bims-tucedo 2022-08-21 papers

bims-tucedo

Biomed News

on Tumor cell dormancy

Issue of 2022‒08‒21
twenty-two papers selected by
Isabel Puig Borreil
Vall d’Hebron Institute of Oncology

Lung Fibroblasts Support Metastasis through Immune Microenvironment Remodeling.
SHMT2-mediated mitochondrial serine metabolism drives 5-FU resistance by fueling nucleotide biosynthesis.
Hypoxia-induced lncRNA STEAP3-AS1 activates Wnt/β-catenin signaling to promote colorectal cancer progression by preventing m6A-mediated degradation of STEAP3 mRNA.
Myeloid Cell-associated Resistance to PD-1/PD-L1 Blockade in Urothelial Cancer Revealed Through Bulk and Single-cell RNA Sequencing.
CRISPR/Cas9-based genome-wide screening for deubiquitinase subfamily identifies USP1 regulating MAST1-driven cisplatin-resistance in cancer cells.
Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling.
P21-activated kinase 2-mediated β-catenin signaling promotes cancer stemness and osimertinib resistance in EGFR-mutant non-small-cell lung cancer.
Longitudinal single-cell transcriptomics reveals distinct patterns of recurrence in acute myeloid leukemia.
Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma.
Pharmacological inhibition of NT5C2 reverses genetic and non-genetic drivers of 6-MP resistance in acute lymphoblastic leukemia.
EHMT2 methyltransferase governs cell identity in the lung and is required for KRASG12D tumor development and propagation.
A slow-cycling/quiescent cells subpopulation is involved in glioma invasiveness.
RNA N6 -methyladenosine reader YTHDC1 is essential for TGF-beta-mediated metastasis of triple negative breast cancer.
Reformation of the chondroitin sulfate glycocalyx enables progression of AR-independent prostate cancer.
Cell clusters softening triggers collective cell migration in vivo.
Single-cell transcriptomics reveals the regulative roles of cancer associated fibroblasts in tumor immune microenvironment of recurrent osteosarcoma.
Circular RNA circFIRRE drives osteosarcoma progression and metastasis through tumorigenic-angiogenic coupling.
Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer.
PACT promotes the metastasis of basal-like breast cancer through Rac1 SUMOylation and activation.
hiPSC-derived bone marrow milieu identifies a clinically actionable driver of niche-mediated treatment resistance in leukemia.
Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma.
Predicting response to immunotherapy in gastric cancer via multi-dimensional analyses of the tumour immune microenvironment.

Cancer Discov. 2022 Aug 19. OF1

Lung Fibroblasts Support Metastasis through Immune Microenvironment Remodeling.

COX-2+ lung fibroblasts reprogram myeloid cells to be immunosuppressive and support lung metastasis.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2022-149
Cell Rep. 2022 Aug 16. pii: S2211-1247(22)01050-6. [Epub ahead of print]40(7): 111233

SHMT2-mediated mitochondrial serine metabolism drives 5-FU resistance by fueling nucleotide biosynthesis.

Erica Pranzini, Elisa Pardella, Livio Muccillo, Angela Leo, Ilaria Nesi, Alice Santi, Matteo Parri, Tong Zhang, Alejandro Huerta Uribe, Tiziano Lottini, Lina Sabatino, Anna Caselli, Annarosa Arcangeli, Giovanni Raugei, Vittorio Colantuoni, Paolo Cirri, Paola Chiarugi, Oliver D K Maddocks, Paolo Paoli, Maria Letizia Taddei.

  5-Fluorouracil (5-FU) is a key component of chemotherapy for colorectal cancer (CRC). 5-FU efficacy is established by intracellular levels of folate cofactors and DNA damage repair strategies. However, drug resistance still represents a major challenge. Here, we report that alterations in serine metabolism affect 5-FU sensitivity in in vitro and in vivo CRC models. In particular, 5-FU-resistant CRC cells display a strong serine dependency achieved either by upregulating endogenous serine synthesis or increasing exogenous serine uptake. Importantly, regardless of the serine feeder strategy, serine hydroxymethyltransferase-2 (SHMT2)-driven compartmentalization of one-carbon metabolism inside the mitochondria represents a specific adaptation of resistant cells to support purine biosynthesis and potentiate DNA damage response. Interfering with serine availability or affecting its mitochondrial metabolism revert 5-FU resistance. These data disclose a relevant mechanism of mitochondrial serine use supporting 5-FU resistance in CRC and provide perspectives for therapeutic approaches.

