Article
Oncology
Ming Liang Oon, Jing Quan Lim, Bernett Lee, Sai Mun Leong, Gwyneth Shook-Ting Soon, Zi Wei Wong, Evelyn Huizi Lim, Zhenhua Li, Allen Eng Juh Yeoh, Shangying Chen, Kenneth Hon Kim Ban, Tae-Hoon Chung, Soo-Yong Tan, Shih-Sung Chuang, Seiichi Kato, Shigeo Nakamura, Emiko Takahashi, Yong-Howe Ho, Joseph D. Khoury, Rex K. H. Au-Yeung, Chee-Leong Cheng, Soon-Thye Lim, Wee-Joo Chng, Claudio Tripodo, Olaf Rotzschke, Choon Kiat Ong, Siok-Bian Ng
Summary: T-cells play a critical role in defending the human body against pathogens, with T-cell lymphomas characterized by malignant T-cells proliferating and forming genetically identical populations with the same TCR rearrangement pattern. A novel segmentation and copy number computation algorithm has been developed to accurately identify different TCR rearrangement patterns using whole genome sequencing data, potentially improving diagnostic accuracy for TCLs and having broader applications in hematology.
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
Biotechnology & Applied Microbiology
Xinghao Chen, Yan Dong, Yali Huang, Jianmin Fan, Minsheng Yang, Jun Zhang
Summary: This study conducted genome resequencing of transgenic poplar 741 line Pb29, identifying two T-DNA insertion sites without chromosomal rearrangement. It was found that Pb29 genome only contains the BtCry1AC gene, with minimal impact on the expression levels of surrounding genes.
Article
Oncology
Fumiko Arakawa, Hiroaki Miyoshi, Noriaki Yoshida, Kazutaka Nakashima, Yosaku Watatani, Takuya Furuta, Kyohei Yamada, Mayuko Moritsubo, Mai Takeuchi, Eriko Yanagida, Yasumasa Shimasaki, Kei Kohno, Keisuke Kataoka, Koichi Ohshima
Summary: Telomere length is maintained by telomerase, with TERT playing a critical role in its activation. TERT expression was found to be higher in AITL and TERT promoter mutations were observed in PTCL-NOS cases. However, no clear relationship was found between the TERT genomic abnormalities and protein expression in PTCL cases. TERT expression tended to have a poor prognosis in PTCL-NOS, but further research is needed to clarify this.
Review
Dermatology
M. H. Vermeer, J. P. Nicolay, J. J. Scarisbrick, P. L. Zinzani
Summary: Mycosis fungoides (MF) and Sezary syndrome (SS) are well-studied subtypes of cutaneous T-cell lymphoma. Accurate quantification of blood involvement is crucial for diagnosis, staging, prognosis, and treatment response assessment. Flow cytometry-based classifications are being developed to improve the assessment of blood involvement and treatment response in MF and SS.
BRITISH JOURNAL OF DERMATOLOGY
(2021)
Article
Hematology
Yuma Sakamoto, Takashi Ishida, Ayako Masaki, Morishige Takeshita, Hiromi Iwasaki, Kentaro Yonekura, Yukie Tashiro, Asahi Ito, Shigeru Kusumoto, Atae Utsunomiya, Shinsuke Iida, Ryuzo Ueda, Hiroshi Inagaki
Summary: Studies have shown that alterations of the CD28 gene are closely related to patient age, prognosis, and subtype in adult T-cell leukaemia/lymphoma. Patients with CD28 gene alterations tend to have a worse prognosis, especially in chronic or smouldering ATL subtypes.
BRITISH JOURNAL OF HAEMATOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Shuichi Nakai, Eiji Kiyohara, Rei Watanabe
Summary: CTCL is a heterogeneous group of non-Hodgkin lymphoma, mainly including MF and SS, with malignant cells possibly originating from different T cell phenotypes. The pathogenesis and therapeutic strategies for CTCL remain unclear due to the similar characteristics between malignant cells and anti-tumor T cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Tina Petrogiannis-Haliotis, Kevin Pehr, David Roberge, Ryan N. Rys, Yury Monczak, Gizelle Popradi, Lissa Ajjamada, Naciba Benlimame, Christiane Querfeld, Nathalie Johnson, Hans Knecht
Summary: We present a case of CD4+ small/medium-sized pleomorphic lymphoma with extensive lesions in the legs. Immunohistochemistry and flow cytometry analysis showed distinct CD4+ and CD8+ T-cell populations with no CD4/CD8 co-expression. TCR gene rearrangement studies confirmed the neoplastic population to be of T-cytotoxic cell lineage, representing a previously undescribed type of CTCL.
