bims-instec 2022-11-13 papers

bims-instec

Biomed News

on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration

Issue of 2022–11–13
thirty-one papers selected by
Maria-Virginia Giolito, Free University of Brussels

The extracellular matrix controls stem cell specification and crypt morphology in the developing and adult mouse gut.
Molecular characterization of acquired resistance to KRAS G12C-EGFR inhibition in colorectal cancer.
Metastatic recurrence in colorectal cancer arises from residual EMP1+ cells.
Axin1 protects colon carcinogenesis by an immune-mediated effect.
Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier.
Resistance Mechanisms to Anti-EGFR Therapy in RAS/RAF Wildtype Colorectal Cancer Vary by Regimen and Line of Therapy.
Mapping prohormone processing by proteases in human enteroendocrine cells using genetically engineered organoid models.
Workflow for Quantitative Proteomic Analysis of Intestinal Organoids Using SILAC.
Olfactomedin 4 associates with expression of differentiation markers but not with properties of cancer stemness, EMT nor metastatic spread in colorectal cancer.
Advancing immune checkpoint blockade in colorectal cancer therapy with nanotechnology.
Directed evolution identifies high-affinity cystine-knot peptide agonists and antagonists of Wnt/β-catenin signaling.
pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation.
Genotype-tailored ERK/MAPK pathway and HDAC inhibition rewires the apoptotic rheostat to trigger colorectal cancer cell death.
Rac1 promotes the reprogramming of glucose metabolism and the growth of colon cancer cells through up-regulating SOX9.
Examination of the Effect of Proton Pump Inhibitors on the Anticancer Activity of Oxaliplatin.
Nuclear Membrane Protein SUN5 Is Highly Expressed and Promotes Proliferation and Migration in Colorectal Cancer by Regulating the ERK Pathway.
Advances in immunotherapy for MMR proficient colorectal cancer.
The Validity of Surrogate Endpoints in Sub Groups of Metastatic Colorectal Cancer Patients Defined by Treatment Class and KRAS Status.
Regulatory Role of Sphingosine-1-Phosphate and C16:0 Ceramide, in Immunogenic Cell Death of Colon Cancer Cells Induced by Bak/Bax-Activation.
Metabolite activation of tumorigenic signaling pathways in the tumor microenvironment.
Role of AMPK in Regulation of Oxaliplatin-Resistant Human Colorectal Cancer.
Deconvolution of bulk tumors into distinct immune cell states predicts colorectal cancer recurrence.
Risk factors for small intestinal adenocarcinomas that are common in the proximal small intestine.
Developing a taxonomy for colorectal cancer.
Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis.
Gene interaction perturbation network deciphers a high-resolution taxonomy in colorectal cancer.
PD-L1 Expression in High-Risk Early-Stage Colorectal Cancer-Its Clinical and Biological Significance in Immune Microenvironment.
Expression pattern of secretory-cell-related transcriptional signatures in colon adenocarcinomas defines tumor microenvironment characteristics and correlates with clinical outcomes.
Alternative splicing downstream of EMT enhances phenotypic plasticity and malignant behaviour in colon cancer.
Nitroreductase-instructed supramolecular assemblies for microbiome regulation to enhance colorectal cancer treatments.
Loss of SATB2 expression correlates with cytokeratin 7 and PD-L1 tumor cell positivity and aggressiveness in colorectal cancer.

Biol Open. 2022 Sep 29. pii: bio.059544. [Epub ahead of print]

The extracellular matrix controls stem cell specification and crypt morphology in the developing and adult mouse gut.

R Ramadan, V M Wouters, S M van Neerven, N E de Groot, Garcia T Martins, V Muncan, O D Franklin, M Battle, K S Carlson, J Leach, O J Sansom, O Boulard, M Chamaillard, L Vermeulen, J P Medema, D J Huels.

  The rapid of the epithelial gut lining is fueled by stem cells that reside at the base of intestinal crypts. The signal transduction pathways and morphogens that regulate intestinal stem cell self-renewal and differentiation have been extensively characterized. In contrast, although extracellular matrix (ECM) components form an integral part of the intesti-nal stem cell niche, their direct influence on the cellular compo-sition is less well understood. We set out to systematically compare the effect of two ECM classes, interstitial matrix and the basement membrane, on the intestinal epithelium. We found that both collagen I and laminin-containing cultures allow growth of small intestinal epithelial cells with all cell types present in both cultures, albeit at different ratios. The collagen cultures contained a subset of cells enriched in fetal-like markers. In con-trast, laminin increased Lgr5+ stem cells and Paneth cells, and induced crypt-like morphology changes. The transition from a collagen culture to a laminin culture, re-sembles the gut development in vivo. The ECM dramatic remodelling is accompa-nied by a local expression of the laminin receptor ITGA6 in the crypt-forming epithelium. Importantly, deletion of laminin in the adult mouse results in a marked reduction of adult intestinal stem cells. Overall, our data support the hy-pothesis that the formation of intestinal crypts is induced by an increased laminin concentration in the ECM.

Keywords:  Crypt morphology; Extracellular matrix; Intestinal stem cells; Laminin

DOI:  https://doi.org/10.1242/bio.059544
Cancer Discov. 2022 Nov 10. pii: CD-22-0405. [Epub ahead of print]

Molecular characterization of acquired resistance to KRAS G12C-EGFR inhibition in colorectal cancer.

Rona Yaeger, Riccardo Mezzadra, Jenna Sinopoli, Yu Bian, Michelangelo Marasco, Esther Kaplun, Yijun Gao, HuiYong Zhao, Arnaud Da Cruz Paula, Yingjie Zhu, Almudena Chaves Perez, Kalyani Chadalavada, Edison Tse, Sudhir Chowdhry, Sydney Bowker, Qing Chang, Besnik Qeriqi, Britta Weigelt, Gouri J Nanjangud, Michael F Berger, Hirak Der-Torossian, Kenna Anderes, Nicholas D Socci, Jinru Shia, Gregory J Riely, Yonina R Murciano-Goroff, Bob T Li, James G Christensen, Jorge S Reis-Filho, David B Solit, Elisa de Stanchina, Scott W Lowe, Neal Rosen, Sandra Misale.

With the combination of KRAS G12C and EGFR inhibitors, KRAS is becoming a druggable target in colorectal cancer. However, secondary resistance limits its efficacy. Using cell lines, patient-derived xenografts, and patient samples, we detected a heterogeneous pattern of putative resistance alterations expected primarily to prevent inhibition of ERK signaling by drugs at progression. Serial analysis of patient blood samples on treatment demonstrates that most of these alterations are detected at a low frequency except for KRAS G12C amplification, a recurrent resistance mechanism that rises in step with clinical progression. Upon drug withdrawal, resistant cells with KRAS G12C amplification undergo oncogene-induced senescence, and progressing patients experience a rapid fall in levels of this alteration in circulating DNA. In this new state, drug resumption is ineffective as mTOR signaling is elevated. However, our work exposes a potential therapeutic vulnerability, whereby therapies that target the senescence response may overcome acquired resistance.

DOI: https://doi.org/10.1158/2159-8290.CD-22-0405
Nature. 2022 Nov 09.

Metastatic recurrence in colorectal cancer arises from residual EMP1+ cells.

