[HTML][HTML] Allostery: allosteric cancer drivers and innovative allosteric drugs

R Nussinov, M Zhang, R Maloney, Y Liu, CJ Tsai… - Journal of molecular …, 2022 - Elsevier
Here, we discuss the principles of allosteric activating mutations, propagation downstream of
the signals that they prompt, and allosteric drugs, with examples from the Ras signaling …

[HTML][HTML] Allostery, and how to define and measure signal transduction

R Nussinov, CJ Tsai, H Jang - Biophysical chemistry, 2022 - Elsevier
Here we ask: What is productive signaling? How to define it, how to measure it, and most of
all, what are the parameters that determine it? Further, what determines the strength of …

Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality

M Sprang, MA Andrade-Navarro, JF Fontaine - BMC bioinformatics, 2022 - Springer
Background The constant evolving and development of next-generation sequencing
techniques lead to high throughput data composed of datasets that include a large number …

MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia

NT Crump, AL Smith, L Godfrey… - Nature …, 2023 - nature.com
Aberrant enhancer activation is a key mechanism driving oncogene expression in many
cancers. While much is known about the regulation of larger chromosome domains in …

Hepatitis B virus DNA integration as a novel biomarker of hepatitis B virus-mediated pathogenetic properties and a barrier to the current strategies for hepatitis B virus …

R Salpini, S D'Anna, L Benedetti, L Piermatteo… - Frontiers in …, 2022 - frontiersin.org
Chronic infection with Hepatitis B Virus (HBV) is a major cause of liver-related morbidity and
mortality worldwide. HBV-DNA integration into the human genome is recognized as a …

Epigenomic characterization of lymphoid neoplasms

M Duran-Ferrer, JI Martín-Subero - Annual Review of Pathology …, 2024 - annualreviews.org
Lymphoid neoplasms represent a heterogeneous group of disease entities and subtypes
with markedly different molecular and clinical features. Beyond genetic alterations, lymphoid …

Systems medicine dissection of chr1q-amp reveals a novel PBX1-FOXM1 axis for targeted therapy in multiple myeloma

N Trasanidis, A Katsarou, K Ponnusamy… - Blood, The Journal …, 2022 - ashpublications.org
Understanding the biological and clinical impact of copy number aberrations (CNAs) on the
development of precision therapies in cancer remains an unmet challenge. Genetic …

Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma

S **ong, J Zhou, TK Tan, TH Chung, TZ Tan… - Nature …, 2024 - nature.com
Multiple myeloma is a hematological malignancy arising from immunoglobulin-secreting
plasma cells. It remains poorly understood how chromatin rewiring of regulatory elements …

The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma

YJC Chen, GB Bhaskara, Y Lu, K Lin… - Genes & …, 2024 - genesdev.cshlp.org
Despite recent advances in therapeutic treatments, multiple myeloma (MM) remains an
incurable malignancy. Epigenetic factors contribute to the initiation, progression, relapse …

Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma

DA Ang, JM Carter, K Deka, JHL Tan, J Zhou… - Nature …, 2024 - nature.com
In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone
marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro …