bims-instec Biomed News
on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration
Issue of 2022–05–29
fourteen papers selected by
Maria-Virginia Giolito, IRFAC/UMR-S1113 INSERM
  1. p53 wild-type colorectal cancer cells that express a fetal gene signature are associated with metastasis and poor prognosis.
  2. RASSF4 inhibits cell proliferation and increases drug sensitivity in colorectal cancer through YAP/Bcl-2 pathway.
  3. Apelin-driven endothelial cell migration sustains intestinal progenitor cells and tumor growth.
  4. Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer.
  5. Targeted ablation of Lgr5-expressing intestinal stem cells in diphtheria toxin receptor-based mouse and organoid models.
  6. JAM-A signals through the Hippo pathway to regulate intestinal epithelial proliferation.
  7. The epigenetic modifier HDAC2 and the checkpoint kinase ATM determine the responses of microsatellite instable colorectal cancer cells to 5-fluorouracil.
  8. Metformin Enhancement of Therapeutic Effects of 5-Fluorouracil and Oxaliplatin in Colon Cancer Cells and Nude Mice.
  9. Spatial structure impacts adaptive therapy by shaping intra-tumoral competition.
  10. A Three-Genes Signature Predicting Colorectal Cancer Relapse Reveals LEMD1 Promoting CRC Cells Migration by RhoA/ROCK1 Signaling Pathway.
  11. Epithelial de-differentiation triggered by co-ordinate epigenetic inactivation of the EHF and CDX1 transcription factors drives colorectal cancer progression.
  12. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions.
  13. Mutational signatures are markers of drug sensitivity of cancer cells.
  14. Predicting cancer prognosis and drug response from the tumor microbiome.
  1. Nat Commun. 2022 May 23. 13(1): 2866
    p53 wild-type colorectal cancer cells that express a fetal gene signature are associated with metastasis and poor prognosis.
    Laura Solé, Teresa Lobo-Jarne, Daniel Álvarez-Villanueva, Josune Alonso-Marañón, Yolanda Guillén, Marta Guix, Irene Sangrador, Catalina Rozalén, Anna Vert, Antonio Barbachano, Joan Lop, Marta Salido, Beatriz Bellosillo, Raquel García-Romero, Marta Garrido, Jessica González, María Martínez-Iniesta, Erika López-Arribillaga, Ramón Salazar, Clara Montagut, Ferrán Torres, Mar Iglesias, Toni Celià-Terrassa, Alberto Muñoz, Alberto Villanueva, Anna Bigas, Lluís Espinosa.
      Current therapy against colorectal cancer (CRC) is based on DNA-damaging agents that remain ineffective in a proportion of patients. Whether and how non-curative DNA damage-based treatment affects tumor cell behavior and patient outcome is primarily unstudied. Using CRC patient-derived organoids (PDO)s, we show that sublethal doses of chemotherapy (CT) does not select previously resistant tumor populations but induces a quiescent state specifically to TP53 wildtype (WT) cancer cells, which is linked to the acquisition of a YAP1-dependent fetal phenotype. Cells displaying this phenotype exhibit high tumor-initiating and metastatic activity. Nuclear YAP1 and fetal traits are present in a proportion of tumors at diagnosis and predict poor prognosis in patients carrying TP53 WT CRC tumors. We provide data indicating the higher efficacy of CT together with YAP1 inhibitors for eradication of therapy resistant TP53 WT cancer cells. Together these results identify fetal conversion as a useful biomarker for patient prognosis and therapy prescription.
    DOI:  https://doi.org/10.1038/s41467-022-30382-9
  2. J Cell Mol Med. 2022 May 25.
    RASSF4 inhibits cell proliferation and increases drug sensitivity in colorectal cancer through YAP/Bcl-2 pathway.
    Yong Han, Xiaotang Zhang, Minmin Guan, Cheng Huo, Chunlin Yu, Bin Hu, Jianjun Cai.