Keywords:  5-FU resistance; CP: Cancer; DNA damage response; Serine metabolism; colorectal cancer; mitochondrial metabolism; nucleotide metabolism; one-carbon metabolism (OCM)

DOI:  https://doi.org/10.1016/j.celrep.2022.111233
Mol Cancer. 2022 Aug 19. 21(1): 168

Hypoxia-induced lncRNA STEAP3-AS1 activates Wnt/β-catenin signaling to promote colorectal cancer progression by preventing m6A-mediated degradation of STEAP3 mRNA.

Li Zhou, Jingwen Jiang, Zhao Huang, Ping Jin, Liyuan Peng, Maochao Luo, Zhe Zhang, Yan Chen, Na Xie, Wei Gao, Edouard C Nice, Jing-Quan Li, Hai-Ning Chen, Canhua Huang.

  BACKGROUND: Hypoxia, a typical hallmark of solid tumors, exhibits an essential role in the progression of colorectal cancer (CRC), in which the dysregulation of long non-coding RNAs (lncRNAs) is frequently observed. However, the underlying mechanisms are not clearly defined.METHODS: The TCGA database was analyzed to identify differential lncRNA expression involved in hypoxia-induced CRC progression. qRT-PCR was conducted to validate the upregulation of lncRNA STEAP3-AS1 in CRC cell lines and tumor-bearing mouse and zebrafish models under hypoxia. ChIP-qRT-PCR was used to detect the transcriptional activation of STEAP3-AS1 mediated by HIF-1α. RNA-seq, fluorescent in situ hybridization, RNA pulldown, RNA immunoprecipitation, co-immunoprecipitation, immunofluorescence and immunoblot experiments were used to ascertain the involved mechanisms. Functional assays were performed in both in vitro and in vivo models to investigate the regulatory role of STEAP3-AS1/STEAP3/Wnt/β-catenin axis in CRC proliferation and metastasis.
RESULTS: Here, we identified a hypoxia-induced antisense lncRNA STEAP3-AS1 that was highly expressed in clinical CRC tissues and positively correlated with poor prognosis of CRC patients. Upregulation of lncRNA STEAP3-AS1, which was induced by HIF-1α-mediated transcriptional activation, facilitated the proliferation and metastasis of CRC cells both in vitro and in vivo. Mechanistically, STEAP3-AS1 interacted competitively with the YTH domain-containing family protein 2 (YTHDF2), a N6-methyladenosine (m6A) reader, leading to the disassociation of YTHDF2 with STEAP3 mRNA. This effect protected STEAP3 mRNA from m6A-mediated degradation, enabling the high expression of STEAP3 protein and subsequent production of cellular ferrous iron (Fe2+). Increased Fe2+ levels elevated Ser 9 phosphorylation of glycogen synthase kinase 3 beta (GSK3β) and inhibited its kinase activity, thus releasing β-catenin for nuclear translocation and subsequent activation of Wnt signaling to support CRC progression.
CONCLUSIONS: Taken together, our study highlights the mechanisms of lncRNA STEAP3-AS1 in facilitating CRC progression involving the STEAP3-AS1/STEAP3/Wnt/β-catenin axis, which may provide novel diagnostic biomarkers or therapeutic targets to benefit CRC treatment. Hypoxia-induced HIF-1α transcriptionally upregulates the expression of lncRNA STEAP3-AS1, which interacts competitively with YTHDF2, thus upregulating mRNA stability of STEAP3 and consequent STEAP3 protein expression. The enhanced STEAP3 expression results in production of cellular ferrous iron (Fe2+), which induces the Ser 9 phosphorylation and inactivation of GSK3β, releasing β-catenin for nuclear translocation and contributing to subsequent activation of Wnt signaling to promote CRC progression.

Keywords:  Colorectal cancer; Hypoxia; LncRNA STEAPS-AS1; STEAP3; Wnt/β-catenin; YTHDF2; m6A modification

DOI:  https://doi.org/10.1186/s12943-022-01638-1
Clin Cancer Res. 2021 Aug 01. 27(15): 4287-4300

Myeloid Cell-associated Resistance to PD-1/PD-L1 Blockade in Urothelial Cancer Revealed Through Bulk and Single-cell RNA Sequencing.