Adrià Cañellas-Socias, Carme Cortina, Xavier Hernando-Momblona, Sergio Palomo-Ponce, Eoghan J Mulholland, Gemma Turon, Lidia Mateo, Sefora Conti, Olga Roman, Marta Sevillano, Felipe Slebe, Diana Stork, Adrià Caballé-Mestres, Antonio Berenguer-Llergo, Adrián Álvarez-Varela, Nicola Fenderico, Laura Novellasdemunt, Laura Jiménez-Gracia, Tamara Sipka, Lidia Bardia, Patricia Lorden, Julien Colombelli, Holger Heyn, Xavier Trepat, Sabine Tejpar, Elena Sancho, Daniele V F Tauriello, Simon Leedham, Camille Stephan-Otto Attolini, Eduard Batlle.

Around 30-40% of patients with colorectal cancer (CRC) undergoing curative resection of the primary tumour will develop metastases in the subsequent years1. Therapies to prevent disease relapse remain an unmet medical need. Here we uncover the identity and features of the residual tumour cells responsible for CRC relapse. An analysis of single-cell transcriptomes of samples from patients with CRC revealed that the majority of genes associated with a poor prognosis are expressed by a unique tumour cell population that we named high-relapse cells (HRCs). We established a human-like mouse model of microsatellite-stable CRC that undergoes metastatic relapse after surgical resection of the primary tumour. Residual HRCs occult in mouse livers after primary CRC surgery gave rise to multiple cell types over time, including LGR5+ stem-like tumour cells2-4, and caused overt metastatic disease. Using Emp1 (encoding epithelial membrane protein 1) as a marker gene for HRCs, we tracked and selectively eliminated this cell population. Genetic ablation of EMP1high cells prevented metastatic recurrence and mice remained disease-free after surgery. We also found that HRC-rich micrometastases were infiltrated with T cells, yet became progressively immune-excluded during outgrowth. Treatment with neoadjuvant immunotherapy eliminated residual metastatic cells and prevented mice from relapsing after surgery. Together, our findings reveal the cell-state dynamics of residual disease in CRC and anticipate that therapies targeting HRCs may help to avoid metastatic relapse.

DOI: https://doi.org/10.1038/s41586-022-05402-9
Cell Mol Gastroenterol Hepatol. 2022 Nov 07. pii: S2352-345X(22)00231-4. [Epub ahead of print]

Axin1 protects colon carcinogenesis by an immune-mediated effect.

Romain Sanson, Silvia Luna Lazzara, David Cune, Caterina Luana Pitasi, Coralie Trentesaux, Marie Fraudeau, Franck Letourneur, Benjamin Saintpierre, Morgane Le Gall, Pascale Bossard, Benoit Terris, Pascal Finetti, François Bertucci, Emilie Mamessier, Béatrice Romagnolo, Christine Perret.

   BACKGROUND & AIMS: Axin1 is a negative regulator of Wnt/β-catenin signaling with tumor suppressor function. The Wnt pathway has a critical role in the intestine, both during homeostasis and cancer, but the role of Axin1 remains elusive.
METHODS: We assessed the role of Axin1 in normal intestinal homeostasis, with control, epithelial-specific Axin1-knockout mice (Axin1ΔIEC) and Axin2-knockout mice. We evaluated the tumor suppressor function of Axin1 during chemically induced colorectal tumorigenesis and DSS-induced colitis, and performed comparative gene expression profiling by whole-genome RNA sequencing. The clinical relevance of the Axin1-dependent gene expression signature was then tested in a database of 2,239 clinical colorectal cancer (CRC) samples.
RESULTS: We found that Axin1 was dispensable for normal intestinal homeostasis and redundant with Axin2 for the Wnt pathway downregulation. Axin1 deficiency in intestinal epithelial cells rendered mice more susceptible to chemically induced colon carcinogenesis, but reduced DSS-induced colitis by attenuating the induction of a pro-inflammatory program. RNA-seq analyses identified an IFNγ/Th1 immune program controlled by Axin1 that enhances the inflammatory response and protects against colorectal cancer. The Axin1-dependent gene expression signature was applied to human CRC samples and identified a group of patients with potential vulnerability to immune checkpoint blockade therapies.
CONCLUSIONS: Our study establishes, in vivo, that Axin1 have redundant function with Axin2 for Wnt downregulation and infers a new role for Axin1. Physiologically, Axin1 stimulates gut inflammation via an IFNγ/Th1 program that prevent tumor growth. Linked to its T-cell mediated effect, the colonic Axin1 signature offers therapeutic perspectives for CRC.

Keywords:  Axin; Intestinal homeostasis; Wnt/β-catenin pathway; colon carcinogenesis; intestinal inflammation

DOI:  https://doi.org/10.1016/j.jcmgh.2022.10.017
Inflamm Bowel Dis. 2022 Nov 10. pii: izac212. [Epub ahead of print]

Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier.

Scott A Jelinsky, Merel Derksen, Eric Bauman, Carla S Verissimo, Wies T M van Dooremalen, Jamie Lee Roos, Celia Higuera Barón, Celia Caballero-Franco, Bryce G Johnson, Michelle G Rooks, Johanna Pott, Bas Oldenburg, Robert G J Vries, Sylvia F Boj, Marion T Kasaian, Farzin Pourfarzad, Charles V Rosadini.

   BACKGROUND: Patient-derived organoid (PDO) models offer potential to transform drug discovery for inflammatory bowel disease (IBD) but are limited by inconsistencies with differentiation and functional characterization. We profiled molecular and cellular features across a range of intestinal organoid models and examined differentiation and establishment of a functional epithelial barrier.
METHODS: Patient-derived organoids or monolayers were generated from control or IBD patient-derived colon or ileum and were molecularly or functionally profiled. Biological or technical replicates were examined for transcriptional responses under conditions of expansion or differentiation. Cell-type composition was determined by deconvolution of cell-associated gene signatures and histological features. Differentiated control or IBD-derived monolayers were examined for establishment of transepithelial electrical resistance (TEER), loss of barrier integrity in response to a cocktail of interferon (IFN)-γ and tumor necrosis factor (TNF)-α, and prevention of cytokine-induced barrier disruption by the JAK inhibitor, tofacitinib.
RESULTS: In response to differentiation media, intestinal organoids and monolayers displayed gene expression patterns consistent with maturation of epithelial cell types found in the human gut. Upon differentiation, both colon- and ileum-derived monolayers formed functional barriers, with sustained TEER. Barrier integrity was compromised by inflammatory cytokines IFN-γ and TNF-α, and damage was inhibited in a dose-dependent manner by tofacitinib.
CONCLUSIONS: We describe the generation and characterization of human colonic or ileal organoid models capable of functional differentiation to mature epithelial cell types. In monolayer culture, these cells formed a robust epithelial barrier with sustained TEER and responses to pharmacological modulation. Our findings demonstrate that control and IBD patient-derived organoids possess consistent transcriptional and functional profiles that can enable development of epithelial-targeted therapies.

Keywords:  barrier function; cell differentiation; organoids; tofacitinib

DOI:  https://doi.org/10.1093/ibd/izac212
J Clin Oncol. 2022 Nov 09. 101200JCO2201423

Resistance Mechanisms to Anti-EGFR Therapy in RAS/RAF Wildtype Colorectal Cancer Vary by Regimen and Line of Therapy.

Christine M Parseghian, Ryan Sun, Melanie Woods, Stefania Napolitano, Hey Min Lee, Jumanah Alshenaifi, Jason Willis, Shakayla Nunez, Kanwal P Raghav, Van K Morris, John P Shen, Madhulika Eluri, Alexey Sorokin, Preeti Kanikarla, Eduardo Vilar, Marko Rehn, Agnes Ang, Teresa Troiani, Scott Kopetz.