      The RASSF family proteins have been implicated in the development of human cancers. To date, the expression pattern and biological significance of RASSF4 in colorectal cancers (CRC) have not been fully investigated. In the current study, we explored expression pattern of RASSF4 in 118 CRC specimens and 30 adjacent 'normal' colon tissues by immunohistochemistry. The results showed that RASSF4 was downregulated in CRC tissues compared with adjacent 'normal' tissues. RASSF4 downregulation significantly associated with advanced tumour-node-metastasis (TNM) stage, T status, positive node status and high Ki-67 index. Analysis of TCGA dataset also supported RASSF4 downregulation in CRC tissues. Ectopically expressed RASSF4 in LoVo cells inhibited cell growth, colony formation, cell cycle progression and increased the sensitivity to 5-FU treatment. Annexin V/PI apoptosis assay showed that RASSF4 overexpression increased 5-FU-induced apoptosis and downregulated the mitochondrial membrane potential. In addition, Western blot demonstrated that RASSF4 overexpression repressed YAP and Bcl-2 while upregulating p21 expression. YAP knockdown abolished the role of RASSF4 on Bcl-2. ChIP assay showed that TEAD4, a major YAP binding transcription factor, could bind to the promoter regions of Bcl-2. In conclusion, our data showed that RASSF4 was downregulated in human CRC. RASSF4 regulated malignant behaviour through YAP/Bcl-2 signalling in CRC cells.
    Keywords:  Bcl-2; RASSF4; YAP; colorectal cancer
    DOI:  https://doi.org/10.1111/jcmm.17395
  3. Nat Cardiovasc Res. 2022 May;1(5): 476-490
    Apelin-driven endothelial cell migration sustains intestinal progenitor cells and tumor growth.
    Jeremiah Bernier-Latmani, Christophe Cisarovsky, Samantha Mahfoud, Simone Ragusa, Isabelle Dupanloup, David Barras, François Renevey, Sina Nassiri, Pascale Anderle, Mario Leonardo Squadrito, Stefanie Siegert, Suzel Davanture, Alejandra González-Loyola, Nadine Fournier, Sanjiv A Luther, Rui Benedito, Philippe Valet, Bin Zhou, Michele De Palma, Mauro Delorenzi, Christine Sempoux, Tatiana V Petrova.
      Stem and progenitor cells residing in the intestinal crypts drive the majority of colorectal cancers (CRCs), yet vascular contribution to this niche remains largely unexplored. VEGFA is a key driver of physiological and tumor angiogenesis. Accordingly, current anti-angiogenic cancer therapies target the VEGFA pathway. Here we report that in CRC expansion of the stem/progenitor pool in intestinal crypts requires VEGFA-independent growth and remodeling of blood vessels. Epithelial transformation induced expression of the endothelial peptide apelin, directs migration of distant venous endothelial cells towards progenitor niche vessels ensuring optimal perfusion. In the absence of apelin, loss of injury-inducible PROX1+ epithelial progenitors inhibited both incipient and advanced intestinal tumor growth. Our results establish fundamental principles for the reciprocal communication between vasculature and the intestinal progenitor niche and provide a mechanism for resistance to VEGFA-targeting drugs in CRCs.
    DOI:  https://doi.org/10.1038/s44161-022-00061-5
  4. Front Oncol. 2022 ;12 878920
    Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer.
    Paige N Vega, Avlant Nilsson, Manu P Kumar, Hiroaki Niitsu, Alan J Simmons, James Ro, Jiawei Wang, Zhengyi Chen, Brian A Joughin, Wei Li, Eliot T McKinley, Qi Liu, Joseph T Roland, M Kay Washington, Robert J Coffey, Douglas A Lauffenburger, Ken S Lau.
      The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for revealing the complex nature of tumors. In this study, we used single-cell RNA-seq (scRNA-seq) to compare the tumor microenvironments between a mouse model of sporadic colorectal adenoma (Lrig1CreERT2/+;Apc2lox14/+) and a mouse model of inflammation-driven colorectal cancer induced by azoxymethane and dextran sodium sulfate (AOM/DSS). While both models develop tumors in the distal colon, we found that the two tumor types have distinct microenvironments. AOM/DSS tumors have an increased abundance of two populations of cancer-associated fibroblasts (CAFs) compared with APC tumors, and we revealed their divergent spatial association with tumor cells using multiplex immunofluorescence (MxIF) imaging. We also identified a unique squamous cell population in AOM/DSS tumors, whose origins were distinct from anal squamous epithelial cells. These cells were in higher proportions upon administration of a chemotherapy regimen of 5-Fluorouracil/Irinotecan. We used computational inference algorithms to predict cell-cell communication mediated by ligand-receptor interactions and downstream pathway activation, and identified potential mechanistic connections between CAFs and tumor cells, as well as CAFs and squamous epithelial cells. This study provides important preclinical insight into the microenvironment of two distinct models of colorectal tumors and reveals unique roles for CAFs and squamous epithelial cells in the AOM/DSS model of inflammation-driven cancer.