Li Wang, John P Sfakianos, Kristin G Beaumont, Guray Akturk, Amir Horowitz, Robert P Sebra, Adam M Farkas, Sacha Gnjatic, Austin Hake, Sudeh Izadmehr, Peter Wiklund, William K Oh, Peter M Szabo, Megan Wind-Rotolo, Keziban Unsal-Kacmaz, Xin Yao, Eric Schadt, Padmanee Sharma, Nina Bhardwaj, Jun Zhu, Matthew D Galsky.

PURPOSE: To define dominant molecular and cellular features associated with PD-1/PD-L1 blockade resistance in metastatic urothelial cancer.EXPERIMENTAL DESIGN: We pursued an unbiased approach using bulk RNA sequencing data from two clinical trials to discover (IMvigor 210) and validate (CheckMate 275) pretreatment molecular features associated with resistance to PD-1/PD-L1 blockade in metastatic urothelial cancer. We then generated single-cell RNA sequencing (scRNA-seq) data from muscle-invasive bladder cancer specimens to dissect the cellular composition underlying the identified gene signatures.
RESULTS: We identified an adaptive immune response gene signature associated with response and a protumorigenic inflammation gene signature associated with resistance to PD-1/PD-L1 blockade. The adaptive immune response:protumorigenic inflammation signature expression ratio, coined the 2IR score, best correlated with clinical outcomes, and was externally validated. Mapping these bulk gene signatures onto scRNA-seq data uncovered their underlying cellular diversity, with prominent expression of the protumorigenic inflammation signature by myeloid phagocytic cells. However, heterogeneity in expression of adaptive immune and protumorigenic inflammation genes was observed among single myeloid phagocytic cells, quantified as the myeloid single cell immune:protumorigenic inflammation ratio (Msc2IR) score. Single myeloid phagocytic cells with low Msc2IR scores demonstrated upregulation of proinflammatory cytokines/chemokines and downregulation of antigen presentation genes, were unrelated to M1 versus M2 polarization, and were enriched in pretreatment blood samples from patients with PD-L1 blockade-resistant metastatic urothelial cancer.
CONCLUSIONS: The balance of adaptive immunity and protumorigenic inflammation in individual tumor microenvironments is associated with PD-1/PD-L1 resistance in urothelial cancer with the latter linked to a proinflammatory cellular state of myeloid phagocytic cells detectable in tumor and blood. See related commentary by Drake, p. 4139.

DOI: https://doi.org/10.1158/1078-0432.CCR-20-4574
Theranostics. 2022 ;12(13): 5949-5970

CRISPR/Cas9-based genome-wide screening for deubiquitinase subfamily identifies USP1 regulating MAST1-driven cisplatin-resistance in cancer cells.

Apoorvi Tyagi, Kamini Kaushal, Arun Pandian Chandrasekaran, Neha Sarodaya, Soumyadip Das, Chang-Hwan Park, Seok-Ho Hong, Kye-Seong Kim, Suresh Ramakrishna.

  Background: Cisplatin is one of the frontline anticancer agents. However, development of cisplatin-resistance limits the therapeutic efficacy of cisplatin-based treatment. The expression of microtubule-associated serine/threonine kinase 1 (MAST1) is a primary factor driving cisplatin-resistance in cancers by rewiring the MEK pathway. However, the mechanisms responsible for MAST1 regulation in conferring drug resistance is unknown. Methods: We implemented a CRISPR/Cas9-based, genome-wide, dual screening system to identify deubiquitinating enzymes (DUBs) that govern cisplatin resistance and regulate MAST1 protein level. We analyzed K48- and K63-linked polyubiquitination of MAST1 protein and mapped the interacting domain between USP1 and MAST1 by immunoprecipitation assay. The deubiquitinating effect of USP1 on MAST1 protein was validated using rescue experiments, in vitro deubiquitination assay, immunoprecipitation assays, and half-life analysis. Furthermore, USP1-knockout A549 lung cancer cells were generated to validate the deubiquitinating activity of USP1 on MAST1 abundance. The USP1-MAST1 correlation was evaluated using bioinformatics tool and in different human clinical tissues. The potential role of USP1 in regulating MAST1-mediated cisplatin resistance was confirmed using a series of in vitro and in vivo experiments. Finally, the clinical relevance of the USP1-MAST1 axis was validated by application of small-molecule inhibitors in a lung cancer xenograft model in NSG mice. Results: The CRISPR/Cas9-based dual screening system identified USP1 as a novel deubiquitinase that interacts, stabilizes, and extends the half-life of MAST1 by preventing its K48-linked polyubiquitination. The expression analysis across human clinical tissues revealed a positive correlation between USP1 and MAST1. USP1 promotes MAST1-mediated MEK1 activation as an underlying mechanism that contributes to cisplatin-resistance in cancers. Loss of USP1 led to attenuation of MAST1-mediated cisplatin-resistance both in vitro and in vivo. The combined pharmacological inhibition of USP1 and MAST1 using small-molecule inhibitors further abrogated MAST1 level and synergistically enhanced cisplatin efficacy in a mouse xenograft model. Conclusions: Overall, our study highlights the role of USP1 in the development of cisplatin resistance and uncovers the regulatory mechanism of MAST1-mediated cisplatin resistance in cancers. Co-treatment with USP1 and MAST1 inhibitors abrogated tumor growth and synergistically enhanced cisplatin efficacy, suggesting a novel alternative combinatorial therapeutic strategy that could further improve MAST1-based therapy in patients with cisplatin-resistant tumors.

