“Misuse” of RNA-seq data in microbiome studies: A cautionary tale of poly(A)

References

[1] Filardo S, Di Pietro M, Sessa R. Current progresses and challenges for microbiome research in human health: a perspective. Front Cell Infect Microbiol. 2024; 14: 1377012.

[2] Hou K, Wu ZX, Chen XY, Wang JQ, Zhang D, Xiao C, et al. Microbiota in health and diseases. Signal Transduct Target Ther. 2022; 7: 135.

[3] Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, et al. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene. 2024; 43: 1127-1148.

[4] Zare A, Postovit LM, Githaka JM. Robust inflammatory breast cancer gene signature using nonparametric random forest analysis. Breast Cancer Res. 2021; 23: 92.

[5] Pirayeshfard L, Luo S, Githaka JM, Saini A, Touret N, Goping IS, et al. Comparing the BAD protein interactomes in 2D and 3D cell culture using proximity labeling. J Proteome Res. 2024; 23: 3433-3443.

[6] Galloway-Peña J, Hanson B. Tools for analysis of the microbiome. Dig Dis Sci. 2020; 65: 674-685.

[7] Cao Y, Xia H, Tan X, Shi C, Ma Y, Meng D, et al. Intratumoural microbiota: a new frontier in cancer development and therapy. Signal Transduct Target Ther. 2024; 9: 15.

[8] Mofayezi A, Jadaliha M, Zangeneh F, Khoddami V. Poly(A) tale: from A to A; RNA polyadenylation in prokaryotes and eukaryotes. Wiley Interdiscip Rev RNA. 2024; 15: e1846.

[9] Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, et al. Best practices on the differential expression analysis of multi-species RNA-seq. Genome Biol. 2021; 22: 121.

[10] Westermann AJ, Gorski SA, Vogel J. Dual RNA-seq of pathogen and host. Nat Rev Microbiol. 2012; 10: 618-630.

[11] Liebhoff AM, Menden K, Laschtowitz A, Franke A, Schramm C, Bonn S. Pathogen detection in RNA-seq data with pathonoia. BMC Bioinformatics. 2023; 24: 53.

[12] Hoyd R, Wheeler CE, Liu Y, Jagjit Singh MS, Muniak M, Jin N, et al. Exogenous sequences in tumors and immune cells (exotic): a tool for estimating the microbe abundances in tumor RNA-seq data. Cancer res commun. 2023; 3: 2375-2385.

[13] Zhang S, Liu X, Zhao Y, Wang P, Yu R, Xu P, et al. Microbiome characteristics description of COVID-19 patients based on bulk RNA-seq and scRNA-Seq data. Comput Biol Med. 2023; 165: 107400.

[14] Yu D, Wang T, Liang D, Mei Y, Zou W, Guo S. The landscape of microbial composition and associated factors in pancreatic ductal adenocarcinoma using RNA-seq data. Front Oncol. 2021; 11: 651350.

[15] Ai B, Mei Y, Liang D, Wang T, Cai H, Yu D. Uncovering the special microbiota associated with occurrence and progression of gastric cancer by using RNA-sequencing. Sci Rep. 2023; 13: 5722.

[16] Dravillas CE, Coleman SS, Hoyd R, Caryotakis G, Denko L, Chan CHF, et al. The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors. Cancer Res Commun. 2024; 4: 1978-1990.

[17] Yao R, Ai B, Wang Z, Shen B, Xue G, Yu D. Uncovering microbial composition of the tissue microenvironment in bladder cancer using RNA sequencing data. J Cancer. 2024; 15: 2431-2441.

[18] Fedorova M, Snezhkina A, Kalinin D, Pudova E, Lantsova M, Krasnov G, et al. Intratumoral microbiome in head and neck paragangliomas. Int J Mol Sci. 2024; 25: 9180.

[19] Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genet. 2013; 45: 1113-1120.

[20] Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, et al. Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature. 2020; 579: 567-574.

[21] Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, et al. Major data analysis errors invalidate cancer microbiome findings. mBio. 2023; 14: e0160723.

[22] Gihawi A, Cooper CS, Brewer DS. Caution regarding the specificities of pan-cancer microbial structure. Microb Genom. 2023; 9: mgen001088.

[23] Shin D, Kim J, Lee JH, Kim JI, Oh YM. Profiling of microbial landscape in lung of chronic obstructive pulmonary disease patients using RNA sequencing. Int J Chronic Obstruct Pulm Dis. 2023; 18: 2531-2542.

[24] Robinson KM, Crabtree J, Mattick JSA, Anderson KE, Dunning Hotopp JC. Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data. Microbiome. 2017; 5: 9.

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