zhang, Hairong Bao, Rui Liu, Shanshan Yang, Ya Jiang, Xue Wu, Yaqi Li, Long Zhang, Fengwei Tan, Qi Xue, Fangqi Liu, Sanjun Cai, Shugeng Gao, Junjie Peng, Jian Zhou, Yang Shao
Summary: This study developed a robust machine learning model for multi-cancer early detection using cell-free DNA fragmentomics. The model showed high accuracy and sensitivity in detecting early-stage and small-size tumors. This research has significant implications for the development of cancer early screening in clinical practice.
Article
Biochemistry & Molecular Biology
Alejandro Ceron-Noriega, Miguel V. Almeida, Michal Levin, Falk Butter
Summary: Nematodes are a diverse group of animals with over 24,000 described species, but most of them lack comprehensive gene annotations. This study used proteotranscriptomics to improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genomes. The methodology was validated by identifying two previously undescribed genes in the model organism Caenorhabditis elegans. Extensive analysis of the comprehensive proteome annotation provided new insights into the evolutionary processes of this metazoan group.
Article
Biology
Darren J. Walsh, David J. Bernard, Faith Pangilinan, Madison Esposito, Denise Harold, Anne Parle-McDermott, Lawrence C. Brody
Summary: The analysis of somatic variation in the mitochondrial genome requires deep sequencing of mitochondrial DNA. This study presents a PCR-free method for ultra-deep sequencing coverage of the mitochondrial genome, using isolated intact mitochondria and a sequence-independent approach. The method avoids false-heteroplasmy calls caused by long-range PCR amplification and enables researchers to identify low frequency heteroplasmy without introducing PCR biases or NUMT contamination.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Xiangnan Wang, Xin Yi, Zhimei Huang, Jianjun He, Zhenkun Wu, Xia Chu, Jian-Hui Jiang
Summary: In this study, a repaired and activated DNAzyme (RADzyme) was developed by incorporating single methyl lesions at designated positions. This technology allowed the development of a fluorogenic RADzyme sensor for monitoring DNA repair, facilitating evaluation of repair activity in different cells and under drug treatment. This strategy provides a simple and versatile tool for the study of DNA repair biology, clinical diagnosis, and therapeutic assessment.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Lihao Guo, Zekun Li, Wenwen Hu, Taoping Liu, Youbin Zheng, Miaomiao Yuan, Yujie Dai, Ruizhi Ning, Yujin Zhu, Keyu Tao, Min Zhang, Tao Du, Lu Zhang, Chen Su, Hossam Haick, Weiwei Wu
Summary: This study presents the design and production of a multifunctional high-performance pressure sensor with dual microstructures of surface micro-bumps and internal hollow pores in a conductive material, an MXene. The sensor demonstrates ultra-high sensitivity, wide detection range, and stability in various human physiological and anatomical movement types. Data mining methods are used to extract gesture behavioral information and physiological information from the sensor signals, showing potential for motor function assessment and human-robot interaction applications.
JOURNAL OF MATERIALS CHEMISTRY A
(2021)
Article
Oncology
Adar Yaacov, Oriya Vardi, Britny Blumenfeld, Avraham Greenberg, Dashiell J. Massey, Amnon Koren, Sheera Adar, Itamar Simon, Shai Rosenberg
Summary: This study systematically analyzed the mutational landscape of tumors and identified the association between mutational processes and replication timing. A novel method was developed to improve understanding of the etiology of mutational signatures.
Article
Medicine, General & Internal
Wei Guo, Xin Chen, Rui Liu, Naixin Liang, Qianli Ma, Hua Bao, Xiuxiu Xu, Xue Wu, Shanshan Yang, Yang Shao, Fengwei Tan, Qi Xue, Shugeng Gao, Jie He
Summary: A predictive model based on cfDNA fragmentomics was developed for early-stage lung adenocarcinoma (LUAD) detection. The model showed high sensitivity for early lesions and small-sized tumors and remained effective even with reduced sequencing depth.