    Keywords:  adaptive immunity; cancer associated fibroblasts (CAF); colorectal cancer; inflammation; squamous cells; stem cells; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2022.878920
  5. STAR Protoc. 2022 Jun 17. 3(2): 101411
    Targeted ablation of Lgr5-expressing intestinal stem cells in diphtheria toxin receptor-based mouse and organoid models.
    Hui Yi Grace Lim, Swathi Yada, Nick Barker.
      Intestinal cells marked by Lgr5 function as tissue-resident stem cells that sustain the homeostatic replenishment of the epithelium. By incorporating a diphtheria toxin receptor (DTR) cassette linked to the Lgr5 coding region, native Lgr5-expressing cells are susceptible to ablation upon DT administration in vivo. A similar strategy can be used for Lgr5-expressing cells within organoids established from DTR models. Together, these in vivo and in vitro approaches will facilitate dissection of the roles of Lgr5-expressing cells residing in different tissue compartments. For complete details on the use and execution of this protocol, please refer to Tan et al. (2021).
    Keywords:  Organoids; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2022.101411
  6. iScience. 2022 May 20. 25(5): 104316
    JAM-A signals through the Hippo pathway to regulate intestinal epithelial proliferation.
    Shuling Fan, Michelle Sydney Smith, Justin Keeney, Monique N O'Leary, Asma Nusrat, Charles A Parkos.
      JAM-A is a tight-junction-associated protein that contributes to regulation of intestinal homeostasis. We report that JAM-A interacts with NF2 and LATS1, functioning as an initiator of the Hippo signaling pathway, well-known for regulation of proliferation. Consistent with these findings, we observed increased YAP activity in JAM-A-deficient intestinal epithelial cells (IEC). Furthermore, overexpression of a dimerization-deficient mutant, JAM-A-DL1, failed to initiate Hippo signaling, phenocopying JAM-A-deficient IEC, whereas overexpression of JAM-A-WT activated Hippo signaling and suppressed proliferation. Lastly, we identify EVI1, a transcription factor reported to promote cellular proliferation, as a contributor to the pro-proliferative phenotype in JAM-A-DL1 overexpressing IEC downstream of YAP. Collectively, our findings establish a new role for JAM-A as a cell-cell contact sensor, raising implications for understanding the contribution(s) of JAM-A to IEC proliferation in the mammalian epithelium.
    Keywords:  Biochemistry; Biological sciences; Cell biology
    DOI:  https://doi.org/10.1016/j.isci.2022.104316
  7. Cell Biol Toxicol. 2022 May 24.
    The epigenetic modifier HDAC2 and the checkpoint kinase ATM determine the responses of microsatellite instable colorectal cancer cells to 5-fluorouracil.
    Nicole Kiweler, Helena Schwarz, Alexandra Nguyen, Stephanie Matschos, Christina Mullins, Andrea Piée-Staffa, Christina Brachetti, Wynand P Roos, Günter Schneider, Michael Linnebacher, Walburgis Brenner, Oliver H Krämer.
      The epigenetic modifier histone deacetylase-2 (HDAC2) is frequently dysregulated in colon cancer cells. Microsatellite instability (MSI), an unfaithful replication of DNA at nucleotide repeats, occurs in about 15% of human colon tumors. MSI promotes a genetic frameshift and consequently a loss of HDAC2 in up to 43% of these tumors. We show that long-term and short-term cultures of colorectal cancers with MSI contain subpopulations of cells lacking HDAC2. These can be isolated as single cell-derived, proliferating populations. Xenografted patient-derived colon cancer tissues with MSI also show variable patterns of HDAC2 expression in mice. HDAC2-positive and HDAC2-negative RKO cells respond similarly to pharmacological inhibitors of the class I HDACs HDAC1/HDAC2/HDAC3. In contrast to this similarity, HDAC2-negative and HDAC2-positive RKO cells undergo differential cell cycle arrest and apoptosis induction in response to the frequently used chemotherapeutic 5-fluorouracil, which becomes incorporated into and damages RNA and DNA. 5-fluorouracil causes an enrichment of HDAC2-negative RKO cells in vitro and in a subset of primary colorectal tumors in mice. 5-fluorouracil induces the phosphorylation of KAP1, a target of the checkpoint kinase ataxia-telangiectasia mutated (ATM), stronger in HDAC2-negative cells than in their HDAC2-positive counterparts. Pharmacological inhibition of ATM sensitizes RKO cells to cytotoxic effects of 5-fluorouracil. These findings demonstrate that HDAC2 and ATM modulate the responses of colorectal cancer cells towards 5-FU.
    Keywords:  5-FU; ATM; Clonal evolution; DNA replication stress; HDAC2; Histone acetylation; KAP1; KU-60019; PR130; Tumor heterogeneity
    DOI:  https://doi.org/10.1007/s10565-022-09731-3
  8. Biomedicines. 2022 Apr 20. pii: 955. [Epub ahead of print]10(5):
    Metformin Enhancement of Therapeutic Effects of 5-Fluorouracil and Oxaliplatin in Colon Cancer Cells and Nude Mice.
    Kwan-Ling Yip, Tsen-Ni Tsai, I-Ping Yang, Zhi-Feng Miao, Yen-Cheng Chen, Ching-Chun Li, Wei-Chih Su, Tsung-Kun Chang, Ching-Wen Huang, Hsiang-Lin Tsai, Yung-Sung Yeh, Jaw-Yuan Wang.
      Studies have demonstrated that metformin has antitumor effects in addition to therapeutic effects on hyperglycemia; however, few studies have explored the effects of metformin in chemotherapy. Therefore, we hypothesized that the administration of metformin would enhance the therapeutic effects of 5-fluorouracil and oxaliplatin (FuOx) to inhibit the growth of colorectal cancer (CRC) cells in vitro and in vivo. The results of our in vitro experiments demonstrated that metformin significantly increased the effects of FuOx with respect to cell proliferation (p < 0.05), colony formation (p < 0.05), and migration (p < 0.01) and induced cell cycle arrest in the G0/G1 phase in HT29 cells and the S phase in SW480 and SW620 cells (p < 0.05). Flow cytometry analysis revealed that metformin combined with FuOx induced late apoptosis (p < 0.05) by mediating mitochondria-related Mcl-1 and Bim protein expression. Furthermore, in vivo, metformin combined with FuOx more notably reduced tumor volume than FuOx or metformin alone did in BALB/c mice (p < 0.05). These findings demonstrate that metformin may act as an adjunctive agent to enhance the chemosensitivity of CRC cells to FuOx. However, further clinical trials are warranted to validate the clinical implications of the findings.
    Keywords:  5-fluorouracil/oxaliplatin; chemotherapy; colorectal cancer; metformin
    DOI:  https://doi.org/10.3390/biomedicines10050955
  9. Commun Med (Lond). 2022 ;2 46
    Spatial structure impacts adaptive therapy by shaping intra-tumoral competition.
    Maximilian A R Strobl, Jill Gallaher, Jeffrey West, Mark Robertson-Tessi, Philip K Maini, Alexander R A Anderson.
       Background: Adaptive therapy aims to tackle cancer drug resistance by leveraging resource competition between drug-sensitive and resistant cells. Here, we present a theoretical study of intra-tumoral competition during adaptive therapy, to investigate under which circumstances it will be superior to aggressive treatment.
    Methods: We develop and analyse a simple, 2-D, on-lattice, agent-based tumour model in which cells are classified as fully drug-sensitive or resistant. Subsequently, we compare this model to its corresponding non-spatial ordinary differential equation model, and fit it to longitudinal prostate-specific antigen data from 65 prostate cancer patients undergoing intermittent androgen deprivation therapy following biochemical recurrence.