PURPOSE: Acquired resistance to anti-EGFR therapy (EGFRi) in CRC has previously been explained by the model of acquiring new mutations in KRAS/NRAS/EGFR, among other MAPK-pathway members. However, this was primarily based on single-agent EGFRi trials and little is known about the resistance mechanisms of EGFRi combined with effective cytotoxic chemotherapy in previously untreated patients.
METHODS: We analyzed paired plasma samples from RAS/BRAF/EGFR wild-type mCRC patients enrolled in three large randomized trials evaluating EGFRi in the first-line in combination with chemotherapy and as a single-agent in third-line. The mutational signature of the alterations acquired with therapy was evaluated. CRC cell lines with resistance to cetuximab, FOLFOX, and SN38 were developed, and transcriptional changes profiled.
RESULTS: Patients whose tumors were treated with and responded to EGFRi alone were more likely to develop acquired mutations (46%) compared to those treated in combination with cytotoxic chemotherapy (9%). Further, contrary to the generally accepted hypothesis of the clonal evolution of acquired resistance, we demonstrate that baseline resistant subclonal mutations rarely expanded to become clonal at progression, and most remained subclonal or disappeared. Consistent with this clinical finding, preclinical models with acquired resistance to either cetuximab or chemotherapy were cross-resistant to the alternate agents, with transcriptomic profiles consistent with epithelial-to-mesenchymal transition (EMT). In contrast, commonly acquired resistance alterations in the MAPK pathway do not impact sensitivity to cytotoxic chemotherapy.
CONCLUSION: These findings support a model of resistance whereby transcriptomic mechanisms of resistance predominate in the presence of active cytotoxic chemotherapy combined with EGFRi, with a greater predominance of acquired MAPK mutations after single-agent EGFRi. The proposed model has implications for prospective studies evaluating EGFRi rechallenge strategies guided by acquired MAPK mutations, and highlights the need to address transcriptional mechanisms of resistance.

DOI: https://doi.org/10.1200/JCO.22.01423
Proc Natl Acad Sci U S A. 2022 11 16. 119(46): e2212057119

Mapping prohormone processing by proteases in human enteroendocrine cells using genetically engineered organoid models.

Joep Beumer, Julia Bauzá-Martinez, Tim S Veth, Veerle Geurts, Charelle Boot, Hannah Gilliam-Vigh, Steen S Poulsen, Filip K Knop, Wei Wu, Hans Clevers.

  Enteroendocrine cells (EECs) secrete hormones in response to ingested nutrients to control physiological processes such as appetite and insulin release. EEC hormones are synthesized as large proproteins that undergo proteolytic processing to generate bioactive peptides. Mutations in EEC-enriched proteases are associated with endocrinopathies. Due to the relative rarity of EECs and a paucity of in vitro models, intestinal prohormone processing remains challenging to assess. Here, human gut organoids in which EECs can efficiently be induced are subjected to CRISPR-Cas9-mediated modification of EEC-expressed endopeptidase and exopeptidase genes. We employ mass spectrometry-based analyses to monitor peptide processing and identify glucagon production in intestinal EECs, stimulated upon bone morphogenic protein (BMP) signaling. We map the substrates and products of major EECs endo- and exopeptidases. Our studies provide a comprehensive description of peptide hormones produced by human EECs and define the roles of specific proteases in their generation.

Keywords:  CRISPR-Cas9; enteroendocrine cells; intestinal organoids; peptidomics; prohormone processing

DOI:  https://doi.org/10.1073/pnas.2212057119
Methods Mol Biol. 2023 ;2603 151-161

Workflow for Quantitative Proteomic Analysis of Intestinal Organoids Using SILAC.

Alexis Gonneaud, Claude Asselin, Véronique Giroux, François-Michel Boisvert.

  Stable isotope labeling by amino acids in cell culture (SILAC) is a strategic quantitative mass spectrometry method to analyze multiple protein samples in different conditions simultaneously. In recent years, 3D cell growth culture conditions have been developed to establish intestinal organoids from isolated crypts, which mimic the intestine's cell composition and organization. Organoids, isolated from normal or diseased tissues, can be used to compare cell distribution and differentiation, signaling pathways, and cell responses to pharmacological agents, therapeutic drugs, endogenous or exogenous metabolites, and environmental stresses, among others. Here, we describe the process of generating SILAC organoids from the mouse small intestine.

Keywords:  Intestinal organoids; Mass spectrometry; Proteomics; SILAC

DOI:  https://doi.org/10.1007/978-1-0716-2863-8_12
J Pathol Clin Res. 2022 Nov 08.

Olfactomedin 4 associates with expression of differentiation markers but not with properties of cancer stemness, EMT nor metastatic spread in colorectal cancer.

Stefanie Jaitner, Elise Pretzsch, Jens Neumann, Achim Schäffauer, Matthias Schiemann, Martin Angele, Jörg Kumbrink, Sarah Schwitalla, Florian R Greten, Lydia Brandl, Frederick Klauschen, David Horst, Thomas Kirchner, Andreas Jung.

  Tumor stem cells play a pivotal role in carcinogenesis and metastatic spread in colorectal cancer (CRC). Olfactomedin 4 (OLFM4) is co-expressed with the established stem cell marker leucine-rich repeat-containing G protein-coupled receptor 5 at the bottom of intestinal crypts and has been suggested as a surrogate for cancer stemness and a biomarker in gastrointestinal tumors associated with prognosis. Therefore, it was the aim of the present study to clarify whether OLFM4 is involved in carcinogenesis and metastatic spread in CRC. We used a combined approach of functional assays using forced OLFM4 overexpression in human CRC cell lines, xenograft mice, and an immunohistochemical approach using patient tissues to investigate the impact of OLFM4 on stemness, canonical Wnt signaling, properties of metastasis and differentiation as well as prognosis. OLFM4 expression correlated weakly with tumor grade in one patient cohort (metastasis collection: p = 0.05; pooled analysis of metastasis collection and survival collection: p = 0.19) and paralleled the expression of differentiation markers (FABP2, MUC2, and CK20) (p = 0.002) but did not correlate with stemness-associated markers. Further analyses in CRC cells lines as well as xenograft mice including forced overexpression of OLFM4 revealed that OLFM4 neither altered the expression of markers of stemness nor epithelial-mesenchymal transition, nor did OLFM4 itself drive proliferation, migration, or colony formation, which are all prerequisites of carcinogenesis and tumor progression. In line with this, we found no significant correlation between OLFM4 expression, metastasis, and patient survival. In summary, expression of OLFM4 in human CRC seems to be characteristic of differentiation marker expression in CRC but is not a driver of carcinogenesis nor metastatic spread.

Keywords:  OLFM4; colorectal cancer; olfactomedin 4; stem cells; stemness

DOI:  https://doi.org/10.1002/cjp2.300
Front Immunol. 2022 ;13 1027124

Advancing immune checkpoint blockade in colorectal cancer therapy with nanotechnology.

Zefan Liu, Yucheng Xiang, Yaxian Zheng, Xin Kang.