Keywords:  Apoptosis; DNA damage; DUB inhibitor; clinical tumor samples; drug resistance; kinase inhibitor; ubiquitin proteasome system

DOI:  https://doi.org/10.7150/thno.72826
Science. 2022 Aug 18. eabn0478

Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling.

Joseph M Chan, Samir Zaidi, Jillian R Love, Jimmy L Zhao, Manu Setty, Kristine M Wadosky, Anuradha Gopalan, Zi-Ning Choo, Sitara Persad, Jungmin Choi, Justin LaClair, Kayla E Lawrence, Ojasvi Chaudhary, Tianhao Xu, Ignas Masilionis, Irina Linkov, Shangqian Wang, Cindy Lee, Afsar Barlas, Michael J Morris, Linas Mazutis, Ronan Chaligne, Yu Chen, David W Goodrich, Wouter R Karthaus, Dana Pe'er, Charles L Sawyers.

Drug resistance in cancer is often linked to changes in tumor cell state or lineage, but the molecular mechanisms driving this plasticity remain unclear. Using murine organoid and genetically engineered mouse models, we investigated the causes of lineage plasticity in prostate cancer and its relationship to antiandrogen resistance. We found that plasticity initiates in an epithelial population defined by mixed luminal-basal phenotype and that it depends on elevated JAK and FGFR activity. Organoid cultures from patients with castration-resistant disease harboring mixed-lineage cells reproduce the dependency observed in mice, by upregulating luminal gene expression upon JAK and FGFR inhibitor treatment. Single-cell analysis confirms the presence of mixed lineage cells with elevated JAK/STAT and FGFR signaling in a subset of patients with metastatic disease, with implications for stratifying patients for clinical trials.

DOI: https://doi.org/10.1126/science.abn0478
Oncogene. 2022 Aug 19.

P21-activated kinase 2-mediated β-catenin signaling promotes cancer stemness and osimertinib resistance in EGFR-mutant non-small-cell lung cancer.

Yanmei Yi, Pan Li, Yuanfeng Huang, Danyang Chen, Siwen Fan, Jun Wang, Minqiang Yang, Shanshan Zeng, Jin Deng, Xinwu Lv, Kai Luo, Zhiwei He, Hao Liu.

Osimertinib (AZD9291) is a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), used for treating patients with advanced non-small-cell lung cancer (NSCLC) harboring EGFR-activating mutations or the resistant T790M mutation. However, acquired resistance to osimertinib is inevitable in EGFR-mutant NSCLC. By employing a global mass spectrometry-based phosphoproteomics approach, we identified that the activated p21-activated kinase 2 (PAK2)/β-catenin axis acts as a driver of osimertinib resistance. We found that PAK2 directly phosphorylates β-catenin and increases the nuclear localization of β-catenin, leading to the increased expression and transcriptional activity of β-catenin, which in turn enhances cancer stem-like properties and osimertinib resistance. Moreover, we revealed that HER3 as an upstream regulator of PAK2, drives the activation of PAK2/β-catenin pathways in osimertinib-resistant cells. The clinical relevance of these findings was further confirmed by examining tissue specimens from patients with EGFR-mutant NSCLC. The results demonstrated that the levels of HER3, phospho-PAK2 (p-PAK2) and β-catenin in the tissues from patients with EGFR-mutant NSCLC, that had relapsed after treatment with osimertinib, were elevated compared to those of the corresponding untreated tissues. Additionally, the high levels of HER3, p-PAK2 and β-catenin correlated with shorter progression-free survival (PFS) in patients with EGFR-TKI-treated NSCLC. We additionally observed that the suppression of PAK2 via knockdown or pharmacological targeting with PAK inhibitors markedly restored the response of osimertinib-resistant NSCLC cells to osimertinib both in vitro and in vivo. In conclusion, these results indicated that the PAK2-mediated activation of β-catenin is important for osimertinib resistance and targeting the HER3/PAK2/β-catenin pathway has potential therapeutic value in NSCLCs with acquired resistance to osimertinib.