    Results: Leveraging the individual-based nature of our model, we explicitly demonstrate competitive suppression of resistance during adaptive therapy, and examine how different factors, such as the initial resistance fraction or resistance costs, alter competition. This not only corroborates our theoretical understanding of adaptive therapy, but also reveals that competition of resistant cells with each other may play a more important role in adaptive therapy in solid tumours than was previously thought. To conclude, we present two case studies, which demonstrate the implications of our work for: (i) mathematical modelling of adaptive therapy, and (ii) the intra-tumoral dynamics in prostate cancer patients during intermittent androgen deprivation treatment, a precursor of adaptive therapy.
    Conclusion: Our work shows that the tumour's spatial architecture is an important factor in adaptive therapy and provides insights into how adaptive therapy leverages both inter- and intra-specific competition to control resistance.
    Keywords:  Cancer therapeutic resistance; Dynamical systems; Prostate cancer; Tumour heterogeneity
    DOI:  https://doi.org/10.1038/s43856-022-00110-x
  10. Front Oncol. 2022 ;12 823696
    A Three-Genes Signature Predicting Colorectal Cancer Relapse Reveals LEMD1 Promoting CRC Cells Migration by RhoA/ROCK1 Signaling Pathway.
    Hui Zhang, Chenxin Xu, Feng Jiang, Jifeng Feng.
       Objective: Colorectal cancer (CRC) patients that experience early relapse consistently exhibit poor survival. However, no effective approach has been developed for the diagnosis and prognosis prediction of postoperative relapsed CRC.
    Methods: Multiple datasets from the GEO database and TCGA database were utilized for bioinformatics analysis. WGCNA analyses and RRA analysis were performed to identify key genes. The COX/Lasso regression model was used to construct the recurrence model. Subsequent in vitro experiments further validated the potential role of the hub genes in CRC.
    Results: A comprehensive analysis was performed on multiple CRC datasets and a CRC recurrence model was constructed containing LEMD1, SERPINE1, and SIAE. After further validation in two independent databases, we selected LEMD1 for in vitro experiments and found that LEMD1 could regulate CRC cell proliferation, migration, invasion, and promote EMT transition. The Rho-GTPase pulldown experiments further indicated that LEMD1 could affect RhoA activity and regulate cytoskeletal dynamics. Finally, we demonstrated that LEMD1 promoted CRC cell migration through the RhoA/ROCK1 signaling pathway.
    Conclusions: In this study, a CRC relapse model consisting of LEMD1, SERPINE1, and SIAE was constructed by comprehensive analysis of multiple CRC datasets. LEMD1 could promote CRC cell migration through the RhoA/ROCK signaling pathway.
    Keywords:  EMT; LEMD1; RhoA; colorectal cancer; metastasis; relapse model
    DOI:  https://doi.org/10.3389/fonc.2022.823696
  11. Cell Death Differ. 2022 May 23.
    Epithelial de-differentiation triggered by co-ordinate epigenetic inactivation of the EHF and CDX1 transcription factors drives colorectal cancer progression.
    Ian Y Luk, Laura J Jenkins, Kael L Schoffer, Irvin Ng, Janson W T Tse, Dmitri Mouradov, Stanislaw Kaczmarczyk, Rebecca Nightingale, Allan D Burrows, Robin L Anderson, Diego Arango, Higinio Dopeso, Larry Croft, Mark F Richardson, Oliver M Sieber, Yang Liao, Jennifer K Mooi, Natalia Vukelic, Camilla M Reehorst, Shoukat Afshar-Sterle, Vicki L J Whitehall, Lochlan Fennell, Helen E Abud, Niall C Tebbutt, Wayne A Phillips, David S Williams, Wei Shi, Lisa A Mielke, Matthias Ernst, Amardeep S Dhillon, Nicholas J Clemons, John M Mariadason.