  Immune checkpoint blockade (ICB) has gained unparalleled success in the treatment of colorectal cancer (CRC). However, undesired side effects, unsatisfactory response rates, tumor metastasis, and drug resistance still hinder the further application of ICB therapy against CRC. Advancing ICB with nanotechnology can be game-changing. With the development of immuno-oncology and nanomaterials, various nanoplatforms have been fabricated to enhance the efficacy of ICB in CRC treatment. Herein, this review systematically summarizes these recent nano-strategies according to their mechanisms. Despite their diverse and complex designs, these nanoplatforms have four main mechanisms in enhancing ICB: 1) targeting immune checkpoint inhibitors (ICIs) to tumor foci, 2) increasing tumor immunogenicity, 3) remodeling tumor microenvironment, and 4) pre-sensitizing immune systems. Importantly, advantages of nanotechnology in CRC, such as innovating the mode-of-actions of ICB, modulating intestinal microbiome, and integrating the whole process of antigen presentation, are highlighted in this review. In general, this review describes the latest applications of nanotechnology for CRC immunotherapy, and may shed light on the future design of ICB platforms.

Keywords:  colorectal cancer; drug delivery; immune checkpoint inhibitors; nanotechnology; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2022.1027124
Proc Natl Acad Sci U S A. 2022 11 16. 119(46): e2207327119

Directed evolution identifies high-affinity cystine-knot peptide agonists and antagonists of Wnt/β-catenin signaling.

Simon Hansen, Yingnan Zhang, Sunhee Hwang, Ahmad Nabhan, Wanqing Li, Jakob Fuhrmann, Yvonne Kschonsak, Lijuan Zhou, Aaron H Nile, Xinxin Gao, Robert Piskol, Felipe de Sousa E Melo, Frederic J de Sauvage, Rami N Hannoush.

  Developing peptide-based tools to fine-tune growth signaling pathways, in particular molecules with exquisite selectivity and high affinities, opens up opportunities for cellular reprogramming in tissue regeneration. Here, we present a library based on cystine-knot peptides (CKPs) that incorporate multiple loops for randomization and selection via directed evolution. Resulting binders could be assembled into multimeric structures to fine-tune cellular signaling. An example is presented for the Wnt pathway, which plays a key role in the homeostasis and regeneration of tissues such as lung, skin, and intestine. We discovered picomolar affinity CKP agonists of the human LPR6 receptor by exploring the limits of the topological manipulation of LRP6 dimerization. Structural analyses revealed that the agonists bind at the first β-propeller domain of LRP6, mimicking the natural Wnt inhibitors DKK1 and SOST. However, the CKP agonists exhibit a different mode of action as they amplify the signaling of natural Wnt ligands but do not activate the pathway by themselves. In an alveolosphere organoid model, the CKP agonists induced alveolar stem cell activity. They also stimulated growth in primary human intestinal organoids. The approach described here advances the important frontier of next-generation agonist design and could be applied to other signaling pathways to discover tunable agonist ligands.

Keywords:  Wnt; agonist; directed evolution; peptide; phage display; regeneration; stem cells

DOI:  https://doi.org/10.1073/pnas.2207327119
Nat Commun. 2022 Nov 11. 13(1): 6840

pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation.

Olga Boix, Marion Martinez, Santiago Vidal, Marta Giménez-Alejandre, Lluís Palenzuela, Laura Lorenzo-Sanz, Laura Quevedo, Olivier Moscoso, Jorge Ruiz-Orera, Pilar Ximénez-Embún, Nikaoly Ciriaco, Paolo Nuciforo, Camille Stephan-Otto Attolini, M Mar Albà, Javier Muñoz, Tian V Tian, Ignacio Varela, Ana Vivancos, Santiago Ramón Y Cajal, Purificación Muñoz, Carmen Rivas, María Abad.

The human transcriptome contains thousands of small open reading frames (sORFs) that encode microproteins whose functions remain largely unexplored. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary conserved ubiquitin-like protein (UBL) expressed in many epithelia and upregulated upon differentiation and under cellular stress. By gain- and loss-of-function studies, we demonstrate that pTINCR is a key inducer of epithelial differentiation in vitro and in vivo. Interestingly, low expression of TINCR associates with worse prognosis in several epithelial cancers, and pTINCR overexpression reduces malignancy in patient-derived xenografts. At the molecular level, pTINCR binds to SUMO through its SUMO interacting motif (SIM) and to CDC42, a Rho-GTPase critical for actin cytoskeleton remodeling and epithelial differentiation. Moreover, pTINCR increases CDC42 SUMOylation and promotes its activation, triggering a pro-differentiation cascade. Our findings suggest that the microproteome is a source of new regulators of cell identity relevant for cancer.

DOI: https://doi.org/10.1038/s41467-022-34529-6
Mol Cancer Ther. 2022 Nov 07. pii: MCT-22-0101. [Epub ahead of print]

Genotype-tailored ERK/MAPK pathway and HDAC inhibition rewires the apoptotic rheostat to trigger colorectal cancer cell death.

Laura J Jenkins, Ian Y Luk, Walter D Fairlie, Erinna F Lee, Michelle Palmieri, Kael L Schoffer, Tao Tan, Irvin Ng, Natalia Vukelic, Sharon Tran, Janson Wt Tse, Rebecca Nightingale, Zakia Alam, Fiona Chionh, George Iatropoulos, Matthias Ernst, Shoukat Afshar-Sterle, Jayesh Desai, Peter Gibbs, Oliver M Sieber, Amardeep S Dhillon, Niall C Tebbutt, John M Mariadason.

The EGFR/RAS/MEK/ERK signalling pathway (ERK/MAPK) is hyper-activated in most colorectal cancers (CRCs). A current limitation of inhibitors of this pathway is that they primarily induce cytostatic effects in CRC cells. Nevertheless, these drugs do induce expression of pro-apoptotic factors, suggesting they may prime CRC cells to undergo apoptosis. As histone deacetylase inhibitors (HDACi) induce expression of multiple pro-apoptotic proteins, we examined whether they could synergize with ERK/MAPK inhibitors to trigger CRC cell apoptosis. Combined MEK/ERK and HDAC inhibition synergistically induced apoptosis in CRC cell lines and patient-derived tumour organoids in vitro, and attenuated Apc-initiated adenoma formation in vivo. Mechanistically, combined MAPK/HDAC inhibition enhanced expression of the BH3-only pro-apoptotic proteins BIM and BMF, and their knockdown significantly attenuated MAPK/HDAC inhibitor-induced apoptosis. Importantly, we demonstrate that the paradigm of combined MAPK/HDAC inhibitor treatment to induce apoptosis can be tailored to specific MAPK genotypes in CRCs, by combining a HDAC inhibitor with either an EGFR, KRASG12C or BRAFV600 inhibitor in KRAS/BRAFWT; KRASG12C, BRAFV600E CRC cell lines respectively. These findings identify a series of ERK/MAPK genotype tailored treatment strategies that can readily undergo clinical testing for the treatment of colorectal cancer. .

DOI: https://doi.org/10.1158/1535-7163.MCT-22-0101
Cancer Sci. 2022 Nov 12.

Rac1 promotes the reprogramming of glucose metabolism and the growth of colon cancer cells through up-regulating SOX9.

Jiaxin Liang, Qiang Liu, Longzheng Xia, Jinguan Lin, Linda Oyang, Shiming Tan, Qiu Peng, Xianjie Jiang, Xuemeng Xu, Nayiyuan Wu, Yanyan Tang, Min Su, Xia Luo, Yiqing Yang, Qianjin Liao, Yujuan Zhou.