Article
Medicine, General & Internal
H. Dean Hosgood, Meghan Davitt, Richard Cawthon, Stephanie J. Weinstein, Batel Blechter, Jason Y. Y. Wong, Mohammad L. Rahman, Wei Hu, Satu Mannisto, Demetrius Albanes, Nathaniel Rothman, Qing Lan
Summary: This study suggests that a higher fraction of mitochondrial DNA with breaks is associated with an increased risk of non-Hodgkin lymphoma (NHL).
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Review
Oncology
Pan Lai, Yang Wang
Summary: Cutaneous T-cell lymphomas are a heterogeneous group of skin-homing non-Hodgkin lymphomas with limited treatment options and poor prognosis. Epigenetics play a crucial role in the development and treatment of this refractory disease.
CANCER BIOLOGY & MEDICINE
(2021)
Article
Medicine, General & Internal
Alfredo Rivas-Delgado, Ferran Nadeu, Marcio Andrade-Campos, Cristina Lopez, Anna Enjuanes, Pablo Mozas, Gerard Frigola, Luis Colomo, Blanca Sanchez-Gonzalez, Neus Villamor, Silvia Bea, Elias Campo, Antonio Salar, Eva Gine, Armando Lopez-Guillermo, Beatriz Bellosillo
Summary: High-throughput sequencing of cfDNA in lymphomas, particularly in PMBL, is a promising noninvasive approach for genomic characterization. This study demonstrates that cfDNA can accurately detect mutations and copy number alterations in PMBL patients, providing a valuable alternative source for disease characterization.
Article
Multidisciplinary Sciences
Matthew H. Larson, Wenying Pan, Hyunsung John Kim, Ruth E. Mauntz, Sarah M. Stuart, Monica Pimentel, Yiqi Zhou, Per Knudsgaard, Vasiliki Demas, Alexander M. Aravanis, Arash Jamshidi
Summary: Cell-free RNA is a promising analyte for cancer detection, with the potential to identify tissue- and subtype-specific biomarkers in breast and lung cancer patients. The presence of dark channel biomarker (DCB) genes in cfRNA from individuals with cancer suggests they could enhance cancer detection in patients with low levels of circulating tumor DNA.
NATURE COMMUNICATIONS
(2021)
Article
Hematology
Lennart Raman, Malaika Van der Linden, Ciel De Vriendt, Bliede Van den Broeck, Kristoff Muylle, Dries Deeren, Franceska Dedeurwaerdere, Sofie Verbeke, Amelie Dendooven, Katrien De Grove, Saskia Baert, Kathleen Claes, Bjorn Menten, Fritz Offner, Jo Van Dorpe
Summary: This study explored the use of shallow-depth sequencing of cell-free DNA for the diagnosis of lymphoma and disease follow-up. It found that liquid biopsies showed detectable copy number alterations and viral read fractions in HL and DLBCL patients. The study also demonstrated the potential of liquid biopsy-derived copy numbers in aiding diagnosis and differentiating HL from DLBCL, achieving a sensitivity of 100% compared to the current standard.
Article
Ecology
Paul E. Schavemaker, Sergio A. Munoz-Gomez
Summary: By analyzing the energetic constraints on cell size, the implications of genome architecture, and the presence of endosymbionts, the authors suggest that mitochondria were not necessary for the initial origin of eukaryotes, but played a role in their diversification and expansion.
NATURE ECOLOGY & EVOLUTION
(2022)
Letter
Dermatology
F. N. Mirza, S. Yumeen, M. Girardi
BRITISH JOURNAL OF DERMATOLOGY
(2021)
Letter
Dermatology
Fatima N. Mirza, Sara Yumeen, Julia M. Lewis, Amber Loren O. King, Sa Rang Kim, Kacie R. Carlson, Sheila Umlauf, Yulia V. Surovtseva, Francine M. Foss, Michael Girardi
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2021)
Article
Hematology
Sara Yumeen, Fatima N. Mirza, Julia M. Lewis, Amber Loren O. King, Sa Rang Kim, Kacie R. Carlson, Sheila R. Umlauf, Yulia Surovtseva, Francine M. Foss, Michael Girardi
Article
Otorhinolaryngology
Daniel Jacobs, Kelly Olino, Henry S. Park, James Clune, Shayan Cheraghlou, Michael Girardi, Barbara Burtness, Harriet Kluger, Benjamin L. Judson
Summary: The study suggests that patients evaluated at academic centers and institutions with high melanoma case volumes are more likely to receive guideline-recommended care, which is associated with improved overall survival. However, the percentage of patients receiving guideline-compliant primary tumor excision and lymph node evaluation has plateaued at approximately 50% since 2012.