DOI: https://doi.org/10.1038/s41388-022-02438-z
Mol Cancer. 2022 Aug 19. 21(1): 166

Longitudinal single-cell transcriptomics reveals distinct patterns of recurrence in acute myeloid leukemia.

Yanan Zhai, Prashant Singh, Anna Dolnik, Peter Brazda, Nader Atlasy, Nunzio Del Gaudio, Konstanze Döhner, Hartmut Döhner, Saverio Minucci, Joost Martens, Lucia Altucci, Wout Megchelenbrink, Lars Bullinger, Hendrik G Stunnenberg.

  BACKGROUND: Acute myeloid leukemia (AML) is a heterogeneous and aggressive blood cancer that results from diverse genetic aberrations in the hematopoietic stem or progenitor cells (HSPCs) leading to the expansion of blasts in the hematopoietic system. The heterogeneity and evolution of cancer blasts can render therapeutic interventions ineffective in a yet poorly understood patient-specific manner. In this study, we investigated the clonal heterogeneity of diagnosis (Dx) and relapse (Re) pairs at genetic and transcriptional levels, and unveiled the underlying pathways and genes contributing to recurrence.METHODS: Whole-exome sequencing was used to detect somatic mutations and large copy number variations (CNVs). Single cell RNA-seq was performed to investigate the clonal heterogeneity between Dx-Re pairs and amongst patients.
RESULTS: scRNA-seq analysis revealed extensive expression differences between patients and Dx-Re pairs, even for those with the same -presumed- initiating events. Transcriptional differences between and within patients are associated with clonal composition and evolution, with the most striking differences in patients that gained large-scale copy number variations at relapse. These differences appear to have significant molecular implications, exemplified by a DNMT3A/FLT3-ITD patient where the leukemia switched from an AP-1 regulated clone at Dx to a mTOR signaling driven clone at Re. The two distinct AML1-ETO pairs share genes related to hematopoietic stem cell maintenance and cell migration suggesting that the Re leukemic stem cell-like (LSC-like) cells evolved from the Dx cells.
CONCLUSIONS: In summary, the single cell RNA data underpinned the tumor heterogeneity not only amongst patient blasts with similar initiating mutations but also between each Dx-Re pair. Our results suggest alternatively and currently unappreciated and unexplored mechanisms leading to therapeutic resistance and AML recurrence.

Keywords:  Acute myeloid Leukemia; Genome analysis; Leukemic stem cells; Recurrence; Single-cell RNA sequencing

DOI:  https://doi.org/10.1186/s12943-022-01635-4
Nat Commun. 2022 Aug 20. 13(1): 4897

Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma.

Laura Yerly, Christine Pich-Bavastro, Jeremy Di Domizio, Tania Wyss, Stéphanie Tissot-Renaud, Michael Cangkrama, Michel Gilliet, Sabine Werner, François Kuonen.

Tumors invade the surrounding tissues to progress, but the heterogeneity of cell types at the tumor-stroma interface and the complexity of their potential interactions hampered mechanistic insight required for efficient therapeutic targeting. Here, combining single-cell and spatial transcriptomics on human basal cell carcinomas, we define the cellular contributors of tumor progression. In the invasive niche, tumor cells exhibit a collective migration phenotype, characterized by the expression of cell-cell junction complexes. In physical proximity, we identify cancer-associated fibroblasts with extracellular matrix-remodeling features. Tumor cells strongly express the cytokine Activin A, and increased Activin A-induced gene signature is found in adjacent cancer-associated fibroblast subpopulations. Altogether, our data identify the cell populations and their transcriptional reprogramming contributing to the spatial organization of the basal cell carcinoma invasive niche. They also demonstrate the power of integrated spatial and single-cell multi-omics to decipher cancer-specific invasive properties and develop targeted therapies.