  Metabolic reprogramming is the survival rule of tumor cells, and tumor cells can meet their high metabolic requirements by changing the energy metabolism mode. Metabolic reprogramming of tumor cells is an important biochemical basis of tumor malignant phenotypes. Ras-related C3 botulinum toxin substrate 1 (Rac1) is abnormally expressed in a variety of tumors and plays an important role in the proliferation, invasion and migration of tumor cells. However, the role of Rac1 in tumor metabolic reprogramming is still unclear. Herein, we revealed that Rac1 was highly expressed in colon cancer tissues and cell lines. Rac1 promotes the proliferation, migration and invasion of colon cancer cells by upregulating SOX9, which as a transcription factor can directly bind to the promoters of HK2 and G6PD genes and regulate their transcriptional activity. Rac1 upregulates the expression of SOX9 through the PI3K/AKT signaling pathway. Moreover, Rac1 can promote glycolysis and the activation of pentose phosphate pathway in colon cancer cells by mediating the axis of SOX9/HK2/G6PD. These findings reveal novel regulatory axes involving Rac1/SOX9/HK2/G6PD in the development and progression of colon cancer, providing novel promising therapeutic targets.

Keywords:  Rac1; SOX9; glycolysis; metabolic reprogramming; pentose phosphate pathway

DOI:  https://doi.org/10.1111/cas.15652
Cancer Diagn Progn. 2022 Nov-Dec;2(6):2(6): 620-626

Examination of the Effect of Proton Pump Inhibitors on the Anticancer Activity of Oxaliplatin.

Junya Hashizume, Kayoko Sato, Hiroo Nakagawa, Hitomi Harasawa, Takuya Honda, Yukinobu Kodama.

   BACKGROUND/AIM: Oxaliplatin (L-OHP) is absorbed by cancer cells via organic cation transporter1-3 (OCT1-3). However, proton pump inhibitors (PPIs) suppress the function of OCT1-3. This study investigated whether PPIs attenuate the antitumor effect of L-OHP.
PATIENTS AND METHODS: Colorectal cancer patients who received FOLFOX (L-OHP + 5-fluorouracil: 5-FU) + bevacizumab therapy at Nagasaki University Hospital from October 1, 2010 to September 30, 2019 were retrospectively investigated. Patients were categorized into two groups with or without PPIs use. Progression-free survival (PFS) between the two groups was compared using the log-rank test. L-OHP was added to the intestinal epithelial Caco-2 cell line with or without the PPI rabeprazole, and then cell viability was analyzed using the WST-8 cell proliferation assay.
RESULTS: The median PFS was 11.4 months in the group with PPIs and 9.7 months in the group without PPIs (p=0.736). No significant effect of 1-10 μM rabeprazole was observed on the antitumor effect of L-OHP. Plasma concentrations of rabeprazole at clinical doses are 1.0-1.3 μM.
CONCLUSION: Even if L-OHP interacts with PPIs, clinical doses of PPIs were considered to have minimal effect on the antitumor effect of L-OHP.

Keywords:  Proton pump inhibitors; colorectal cancer; organic cation transporters; oxaliplatin

DOI:  https://doi.org/10.21873/cdp.10151
Cancers (Basel). 2022 Oct 31. pii: 5368. [Epub ahead of print]14(21):

Nuclear Membrane Protein SUN5 Is Highly Expressed and Promotes Proliferation and Migration in Colorectal Cancer by Regulating the ERK Pathway.

Xiaoyue Song, Ruhong Li, Gang Liu, Lihua Huang, Peng Li, Wanjiang Feng, Qiujie Gao, Xiaowei Xing.

  SUN5 was first identified as a nuclear envelope protein involved in spermatocyte division. We found that SUN5 was highly expressed in some cancers, but its function and mechanism in cancer development remain unclear. In the present study, we demonstrated that SUN5 was highly expressed in colorectal cancer (CRC) tissues and cells, as indicated by bioinformatics analysis, and SUN5 promoted cell proliferation and migration in vitro. Moreover, the overexpression of SUN5 upregulated phosphorylated ERK1/2 (pERK1/2), whereas the knockdown of SUN5 yielded the opposite results. PD0325901 decreased the level of pERK1/2 to inhibit cell proliferation and migration, which was partially reversed by SUN5 overexpression, indicating that drug resistance existed in patients with high SUN5 expression. The xenograft transplantation experiment showed that SUN5 accelerated tumor formation in vivo. Furthermore, we found that SUN5 regulated the ERK pathway via Nesprin2 mediation and promoted the nuclear translocation of pERK1/2 by interacting with Nup93. Thus, these findings indicated that highly expressed SUN5 promoted CRC proliferation and migration by regulating the ERK pathway, which may contribute to the clinical diagnosis and new treatment strategies for CRC.

Keywords:  ERK1/2; SUN5; colorectal cancer; migration; proliferation

DOI:  https://doi.org/10.3390/cancers14215368
Cancer Treat Rev. 2022 Nov 01. pii: S0305-7372(22)00149-9. [Epub ahead of print]111 102480

Advances in immunotherapy for MMR proficient colorectal cancer.

Hazel Lote, Naureen Starling, Rille Pihlak, Marco Gerlinger.

Survival in mismatch-repair proficient (MMRp) metastatic colorectal cancer (mCRC) remains poor and chemotherapy is the mainstay of treatment. Immunotherapy has demonstrated durable responses and a favourable side-effect profile in various cancer types and multiple clinical trials have been conducted in MMRp mCRC. In this review we summarise emerging trial data which demonstrate promising immunotherapy combinations in MMRp mCRC. We outline barriers to success, evaluate emerging biomarkers and discuss potential strategies to increase the effectiveness of immunotherapy in MMRp mCRC.

DOI: https://doi.org/10.1016/j.ctrv.2022.102480
Cancers (Basel). 2022 Nov 01. pii: 5391. [Epub ahead of print]14(21):

The Validity of Surrogate Endpoints in Sub Groups of Metastatic Colorectal Cancer Patients Defined by Treatment Class and KRAS Status.

Heather Poad, Sam Khan, Lorna Wheaton, Anne Thomas, Michael Sweeting, Sylwia Bujkiewicz.

  Background and Aim: Findings from the literature suggest that the validity of surrogate endpoints in metastatic colorectal cancer (mCRC) may depend on a treatments' mechanism of action. We explore this and the impact of Kirsten rat sarcoma (KRAS) status on surrogacy patterns in mCRC. Methods: A systematic review was undertaken to identify randomized controlled trials (RCTs) for pharmacological therapies in mCRC. Bayesian meta-analytic methods for surrogate endpoint evaluation were used to evaluate surrogate relationships across all RCTs, by KRAS status and treatment class. Surrogate endpoints explored were progression free survival (PFS) as a surrogate endpoint for overall survival (OS), and tumour response (TR) as a surrogate for PFS and OS. Results: 66 RCTs were identified from the systematic review. PFS showed a strong surrogate relationship with OS across all data and in subgroups by KRAS status. The relationship appeared stronger within individual treatment classes compared to the overall analysis. The TR-PFS and TR-OS relationships were found to be weak overall but stronger within the Epidermal Growth Factor Receptor + Chemotherapy (EGFR + Chemo) treatment class; both overall and in the wild type (WT) patients for TR-PFS, but not in patients with the mutant (MT) KRAS status where data were limited. Conclusions: PFS appeared to be a good surrogate endpoint for OS. TR showed a moderate surrogate relationship with PFS and OS for the EGFR + Chemo treatment class. There was some evidence of impact of the mechanism of action on the strength of the surrogacy patterns in mCRC, but little evidence of the impact of KRAS status on the validity of surrogate endpoints.