Article
Multidisciplinary Sciences
Jonathan C. M. Wan, Dennis Stephens, Lingqi Luo, James R. White, Caitlin M. Stewart, Benoit Rousseau, Dana W. Y. Tsui, Luis A. Diaz
Summary: This study investigates mutational signatures in plasma whole genome sequencing and uses machine learning to distinguish cancer patients from healthy individuals, potentially enabling early cancer detection and assessment of cancer risk and etiology.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Jill Rafalko, Erica Soster, Samantha Caldwell, Eyad Almasri, Thomas Westover, Vivian Weinblatt, Philip Cacheris
Summary: This study found that genome-wide cfDNA screening can detect chromosomal abnormalities beyond traditional screening, with an overall PPV of >70% for cases with subchromosomal CNVs. Isolated CNVs had a lower PPV of 61.0% compared to complex CNVs at 93.9%. Detected abnormalities included isolated deletions/duplications and unbalanced structural rearrangements.
GENETICS IN MEDICINE
(2021)
Article
Cell Biology
Burcak Otlu, Marcos Diaz-Gay, Ian Vermes, Erik N. Bergstrom, Maria Zhivagui, Mark Barnes, Ludmil B. Alexandrov
Summary: By integrating mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE, we evaluated the impact of various topographical features on cancer-specific mutational processes. Most mutational signatures were influenced by topographical features, especially those related to similar etiologies. Certain signatures exhibited periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, providing further insights into the underlying mutational processes. Our findings, disseminated via the COSMIC signatures database, offer a comprehensive online resource for exploring the interactions between mutational signatures and topographical features in human cancer.
Article
Biochemistry & Molecular Biology
Samuel K. Powell, Callan O'Shea, Kayla Townsley, Iya Prytkova, Kristina Dobrindt, Rahat Elahi, Marina Iskhakova, Tova Lambert, Aditi Valada, Will Liao, Seok-Man Ho, Paul A. Slesinger, Laura M. Huckins, Schahram Akbarian, Kristen J. Brennand
Summary: Rapid and efficient induction of dopaminergic neurons can be achieved through transient overexpression of lineage-promoting transcription factors combined with stringent selection. These induced dopaminergic neurons provide a critical tool for modeling midbrain dopaminergic neuron development and dysfunction in psychiatric disease.
MOLECULAR PSYCHIATRY
(2023)
Article
Oncology
Alexander C. J. van Akkooi, Tina J. Hieken, Elizabeth M. Burton, Charlotte Ariyan, Paolo A. Ascierto, Salvatore V. M. A. Asero, Christian U. Blank, Matthew S. Block, Genevieve M. Boland, Corrado Caraco, Sydney Chng, B. Scott Davidson, Joao Pedreira Duprat Neto, Mark B. Faries, Jeffrey E. Gershenwald, Dirk J. Grunhagen, David E. Gyorki, Dale Han, Andrew J. Hayes, Winan J. van Houdt, George C. Karakousis, Willem M. C. Klop, Georgina Long, Michael C. Lowe, Alexander M. Menzies, Roger Olofsson Bagge, Thomas E. Pennington, Piotr Rutkowski, Robyn P. M. Saw, Richard A. Scolyer, Kerwin F. Shannon, Vernon K. Sondak, Hussein Tawbi, Alessandro A. E. Testori, Mike T. Tetzlaff, John F. Thompson, Jonathan S. Zager, Charlotte L. Zuur, Jennifer A. Wargo, Andrew J. Spillane, Merrick Ross
Summary: Exciting advances in melanoma systemic therapies have provided opportunities for neoadjuvant systemic treatment in high-risk, resectable metastatic melanomas. This article presents the current state of neoadjuvant systemic therapy for melanoma, focusing on the surgical aspects and the role of surgical oncologists. It summarizes past developments in melanoma treatment and the evidence for neoadjuvant systemic therapy in stage III melanoma, discussing surgical issues, technical aspects, and other important considerations.
ANNALS OF SURGICAL ONCOLOGY
(2022)
Article
Oncology
Melanie Pages, Denisse Rotem, Gregory Gydush, Sarah Reed, Justin Rhoades, Gavin Ha, Christopher Lo, Mark Fleharty, Madeleine Duran, Robert Jones, Sarah Becker, Michaela Haller, Claire E. Sinai, Liliana Goumnerova, Todd R. Golub, J. Christopher Love, Keith L. Ligon, Karen D. Wright, Viktor A. Adalsteinsson, Rameen Beroukhim, Pratiti Bandopadhayay
Summary: The study systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, CSF, and urine. Results showed that most samples had very low levels of somatic mutations, posing a challenge for detection using whole-genome or targeted sequencing methods. Substantial challenges remain in genetically characterizing pediatric brain tumors from liquid biopsies.