OTOLARYNGOLOGY-HEAD AND NECK SURGERY
(2021)
Editorial Material
Dermatology
Sara Yumeen, Fatima N. Mirza, Julia M. Lewis, Michael Giradi
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2020)
Article
Dermatology
Ellen J. Kim, Joan Guitart, Christiane Querfeld, Michael Girardi, Amy Musiek, Oleg E. Akilov, James T. Angello, William L. Bailey, Larisa J. Geskin
Summary: This study analyzed the effect of chlormethine gel in combination with other therapies on efficacy, safety, and health-related quality of life in a real-world setting. The results confirmed that chlormethine gel is an important therapeutic option for patients with mycosis fungoides, reducing the severity of skin lesions and improving health-related quality of life.
AMERICAN JOURNAL OF CLINICAL DERMATOLOGY
(2021)
Article
Multidisciplinary Sciences
Jamie K. Hu, Hee-Won Suh, Munibah Qureshi, Julia M. Lewis, Sharon Yaqoob, Zoe M. Moscato, Sofia Griff, Alison K. Lee, Emily S. Yin, W. Mark Saltzman, Michael Girardi
Summary: The development of a bioadhesive nanoparticle (BNP) drug delivery system significantly increased the therapeutic efficacy of intratumoral drug delivery by enhancing binding to SCC tumor cell surfaces and matrix proteins. In a mouse model, BNP-CPT markedly reduced tumor burden and showed signs of histologic cure in a portion of the lesions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Dermatology
Shayan Cheraghlou, Sean R. Christensen, David J. Leffell, Michael Girardi
Summary: This study evaluated the association of treatment center academic affiliation and case volume with long-term patient survival after Mohs micrographic surgery for T1a-T2a invasive melanoma. The results showed that patients treated at academic and top decile-volume facilities had improved long-term survival compared to those treated at nonacademic and low-volume facilities. Identification and standardization of practices at these facilities may help reduce survival differences between centers.
Article
Dermatology
Shayan Cheraghlou, Praneeth Sadda, George O. Agogo, Michael Girardi
Summary: By utilizing a modified CART algorithm on data points in the NCDB, novel prognostic factors for Merkel cell carcinoma were identified, leading to the proposal of specific prognostic strata. This risk-stratified grouping showed strong predictive power for survival and demonstrated a high degree of within-group homogeneity and survival prediction.
AUSTRALASIAN JOURNAL OF DERMATOLOGY
(2021)
Letter
Dermatology
Amber Loren Ong King, Fatima N. Mirza, Julia M. Lewis, Shiela Umlauf, Yulia Surovtseva, Kacie R. Carlson, Francine M. Foss, Michael Girardi
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Multidisciplinary Sciences
Julia M. Lewis, Patrick F. Monico, Fatima N. Mirza, Suzanne Xu, Sara Yumeen, Jack L. Turban, Anjela Galan, Michael Girardi
Summary: Chronic UV exposure leads to a shift in the immune response towards ROR gamma t+ IL-22/IL-17A-producing cells, which are associated with mutant KC growth, and targeting these immune components may represent potential strategies for skin cancer prevention.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Hematology
Jingjing Ren, Rihao Qu, Nur-Taz Rahman, Julia M. Lewis, Amber Loren Ong King, Xiaofeng Liao, Fatima N. Mirza, Kacie R. Carlson, Yaqing Huang, Scott Gigante, Benjamin Evans, Barani Kumar Rajendran, Suzanne Xu, Guilin Wang, Francine M. Foss, William Damsky, Yuval Kluger, Smita Krishnaswamy, Michael Girardi
Summary: The incidence of cutaneous T-cell lymphoma (CTCL) increases with age and blood involvement is associated with a worse prognosis. In this study, we analyzed the transcriptomic profiles and T-cell receptor (TCR) sequences of CD4+ T cells from CTCL patients, revealing common features of the disease and potential therapeutic targets.
Letter
Dermatology
Suzanne Xu, Jingjing Ren, Julia M. Lewis, Kacie R. Carlson, Michael Girardi
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Meeting Abstract
Dermatology
J. Ren, R. Qu, N. Rahman, J. Lewis, A. King, X. Liao
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Review
Biology
Kathleen Suozzi, Jack Turban, Michael Girardi
YALE JOURNAL OF BIOLOGY AND MEDICINE
(2020)