Keywords:  bayesian meta-analysis; health technology assessment; metastatic colorectal cancer; surrogate endpoints

DOI:  https://doi.org/10.3390/cancers14215391
Cancers (Basel). 2022 Oct 22. pii: 5182. [Epub ahead of print]14(21):

Regulatory Role of Sphingosine-1-Phosphate and C16:0 Ceramide, in Immunogenic Cell Death of Colon Cancer Cells Induced by Bak/Bax-Activation.

Jeremy A Hengst, Asvelt J Nduwumwami, Jong K Yun.

  We recently identified the sphingosine kinases (SphK1/2) as key intracellular regulators of immunogenic cell death (ICD) in colorectal cancer (CRC) cells. To better understand the mechanism by which SphK inhibition enhances ICD, we focused on the intracellular signaling pathways leading to cell surface exposure of calreticulin (ectoCRT). Herein, we demonstrate that ABT-263 and AZD-5991, inhibitors of Bcl-2/Bcl-XL and Mcl-1, respectively, induce the production of ectoCRT, indicative of ICD. Inhibition of SphK1 significantly enhanced ABT/AZD-induced ectoCRT production, in a caspase 8-dependent manner. Mechanistically, we demonstrate that ABT/AZD-induced Bak/Bax activation stimulates pro-survival SphK1/sphingosine-1-phosphate (S1P) signaling, which attenuates ectoCRT production. Additionally, we identified a regulatory role for ceramide synthase 6 (CerS6)/C16:0 ceramide in transporting of ectoCRT to the cell surface. Together, these results indicate that the sphingolipid metabolic regulators of the sphingolipid rheostat, S1P and C16:0 ceramide, influence survival/death decisions of CRC cells in response to ICD-inducing chemotherapeutic agents. Importantly, SphK1, which produces S1P, is a stress-responsive pro-survival lipid kinase that suppresses ICD. While ceramide, produced by the inhibition of SphK1 is required for production of the cell surface marker of ICD, ectoCRT. Thus, inhibition of SphK1 represents a means to enhance the therapeutic efficacy of ICD-inducing agents.

Keywords:  Bak; Bax; cell signaling; ceramide; colorectal cancer; immunogenic cell death; inflammation; sphingolipids; sphingosine phosphate

DOI:  https://doi.org/10.3390/cancers14215182
Sci Signal. 2022 Nov 08. 15(759): eabj4220

Metabolite activation of tumorigenic signaling pathways in the tumor microenvironment.

Vivien Low, Zhongchi Li, John Blenis.

The role of metabolites exchanged in the tumor microenvironment is largely thought of as fuels to drive the increased biosynthetic and bioenergetic demands of growing tumors. However, this view is shifting as metabolites are increasingly shown to function as signaling molecules that directly regulate oncogenic pathways. Combined with our growing understanding of the essential role of stromal cells, this shift has led to increased interest in how the collective and interconnected metabolome of the tumor microenvironment can drive malignant transformation, epithelial-to-mesenchymal transition, drug resistance, immune evasion, and metastasis. In this review, we discuss how metabolite exchange between tumors and various cell types in the tumor microenvironment-such as fibroblasts, adipocytes, and immune cells-can activate signaling pathways that drive cancer progression.

DOI: https://doi.org/10.1126/scisignal.abj4220
Biomedicines. 2022 Oct 25. pii: 2690. [Epub ahead of print]10(11):

Role of AMPK in Regulation of Oxaliplatin-Resistant Human Colorectal Cancer.

Sun Young Park, Ye Seo Chung, So Yeon Park, So Hee Kim.

  Oxaliplatin is a platinum analog that can interfere with DNA replication and transcription. Continuous exposure to oxaliplatin results in chemoresistance; however, this mechanism is not well known. In this study, oxaliplatin-resistant (OR) colorectal cancer (CRC) cells of HCT116, HT29, SW480 and SW620 were established by gradually increasing the drug concentration to 2.5 μM. The inhibitory concentrations of cell growth by 50% (IC50) of oxaliplatin were 4.40-12.7-fold significantly higher in OR CRC cells as compared to their respective parental (PT) CRC cells. Phospho-Akt and phospho-mammalian target of rapamycin (mTOR) decreased in PT CRC cells but was overexpressed in OR CRC cells in response to oxaliplatin. In addition, an oxaliplatin-mediated decrease in phospho-AMP-activated protein kinase (AMPK) in PT CRC cells induced autophagy. Contrastingly, an increased phospho-AMPK in OR CRC cells was accompanied by a decrease in LC3B, further inducing the activity of glycolytic enzymes, such as glucose transporter 1 (GLUT1), 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) and phosphofructokinase 1 (PFK1), to mediate cell survival. Inhibition of AMPK in OR CRC cells induced autophagy through inactivation of Akt/mTOR pathway and a decrease in GLUT1, PFKFB3, and PFK1. Collectively, targeting AMPK may provide solutions to overcome chemoresistance in OR CRC cells and restore chemosensitivity to anticancer drugs.

Keywords:  AMPK; Akt-mTOR; autophagy; chemoresistance; colorectal cancer; glycolysis; oxaliplatin

DOI:  https://doi.org/10.3390/biomedicines10112690
iScience. 2022 Nov 18. 25(11): 105392

Deconvolution of bulk tumors into distinct immune cell states predicts colorectal cancer recurrence.

Donghyo Kim, Jinho Kim, Juhun Lee, Seong Kyu Han, Kwanghwan Lee, JungHo Kong, Yeon Jeong Kim, Woo Yong Lee, Seong Hyeon Yun, Hee Cheol Kim, Hye Kyung Hong, Yong Beom Cho, Donghyun Park, Sanguk Kim.

  Predicting colorectal cancer recurrence after tumor resection is crucial because it promotes the administration of proper subsequent treatment or management to improve the clinical outcomes of patients. Several clinical or molecular factors, including tumor stage, metastasis, and microsatellite instability status, have been used to assess the risk of recurrence, although their predictive ability is limited. Here, we predicted colorectal cancer recurrence based on cellular deconvolution of bulk tumors into two distinct immune cell states: cancer-associated (tumor-infiltrating immune cell-like) and noncancer-associated (peripheral blood mononuclear cell-like). Prediction model performed significantly better when immune cells were deconvoluted into two states rather than a single state, suggesting that the difference in cancer recurrence was better explained by distinct states of immune cells. It indicates the importance of distinguishing immune cell states using cellular deconvolution to improve the prediction of colorectal cancer recurrence.

Keywords:  Biocomputational method; Bioinformatics; Cancer systems biology; Health informatics; Health sciences; Immunology; Oncology; Systems biology

DOI:  https://doi.org/10.1016/j.isci.2022.105392
World J Gastroenterol. 2022 Oct 21. 28(39): 5658-5665

Risk factors for small intestinal adenocarcinomas that are common in the proximal small intestine.

Shunji Fujimori, Ryohei Hamakubo, Aitoshi Hoshimoto, Takayoshi Nishimoto, Jun Omori, Naohiko Akimoto, Shu Tanaka, Atsushi Tatsuguchi, Katsuhiko Iwakiri.