Article
Endocrinology & Metabolism
Elizabeth H. Stover, Coyin Oh, Paula Keskula, Atish D. Choudhury, Yuen-Yi Tseng, Viktor A. Adalsteinsson, Jens G. Lohr, Aaron R. Thorner, Matthew Ducar, Gregory Kryukov, Gavin Ha, Mara Rosenberg, Samuel S. Freeman, Zhenwei Zhang, Xiaoyun Wu, Eliezer M. Van Allen, David Y. Takeda, Massimo Loda, Chin-Lee Wu, Mary-Ellen Taplin, Levi A. Garraway, Jesse S. Boehm, Franklin W. Huang
Summary: In this study, a prostate cancer-specific targeted NGS panel was used to evaluate genetic alterations in primary and metastatic prostate cancer samples, including driver oncogene mutations and ETS family gene fusions, as well as the genetic characteristics of cell lines. This approach provides important information for personalized treatment of prostate cancer.
Article
Public, Environmental & Occupational Health
Beth Frates, David Cron, Carrie Cunningham Lubitz, Genevieve Boland, Sunita Srivastava, Richard A. Hodin, Antonia E. Stephen, Kelsey Carney, Roy Phitayakorn
Summary: Surgeons have faced immense pressure during the COVID pandemic, but it has also prompted a reevaluation of mentoring practices. The team mentoring program at Massachusetts General Hospital's surgery department, which includes a lifestyle medicine expert, has been successful and could be explored by other departments and hospitals.
AMERICAN JOURNAL OF LIFESTYLE MEDICINE
(2023)
Article
Pathology
Jin-Yih Low, Minjeong Ko, Brian Hanaratty, Radhika A. Patel, Akshay Bhamidipati, Christopher M. Heaphy, Erolcan Gayar, John K. Lee, Shan Li, Angelo M. De Marzo, William G. Nelson, Anuj Gupta, Srinivasa Yengnasubramanium, Gavin Ha, Jonathan I. Epstein, Michael C. Haffner
Summary: Basal cell carcinoma (BCC) of the prostate is a rare tumor that differs from the more common acinar adenocarcinoma (AAC) in terms of basal cell differentiation and genomic alterations. Whole genome sequencing of two BCC cases revealed low copy number and mutational burden, recurrent copy number loss of chromosome 16, and mutations in driver genes such as KIT, DENND3, PTPRU, MGA, and CYLD. Depletion of CYLD protein increased proliferation of prostatic basal cells in vitro. These findings highlight the distinct genomic alterations and potential role of chromosome 16 loss in the pathogenesis of prostatic BCC.
AMERICAN JOURNAL OF PATHOLOGY
(2023)
Editorial Material
Oncology
Shoshana T. Levi, Genevieve M. Boland
CLINICAL CANCER RESEARCH
(2023)
Article
Oncology
Catherine N. Zivanov, Anne Coogan, Robin R. Lane, Sara G. Lin, Sarah C. Reed, Marc A. Robinson, Mohana Karlekar, Lauren S. Prescott, Alaina J. Brown
Summary: This study aimed to evaluate the impact of a letter-based advance care planning (ACP) initiative on gynecologic oncology (GO) inpatients. The results showed that providing ACP packets and conducting ACP conversations led by medical students increased the documentation rates of ACP in the electronic medical records (EMR) of patients.
JOURNAL OF CANCER EDUCATION
(2023)
Review
Oncology
Andrew H. Lipsky, Nicole Lamanna
Summary: Targeted therapies have revolutionized the frontline treatment for CLL, reducing reliance on chemoimmunotherapy. Drugs such as ibrutinib, acalabrutinib, and venetoclax have shown efficacy in oral therapy. This review explores novel therapeutic strategies using these agents in combination, highlighting the importance of patient characteristics and study methodology.
Review
Oncology
Sarah C. Reed, Sarah Croessmann, Ben Ho Park
Summary: Clonal hematopoiesis of indeterminate potential (CHIP) is the expansion of leukemia-associated somatic mutations in healthy individuals, which can lead to increased risk of hematologic malignancy, cardiovascular disease, and mortality. Recent research has found high rates of CHIP in patients with solid tumors and suggests a potential role in inflammation and solid tumor biology.