DOI: https://doi.org/10.1038/s41467-022-32670-w
Cancer Discov. 2022 Aug 19. pii: CD-22-0010. [Epub ahead of print]

Pharmacological inhibition of NT5C2 reverses genetic and non-genetic drivers of 6-MP resistance in acute lymphoblastic leukemia.

Clara Reglero, Chelsea L Dieck, Arie Zask, Farhad Forouhar, Anouchka P Laurent, Wen-Hsuan W Lin, Robert Albero, Hannah I Miller, Cindy Ma, Julie M Gastier-Foster, Mignon L Loh, Liang Tong, Brent R Stockwell, Teresa Palomero, Adolfo A Ferrando.

Low intensity maintenance therapy with 6-mercaptopurine (6-MP) limits the occurrence of acute lymphoblastic leukemia (ALL) relapse and is central to the success of multi-agent chemotherapy protocols. Activating mutations in the cytosolic 5' nucleotidase II (NT5C2) gene drive resistance to 6-MP in over 35% of early relapse ALL cases. Here we identify CRCD2 as a first-in-class small molecule NT5C2 nucleotidase inhibitor broadly active against leukemias bearing highly prevalent relapse-associated mutant forms of NT5C2 in vitro and in vivo. Importantly, CRCD2 treatment also enhanced the cytotoxic activity of 6-MP in NT5C2 wild type leukemias leading to the identification of NT5C2 S502 phosphorylation as a novel NT5C2-mediated mechanism of 6-MP resistance in this disease. These results uncover an unanticipated role of non-genetic NT5C2 activation as a driver of 6-MP resistance in ALL and demonstrate the potential of NT5C2 inhibitor therapy for enhancing the efficacy of thiopurine maintenance therapy and overcoming resistance at relapse.

DOI: https://doi.org/10.1158/2159-8290.CD-22-0010
Elife. 2022 Aug 19. pii: e57648. [Epub ahead of print]11

EHMT2 methyltransferase governs cell identity in the lung and is required for KRASG12D tumor development and propagation.

Ariel Pribluda, Anneleen Daemen, Anthony Nelson Lima, Xi Wang, Marc Hafner, Chungkee Poon, Zora Modrusan, Anand Kumar Katakam, Oded Foreman, Jefferey Eastham, Jefferey Hung, Benjamin Haley, Julia T Garcia, Erica L Jackson, Melissa R Junttila.

  Lung development, integrity and repair rely on precise Wnt signaling, which is corrupted in diverse diseases, including cancer. Here, we discover that EHMT2 methyltransferase regulates Wnt signaling in the lung by controlling the transcriptional activity of chromatin-bound β-catenin, through a non-histone substrate in mouse lung. Inhibition of EHMT2 induces transcriptional, morphologic, and molecular changes consistent with alveolar type 2 (AT2) lineage commitment. Mechanistically, EHMT2 activity functions to support regenerative properties of KrasG12D tumors and normal AT2 cells - the predominant cell of origin of this cancer. Consequently, EHMT2 inhibition prevents KrasG12D lung adenocarcinoma tumor formation and propagation and disrupts normal AT2 cell differentiation. Consistent with these findings, low gene EHMT2 expression in human lung adenocarcinoma correlates with enhanced AT2 gene expression and improved prognosis. These data reveal EHMT2 as a critical regulator of Wnt signaling, implicating Ehmt2 as a potential target in lung cancer and other AT2-mediated lung pathologies.

Keywords:  cancer biology; cell biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.57648
Nat Commun. 2022 Aug 15. 13(1): 4767

A slow-cycling/quiescent cells subpopulation is involved in glioma invasiveness.

Francesco Antonica, Lucia Santomaso, Davide Pernici, Linda Petrucci, Giuseppe Aiello, Alessandro Cutarelli, Luciano Conti, Alessandro Romanel, Evelina Miele, Toma Tebaldi, Luca Tiberi.