  The frequency of primary small intestinal adenocarcinoma is increasing but is still low. Its frequency is approximately 3% of that of colorectal adenocarcinoma. Considering that the small intestine occupies 90% of the surface area of the gastrointestinal tract, small intestinal adenocarcinoma is very rare. The main site of small intestinal adenocarcinoma is the proximal small intestine. Based on this characteristic, dietary animal proteins/lipids and bile concentrations are implicated and reported to be involved in carcinogenesis. Since most nutrients are absorbed in the proximal small intestine, the effect of absorbable intestinal content is a suitable explanation for why small intestinal adenocarcinoma is more common in the proximal small intestine. The proportion of aerobic bacteria is high in the proximal small intestine, but the absolute number of bacteria is low. In addition, the length and density of villi are greater in the proximal small intestine. However, the involvement of villi is considered to be low because the number of small intestinal adenocarcinomas is much smaller than that of colorectal adenocarcinomas. On the other hand, the reason for the low incidence of small intestinal adenocarcinoma in the distal small intestine may be that immune organs reside there. Genetic and disease factors increase the likelihood of small intestinal adenocarcinoma. In carcinogenesis experiments in which the positions of the small and large intestines were exchanged, tumors still occurred in the large intestinal mucosa more often. In other words, the influence of the intestinal contents is small, and there is a large difference in epithelial properties between the small intestine and the large intestine. In conclusion, small intestinal adenocarcinoma is rare compared to large intestinal adenocarcinoma due to the nature of the epithelium. It is reasonable to assume that diet is a trigger for small intestinal adenocarcinoma.

Keywords:  Adenocarcinoma; Carcinogenesis; Large intestine; Risk factor; Small intestine

DOI:  https://doi.org/10.3748/wjg.v28.i39.5658
Elife. 2022 Nov 11. pii: e84025. [Epub ahead of print]11

Developing a taxonomy for colorectal cancer.

Jiansong Fang, Dawei Wang, Xiude Fan.

  Analyzing how gene interaction networks are perturbed in individuals can help identify different types of colorectal cancers, paving the way towards personalized care.

Keywords:  biological network; cancer biology; colorectal cancer; gene interaction; human; molecular subtype; precision medicine

DOI:  https://doi.org/10.7554/eLife.84025
Int J Mol Sci. 2022 Oct 31. pii: 13252. [Epub ahead of print]23(21):

Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis.

Kristian Urh, Nina Zidar, Emanuela Boštjančič.

  Cancer stem cells (CSC) play one of the crucial roles in the pathogenesis of various cancers, including colorectal cancer (CRC). Although great efforts have been made regarding our understanding of the cancerogenesis of CRC, CSC involvement in CRC development is still poorly understood. Using bioinformatics and RNA-seq data of normal mucosa, colorectal adenoma, and carcinoma (n = 106) from GEO and TCGA, we identified candidate CSC genes and analyzed pathway enrichment analysis (PEI) and protein-protein interaction analysis (PPI). Identified CSC-related genes were validated using qPCR and tissue samples from 47 patients with adenoma, adenoma with early carcinoma, and carcinoma without and with lymph node metastasis and were compared to normal mucosa. Six CSC-related genes were identified: ANLN, CDK1, ECT2, PDGFD, TNC, and TNXB. ANLN, CDK1, ECT2, and TNC were differentially expressed between adenoma and adenoma with early carcinoma. TNC was differentially expressed in CRC without lymph node metastases whereas ANLN, CDK1, and PDGFD were differentially expressed in CRC with lymph node metastases compared to normal mucosa. ANLN and PDGFD were differentially expressed between carcinoma without and with lymph node metastasis. Our study identified and validated CSC-related genes that might be involved in early stages of CRC development (ANLN, CDK1, ECT2, TNC) and in development of metastasis (ANLN, PDGFD).

Keywords:  RNA-seq; adenoma-carcinoma progression; bioinformatics analysis; cancer stem cells; colorectal cancer; differentially expressed genes; metastases; qPCR

DOI:  https://doi.org/10.3390/ijms232113252
Elife. 2022 11 08. pii: e81114. [Epub ahead of print]11

Gene interaction perturbation network deciphers a high-resolution taxonomy in colorectal cancer.

Zaoqu Liu, Siyuan Weng, Qin Dang, Hui Xu, Yuqing Ren, Chunguang Guo, Zhe Xing, Zhenqiang Sun, Xinwei Han.

 Molecular subtypes of colorectal cancer (CRC) are currently identified via the snapshot transcriptional profiles, largely ignoring the dynamic changes of gene expressions. Conversely, biological networks remain relatively stable irrespective of time and condition. Here, we introduce an individual-specific gene interaction perturbation network-based (GIN) approach and identify six GIN subtypes (GINS1-6) with distinguishing features: (i) GINS1 (proliferative, 24%~34%), elevated proliferative activity, high tumor purity, immune-desert, PIK3CA mutations, and immunotherapeutic resistance; (ii) GINS2 (stromal-rich, 14%~22%), abundant fibroblasts, immune-suppressed, stem-cell-like, SMAD4 mutations, unfavorable prognosis, high potential of recurrence and metastasis, immunotherapeutic resistance, and sensitive to fluorouracil-based chemotherapy; (iii) GINS3 (KRAS-inactivated, 13%~20%), high tumor purity, immune-desert, activation of EGFR and ephrin receptors, chromosomal instability (CIN), fewer KRAS mutations, SMOC1 methylation, immunotherapeutic resistance, and sensitive to cetuximab and bevacizumab; (iv) GINS4 (mixed, 10%~19%), moderate level of stromal and immune activities, transit-amplifying-like, and TMEM106A methylation; (v) GINS5 (immune-activated, 12%~24%), stronger immune activation, plentiful tumor mutation and neoantigen burden, microsatellite instability and high CpG island methylator phenotype, BRAF mutations, favorable prognosis, and sensitive to immunotherapy and PARP inhibitors; (vi) GINS6, (metabolic, 5%~8%), accumulated fatty acids, enterocyte-like, and BMP activity. Overall, the novel high-resolution taxonomy derived from an interactome perspective could facilitate more effective management of CRC patients.

Keywords: biological network; cancer biology; colorectal cancer; gene interaction; human; molecular subtype; precision medicine

DOI: https://doi.org/10.7554/eLife.81114
Int J Mol Sci. 2022 Oct 31. pii: 13277. [Epub ahead of print]23(21):

PD-L1 Expression in High-Risk Early-Stage Colorectal Cancer-Its Clinical and Biological Significance in Immune Microenvironment.

Bing-Syuan Chung, I-Chuang Liao, Peng-Chan Lin, Shang-Yin Wu, Jui-Wen Kang, Bo-Wen Lin, Po-Chuan Chen, Ren-Hao Chan, Chung-Ta Lee, Meng-Ru Shen, Shang-Hung Chen, Yu-Min Yeh.

  Programmed death-ligand 1 (PD-L1) is an immune checkpoint molecule that can regulate immune responses in the tumor microenvironment (TME); however, the clinical applications of PD-L1 in early-stage colorectal cancer (CRC) remain unclear. In this study, we aimed to investigate the relationship between PD-L1 expression and survival outcome and explore its relevant immune responses in CRC. PD-L1 expression was evaluated by immunohistochemical staining to determine the tumor proportion score and combined positive score (CPS) in a Taiwanese CRC cohort. The oncomine immune response research assay was conducted for immune gene expression analyses. CRC datasets from the TCGA database were reappraised for PD-L1-associated gene enrichment analyses using GSEA. The high expression of PD-L1 (CPS ≥ 5) was associated with longer recurrence-free survival (p = 0.031) and was an independent prognostic factor as revealed by multivariate analysis. High PD-L1 expression was related to six immune-related gene signatures, and CXCL9 is the most significant overexpressed gene in differential analyses. High CXCL9 expression correlated with increased infiltration levels of immune cells in the TME, including CD8+ T lymphocytes and M1 macrophages. These findings suggest that high PD-L1 expression is a prognostic factor of early-stage CRC, and CXCL9 may play a key role in regulating PD-L1 expression.