CLINICAL CANCER RESEARCH
(2023)
Article
Oncology
Michael T. Schweizer, Roman Gulati, Todd Yezefski, Heather H. Cheng, Elahe Mostaghel, Michael C. Haffner, Radhika A. Patel, Navonil De Sarkar, Gavin Ha, Ruth Dumpit, Brianna Woo, Aaron Lin, Patrick Panlasigui, Nerina McDonald, Michael Lai, Katie Nega, Jeannette Hammond, Petros Grivas, Andrew Hsieh, Bruce Montgomery, Peter S. Nelson, Evan Y. Yu
Summary: This study investigated the use of Bipolar androgen therapy (BAT) in metastatic castration-resistant prostate cancer (mCRPC) and found that BAT plus olaparib combination therapy can achieve high response rates and long progression-free survival. The clinical effects of this treatment may be related to DNA damage induction and synergy with PARP inhibitors. The presence or absence of HRR gene mutations does not affect the efficacy.
PROSTATE CANCER AND PROSTATIC DISEASES
(2023)
Article
Oncology
Navonil De Sarkar, Robert D. Patton, Anna-Lisa Doebley, Brian Hanratty, Mohamed Adil, Adam J. Kreitzman, Jay F. Sarthy, Minjeong Ko, Sandipan Brahma, Michael P. Meers, Derek H. Janssens, Lisa S. Ang, Ilsa M. Coleman, Arnab Bose, Ruth F. Dumpit, Jared M. Lucas, Talina A. Nunez, Holly M. Nguyen, Heather M. McClure, Colin C. Pritchard, Michael T. Schweizer, Colm Morrissey, Atish D. Choudhury, Sylvan C. Baca, Jacob E. Berchuck, Matthew L. Freedman, Kami Ahmad, Michael C. Haffner, R. Bruce Montgomery, Eva Corey, Steven Henikoff, Peter S. Nelson, Gavin Ha
Summary: By studying nucleosome positioning patterns in circulating tumor DNA (ctDNA), we identified distinct phenotypes of advanced prostate cancers and developed prediction models for phenotype classification. Nucleosome patterns associated with transcriptional activity were observed in ctDNA, providing insights into gene regulation and potential therapeutic targets. This study demonstrates the diagnostic advantages and precision oncology implications of ctDNA in cancer phenotyping.
Article
Oncology
Azadeh Tabari, Meredith Cox, Brian D'Amore, Arian Mansur, Harika Dabbara, Genevieve Boland, Michael S. Gee, Dania Daye
Summary: Machine learning-based radiomics can predict the response to immune checkpoint inhibitors (ICI) in metastatic melanoma and complement LDH for prognostication. Combining radiomics features with LDH resulted in better prediction of treatment response.
Article
Health Policy & Services
Julie J. J. Lee, Daniel E. E. Sack, Sharon Kam, Sarah C. C. Reed, Babatunde Carew, Cooper Lloyd, Eleanor O. O. Weaver, Robert F. F. Miller
Summary: High medication costs in the United States disproportionately affect uninsured and underinsured patients. Pharmaceutical companies offer patient assistance programs (PAPs) to lower costs for uninsured patients. A study of a student-run free clinic in Nashville, Tennessee over ten years demonstrates the reliable and sustainable use of PAPs to increase patients' access to expensive medications. The study shows significant growth in the number of medications available through PAPs and potential cost savings of over $1.2 million in 2021.
JOURNAL OF COMMUNITY HEALTH
(2023)
Article
Oncology
Francesca Khani, William F. Hooper, Xiaofei Wang, Timothy R. Chu, Minita Shah, Lara Winterkorn, Michael Sigouros, Vincenza Conteduca, David Pisapia, Sara Wobker, Sydney Walker, Julie N. Graff, Brian Robinson, Juan Miguel Mosquera, Andrea Sboner, Olivier Elemento, Nicolas Robine, Himisha Beltran
Summary: In this study, the clinical and molecular characteristics of intracranial metastases in prostate cancer were evaluated. Whole genome sequencing was performed to identify genomic alterations. The results revealed a higher diversity of structural alterations in intracranial metastases compared to primary tumors, with AR and TP53 alterations being frequently observed. Clonality analysis provided insights into the genomic factors contributing to metastatic spread in prostate cancer.
NPJ PRECISION ONCOLOGY
(2023)