Pediatric and adult high-grade gliomas are the most common primary malignant brain tumors, with poor prognosis due to recurrence and tumor infiltration after therapy. Quiescent cells have been implicated in tumor recurrence and treatment resistance, but their direct visualization and targeting remain challenging, precluding their mechanistic study. Here, we identify a population of malignant cells expressing Prominin-1 in a non-proliferating state in pediatric high-grade glioma patients. Using a genetic tool to visualize and ablate quiescent cells in mouse brain cancer and human cancer organoids, we reveal their localization at both the core and the edge of the tumors, and we demonstrate that quiescent cells are involved in infiltration of brain cancer cells. Finally, we find that Harmine, a DYRK1A/B inhibitor, partially decreases the number of quiescent and infiltrating cancer cells. Our data point to a subpopulation of quiescent cells as partially responsible of tumor invasiveness, one of the major causes of brain cancer morbidity.

DOI: https://doi.org/10.1038/s41467-022-32448-0
Theranostics. 2022 ;12(13): 5727-5743

RNA N6 -methyladenosine reader YTHDC1 is essential for TGF-beta-mediated metastasis of triple negative breast cancer.

Brandon Tan, Keren Zhou, Wei Liu, Emily Prince, Ying Qing, Yangchan Li, Li Han, Xi Qin, Rui Su, Sheela Pangeni Pokharel, Lu Yang, Zhicong Zhao, Chao Shen, Wei Li, Zhenhua Chen, Zheng Zhang, Xiaolan Deng, Andrew Small, Kitty Wang, Keith Leung, Chun-Wei Chen, Binghui Shen, Jianjun Chen.

  RNA N6 -methyladenosine (m6A) modification and its regulators fine tune gene expression and contribute to tumorigenesis. This study aims to uncover the essential role and the underlying molecular mechanism(s) of the m6A reader YTHDC1 in promoting triple negative breast cancer (TNBC) metastasis.METHODS: In vitro and in vivo models were employed to determine the pathological function of YTHDC1 in TNBC metastasis. To identify bona fide YTHDC1 target RNAs, we conducted RNA-seq, m6A-seq, and RIP-seq, followed by integrative data analysis and validation assays.
RESULTS: By analyzing The Cancer Genome Atlas (TCGA) dataset, we found that elevated expression of YTHDC1 is positively correlated with poor prognosis in breast cancer patients. Using a mammary fat pad mouse model of TNBC, YTHDC1 significantly promoted lung metastasis of TNBC cells. Through multiple transcriptome-wide sequencing and integrative data analysis, we revealed dysregulation of metastasis-related pathways following YTHDC1 depletion and identified SMAD3 as a bona fide YTHDC1 target RNA. Depletion of YTHDC1 caused nuclear retention of SMAD3 mRNA, leading to lower SMAD3 protein levels. Loss of YTHDC1 led to impaired TGF-β-induced gene expression, leading to inhibition of epithelial-mesenchymal transition (EMT) and suppressed TNBC cell migration and invasion. SMAD3 overexpression was able to restore the response to TGF-β in YTHDC1 depleted TNBC cells. Furthermore, we demonstrated that the oncogenic role of YTHDC1 is mediated through its recognition of m6A as m6A-binding defective mutants of YTHDC1 were unable to rescue the impaired cell migration and invasion of YTHDC1 knockout TNBC cells.
CONCLUSIONS: We show that YTHDC1 plays a critical oncogenic role in TNBC metastasis through promoting the nuclear export and expression of SMAD3 to augment the TGF-β signaling cascade. Overall, our study demonstrates that YTHDC1 is vital for TNBC progression by enhancing TNBC cell survival and TGF-β-mediated EMT via SMAD3 to enable the formation of distant metastasis and highlights the therapeutic potential of targeting the YTHDC1/m6A/SMAD3 axis for TNBC treatment.

Keywords:  N6-methyladenosine; SMAD3; TGF-β; YTHDC1; metastasis

DOI:  https://doi.org/10.7150/thno.71872
Nat Commun. 2022 Aug 13. 13(1): 4760

Reformation of the chondroitin sulfate glycocalyx enables progression of AR-independent prostate cancer.

Nader Al-Nakouzi, Chris Kedong Wang, Htoo Zarni Oo, Irina Nelepcu, Nada Lallous, Charlotte B Spliid, Nastaran Khazamipour, Joey Lo, Sarah Truong, Colin Collins, Desmond Hui, Shaghayegh Esfandnia, Hans Adomat, Thomas Mandel Clausen, Tobias Gustavsson, Swati Choudhary, Robert Dagil, Eva Corey, Yuzhuo Wang, Anne Chauchereau, Ladan Fazli, Jeffrey D Esko, Ali Salanti, Peter S Nelson, Martin E Gleave, Mads Daugaard.

