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Biology subjects

Lamichhane, A.

Publications and source records attributed to Lamichhane, A..

2 recordsLinked to original sources

The impact of patient biology on racial disparities in breast cancer outcome

Hormone receptor positive (HR+) breast cancer is the most common subtype of breast cancer diagnosed globally. Despite effective targeted therapies, HR+ breast cancer remains a leading cause of cancer-related death in women. Long-standing epidemiological research identifies significantly worse outcomes for Black women diagnosed with HR+ breast cancer relative to White women. While structural factors such as access to healthcare and education level contribute to this outcome disparity, it persists even in analyses where these factors are controlled. In-depth analyses of the somatic molecular biology that may underlie these outcome disparities are hampered by a lack of datasets that represent Black patient populations. Here, we generate a HR+ breast cancer patient transcriptomic dataset that overrepresents Black women and controls for access to healthcare and education level. We find that signatures relating to the tumor microenvironment, i.e. collagen deposition and prognostically unfavorable T-cell landscapes are enriched in HR+ tumors from Black women. Importantly, we find, using experimental model systems in vitro and in vivo, that race-aligned collagen deposition patterns are at least partially attributable to tumor cell-intrinsic signaling and critical for Black breast cancer metastasis. We also find that unfavorable T-cell signatures in HR+ tumors from Black women, which have previously been attributed to race and ancestry, are more strongly poverty-aligned. Using multiple independent datasets, we identify STAT4 as a potential master regulator of this poverty-associated tumor immune signature. Together, these findings provide new evidence that somatic molecular biology of breast cancer patients can be modified by multiple structural factors such as self-identified race and poverty burden to promote poor patient outcomes. Integrating an understanding of structural factors into molecular cancer research is critical for implementing truly personalized, and maximally effective, oncology systems.

cancer biology↗

Natural Language Processing-like Deep Learning Aided in Identification and Validation of Thiosulfinate Tolerance Clusters in Diverse Bacteria

Allicin tolerance (alt) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP) - like techniques, such as those used in DeepBGC, offers a promising solution by treating gene clusters like a language, allowing for identifying and collecting gene clusters based on patterns and relationships within the sequences. We curated and validated alt-like clusters in Pantoea ananatis 97-1R (PA), Burkholderia gladioli pv. gladioli FDAARGOS 389 (BG), and Pseudomonas syringae pv. tomato DC3000 -(PTO). Leveraging sequences from the RefSeq bacterial database, we conducted comparative analyses of gene synteny, gene/protein sequences, protein structures, and predicted protein interactions. This approach enabled the discovery of several novel alt-like clusters previously undetectable by other methods, which were further validated experimentally. Our work highlights the effectiveness of NLP-like techniques for identifying underrepresented gene clusters and expands our understanding of the diversity and utility of alt-like clusters in diverse bacterial genera. This work demonstrates the potential of these techniques to simplify the identification process and enhance the applicability of biological data in real-world scenarios. Significance StatementThiosulfinates, like allicin, are potent antifeedants and antimicrobials produced by Allium species and pose a challenge for phytopathogenic bacteria. Phytopathogenic bacteria have been shown to utilize an allicin tolerance (alt) gene cluster to circumvent this host response, leading to economically significant yield losses. Due to the complexity of mining these clusters, we applied techniques akin to natural language processing to analyze Pfam domains and gene proximity. This approach led to the identification of novel alt-like gene clusters, showcasing the potential of artificial intelligence to reveal elusive and underrepresented genetic clusters and enhance our understanding of their diversity and role across various bacterial genera.

pathology↗