Keywords:  CXCL9; PD-L1; colorectal cancer; combined positive score; prognostic biomarker

DOI:  https://doi.org/10.3390/ijms232113277
Mol Oncol. 2022 Nov 08.

Expression pattern of secretory-cell-related transcriptional signatures in colon adenocarcinomas defines tumor microenvironment characteristics and correlates with clinical outcomes.

Rui Zhou, Lingbo Li, Shaoyan Xi, Yue Zhang, Zhihong Liu, Dongqiang Zeng, Huiying Sun, Jianhua Wu, Ling Wang, Min Shi, Jianping Bin, Yulin Liao, Wangjun Liao.

  Despite the connection of secretory cells to distinct mucus-containing colon cancer histological subtypes and the interaction of secretory cells with immune cells in the pathogenesis of intestinal inflammatory diseases, whether the secretory cell signatures are associated with tumor microenvironment (TME) heterogeneity and can aid in colon cancer patient classification have not been investigated. Here, by performing the principal component analysis and consensus clustering analysis, we identified four distinct expression patterns based on secretory cell signatures which were significantly associated with different clinical behaviors, TME landscape, pathway activation, genomic mutations, and DNA methylation characteristics. Subsequently, a "SCS score" model was constructed. The high SCS score indicated a pattern of "secretory cell subtype 2", which was characterized by stromal infiltration and activation, and predicted poor prognosis and low sensitivity to fluorouracil-based chemotherapy and immunotherapy, but high sensitivity to PI3K catalytic subunit inhibitors. In conclusion, our study comprehensively uncovered the tumor heterogeneity related to secretory cell signature expression patterns. Moreover, the SCS score can supplement routine histopathological assessments to guide personalized therapeutic strategies in colon cancer patients.

Keywords:  Chemotherapy; Colon cancer; Immunotherapy; Molecular subtype; Prognosis; Secretory cells

DOI:  https://doi.org/10.1002/1878-0261.13338
Elife. 2022 Nov 08. pii: e82006. [Epub ahead of print]11

Alternative splicing downstream of EMT enhances phenotypic plasticity and malignant behaviour in colon cancer.

Tong Xu, Mathijs Verhagen, Rosalie Joosten, Wenjie Sun, Andrea Sacchetti, Leonel Munoz Sagredo, Véronique Orian-Rousseau, Riccardo Fodde.

  Phenotypic plasticity allows carcinoma cells to transiently acquire the quasi-mesenchymal features necessary to detach from the primary mass and proceed along the invasion-metastasis cascade. A broad spectrum of epigenetic mechanisms is likely to cause the epithelial-to-mesenchymal (EMT) and mesenchymal-to-epithelial (MET) transitions necessary to allow local dissemination and distant metastasis. Here, we report on the role played by alternative splicing (AS) in eliciting phenotypic plasticity in epithelial malignancies with focus on colon cancer. By taking advantage of the coexistence of subpopulations of fully epithelial (EpCAMhi) and quasi-mesenchymal and highly metastatic (EpCAMlo) cells in conventional human cancer cell lines, we here show that the differential expression of ESRP1 and other RNA-binding proteins (RBPs) downstream of the EMT master regulator ZEB1, alters the AS pattern of a broad spectrum of targets including CD44 and NUMB, thus resulting in the generation of specific isoforms functionally associated with increased invasion and metastasis. Additional functional and clinical validation studies indicate that both the newly identified RBPs and the CD44s and NUMB2/4 splicing isoforms promote local invasion and distant metastasis and are associated with poor survival in colon cancer. The systematic elucidation of the spectrum of EMT-related RBPs and AS targets in epithelial cancers, apart from the insights in the mechanisms underlying phenotypic plasticity, will lead to the identification of novel and tumor-specific therapeutic targets.

Keywords:  cancer biology; genetics; genomics; human

DOI:  https://doi.org/10.7554/eLife.82006
Sci Adv. 2022 Nov 11. 8(45): eadd2789

Nitroreductase-instructed supramolecular assemblies for microbiome regulation to enhance colorectal cancer treatments.

Jiali Chen, Pai Zhang, Yan Zhao, Jie Zhao, Xiaobo Wu, Ruijia Zhang, Ruitao Cha, Qingxin Yao, Yuan Gao.

The development of human microbiome has collectively correlated the sophisticated interactions between Fusobacterium nucleatum and colorectal cancers (CRCs). However, the treatment of CRC via disruption of gastrointestinal flora remains less explored. Aiming at the up-regulated activity of nitroreductase in F. nucleatum-infected tumors, here, we developed the nitroreductase-instructed supramolecular self-assembly. The designed assembly precursors underwent enzymatic transformation to form assemblies, which agglutinated F. nucleatum and eradicated the targeted bacteria. These assemblies with anti-F. nucleatum activity could further alleviate the bacteria-induced drug resistance effect, thus sensitizing CRC cells against chemo-drugs. Eventually, in mice bearing F. nucleatum-infected CRC, the local introduction of nitroreductase-instructed assemblies could efficiently inhibit the tumor growth. Overall, this study incorporated nitroreductase to broaden the toolbox of enzyme-instructed supramolecular self-assembly. The local introduction of nitroreductase-instructed assemblies could target F. nucleatum to eliminate its contribution to CRC drug resistance and ameliorate chemotherapy outcomes.

DOI: https://doi.org/10.1126/sciadv.add2789
Sci Rep. 2022 Nov 09. 12(1): 19152

Loss of SATB2 expression correlates with cytokeratin 7 and PD-L1 tumor cell positivity and aggressiveness in colorectal cancer.

Jan Hrudka, Radoslav Matěj, Andrej Nikov, Igor Tomyak, Hana Fišerová, Karolína Jelínková, Petr Waldauf.

Colorectal carcinoma (CRC) is a disease that causes significant morbidity and mortality worldwide. To improve treatment, new biomarkers are needed to allow better patient risk stratification in terms of prognosis. This study aimed to clarify the prognostic significance of colonic-specific transcription factor special AT-rich sequence-binding protein 2 (SATB2), cytoskeletal protein cytokeratin 7 (CK7), and immune checkpoint molecule programmed death-ligand 1 (PD-L1). We analyzed a cohort of 285 patients with surgically treated CRC for quantitative associations among the three markers and five traditional prognostic indicators (i.e., tumor stage, histological grade, variant morphology, laterality, and mismatch-repair/MMR status). The results showed that loss of SATB2 expression had significant negative prognostic implications relative to overall survival (OS) and cancer-specific survival (CSS), significantly shortened 5 years OS and CSS and 10 years CSS in patients with CRC expressing CK7, and borderline insignificantly shortened OS in patients with PD-L1 + CRC. PD-L1 showed a significant negative impact in cases with strong expression (membranous staining in 50-100% of tumor cells). Loss of SATB2 was associated with CK7 expression, advanced tumor stage, mucinous or signet ring cell morphology, high grade, right-sided localization but was borderline insignificant relative to PD-L1 expression. CK7 expression was associated with high grade and SATB2 loss. Additionally, a separate analysis of 248 neoadjuvant therapy-naïve cases was performed with mostly similar results. The loss of SATB2 and CK7 expression were significant negative predictors in the multivariate analysis adjusted for associated parameters and patient age. In summary, loss of SATB2 expression and gain of CK7 and strong PD-L1 expression characterize an aggressive phenotype of CRC.

DOI: https://doi.org/10.1038/s41598-022-22685-0