      Colorectal cancers (CRCs) often display histological features indicative of aberrant differentiation but the molecular underpinnings of this trait and whether it directly drives disease progression is unclear. Here, we identify co-ordinate epigenetic inactivation of two epithelial-specific transcription factors, EHF and CDX1, as a mechanism driving differentiation loss in CRCs. Re-expression of EHF and CDX1 in poorly-differentiated CRC cells induced extensive chromatin remodelling, transcriptional re-programming, and differentiation along the enterocytic lineage, leading to reduced growth and metastasis. Strikingly, EHF and CDX1 were also able to reprogramme non-colonic epithelial cells to express colonic differentiation markers. By contrast, inactivation of EHF and CDX1 in well-differentiated CRC cells triggered tumour de-differentiation. Mechanistically, we demonstrate that EHF physically interacts with CDX1 via its PNT domain, and that these transcription factors co-operatively drive transcription of the colonic differentiation marker, VIL1. Compound genetic deletion of Ehf and Cdx1 in the mouse colon disrupted normal colonic differentiation and significantly enhanced colorectal tumour progression. These findings thus reveal a novel mechanism driving epithelial de-differentiation and tumour progression in CRC.
    DOI:  https://doi.org/10.1038/s41418-022-01016-w
  12. Nat Commun. 2022 May 26. 13(1): 2965
    Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions.
    Ryan J Smith, Hongpan Zhang, Shengen Shawn Hu, Theodora Yung, Roshane Francis, Lilian Lee, Mark W Onaitis, Peter B Dirks, Chongzhi Zang, Tae-Hee Kim.
      Development of the gastrointestinal system occurs after gut tube closure, guided by spatial and temporal control of gene expression. However, it remains unclear what forces regulate these spatiotemporal gene expression patterns. Here we perform single-cell chromatin profiling of the primitive gut tube to reveal organ-specific chromatin patterns that reflect the anatomical patterns of distinct organs. We generate a comprehensive map of epigenomic changes throughout gut development, demonstrating that dynamic chromatin accessibility patterns associate with lineage-specific transcription factor binding events to regulate organ-specific gene expression. Additionally, we show that loss of Sox2 and Cdx2, foregut and hindgut lineage-specific transcription factors, respectively, leads to fate shifts in epigenomic patterns, linking transcription factor binding, chromatin accessibility, and lineage fate decisions in gut development. Notably, abnormal expression of Sox2 in the pancreas and intestine impairs lineage fate decisions in both development and adult homeostasis. Together, our findings define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and adult homeostasis.
    DOI:  https://doi.org/10.1038/s41467-022-30624-w
  13. Nat Commun. 2022 May 25. 13(1): 2926
    Mutational signatures are markers of drug sensitivity of cancer cells.
    Jurica Levatić, Marina Salvadores, Francisco Fuster-Tormo, Fran Supek.
      Genomic analyses have revealed mutational footprints associated with DNA maintenance gone awry, or with mutagen exposures. Because cancer therapeutics often target DNA synthesis or repair, we asked if mutational signatures make useful markers of drug sensitivity. We detect mutational signatures in cancer cell line exomes (where matched healthy tissues are not available) by adjusting for the confounding germline mutation spectra across ancestries. We identify robust associations between various mutational signatures and drug activity across cancer cell lines; these are as numerous as associations with established genetic markers such as driver gene alterations. Signatures of prior exposures to DNA damaging agents - including chemotherapy - tend to associate with drug resistance, while signatures of deficiencies in DNA repair tend to predict sensitivity towards particular therapeutics. Replication analyses across independent drug and CRISPR genetic screening data sets reveal hundreds of robust associations, which are provided as a resource for drug repurposing guided by mutational signature markers.
    DOI:  https://doi.org/10.1038/s41467-022-30582-3
  14. Nat Commun. 2022 May 24. 13(1): 2896
    Predicting cancer prognosis and drug response from the tumor microbiome.
    Leandro C Hermida, E Michael Gertz, Eytan Ruppin.
      Tumor gene expression is predictive of patient prognosis in some cancers. However, RNA-seq and whole genome sequencing data contain not only reads from host tumor and normal tissue, but also reads from the tumor microbiome, which can be used to infer the microbial abundances in each tumor. Here, we show that tumor microbial abundances, alone or in combination with tumor gene expression, can predict cancer prognosis and drug response to some extent-microbial abundances are significantly less predictive of prognosis than gene expression, although similarly as predictive of drug response, but in mostly different cancer-drug combinations. Thus, it appears possible to leverage existing sequencing technology, or develop new protocols, to obtain more non-redundant information about prognosis and drug response from RNA-seq and whole genome sequencing experiments than could be obtained from tumor gene expression or genomic data alone.
    DOI:  https://doi.org/10.1038/s41467-022-30512-3
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