Lineage plasticity of prostate cancer is associated with resistance to androgen receptor (AR) pathway inhibition (ARPI) and supported by a reactive tumor microenvironment. Here we show that changes in chondroitin sulfate (CS), a major glycosaminoglycan component of the tumor cell glycocalyx and extracellular matrix, is AR-regulated and promotes the adaptive progression of castration-resistant prostate cancer (CRPC) after ARPI. AR directly represses transcription of the 4-O-sulfotransferase gene CHST11 under basal androgen conditions, maintaining steady-state CS in prostate adenocarcinomas. When AR signaling is inhibited by ARPI or lost during progression to non-AR-driven CRPC as a consequence of lineage plasticity, CHST11 expression is unleashed, leading to elevated 4-O-sulfated chondroitin levels. Inhibition of the tumor cell CS glycocalyx delays CRPC progression, and impairs growth and motility of prostate cancer after ARPI. Thus, a reactive CS glycocalyx supports adaptive survival and treatment resistance after ARPI, representing a therapeutic opportunity in patients with advanced prostate cancer.

DOI: https://doi.org/10.1038/s41467-022-32530-7
Nat Mater. 2022 Aug 15.

Cell clusters softening triggers collective cell migration in vivo.

Cristian L Marchant, Abdul N Malmi-Kakkada, Jaime A Espina, Elias H Barriga.

Embryogenesis, tissue repair and cancer metastasis rely on collective cell migration. In vitro studies propose that cells are stiffer while migrating in stiff substrates, but softer when plated in compliant surfaces which are typically considered as non-permissive for migration. Here we show that cells within clusters from embryonic tissue dynamically decrease their stiffness in response to the temporal stiffening of their native substrate to initiate collective cell migration. Molecular and mechanical perturbations of embryonic tissues reveal that this unexpected mechanical response involves a mechanosensitive pathway relying on Piezo1-mediated microtubule deacetylation. We further show that decreasing microtubule acetylation and consequently cluster stiffness is sufficient to trigger collective cell migration in soft non-permissive substrates. This suggests that reaching an optimal cluster-to-substrate stiffness ratio is essential to trigger the onset of this collective process. Overall, these in vivo findings challenge the current understanding of collective cell migration and its physiological and pathological roles.

DOI: https://doi.org/10.1038/s41563-022-01323-0
Theranostics. 2022 ;12(13): 5877-5887

Single-cell transcriptomics reveals the regulative roles of cancer associated fibroblasts in tumor immune microenvironment of recurrent osteosarcoma.

Xin Huang, Lutong Wang, Haoyu Guo, Weiyue Zhang, Zengwu Shao.

  Rationale: Osteosarcoma (OS) is the most common primary bone tumor with a poor prognosis, but the detailed mechanism is still unclear. A comprehensive investigation of tumor microenvironment (TME) of OS might help find effective anti-tumor strategies. Single-cell transcriptomics is a powerful new tool to explore TME. Therefore, this study is designed to investigate the TME and gene expression pattern of primary and recurrent OS at the single-cell level. Methods: The single-cell RNA sequencing and bioinformatic analysis were conducted to investigate the cellular constitution of primary, recurrent, and lung metastatic OS lesions according to the datasets of GSE152048 and GSE162454. TIMER database was used to investigate the role of LOX in the prognosis of sarcoma. The functions of related cells and markers were further confirmed by in vitro and in vivo experiments. Results: Cancer associated fibroblasts (CAFs) were found with a higher infiltrating level in recurrent OS, and were enriched in the epithelial-mesenchymal transition (EMT) pathway. CAFs showed remarkably increased expression of LOX, which might lead to EMT and poor prognosis of OS. Mechanically, LOX regulated the function of CAFs and macrophage polarization to remodel the tumor immune microenvironment. Moreover, LOX inhibitor could inhibit migration and promote apoptosis of OS both in vitro and in vivo. Conclusions: This study revealed the heterogeneity of recurrent OS and highlighted an innovative mechanism that CAFs regulate EMT of OS via LOX. Targeting LOX of CAFs showed promising efficacy in remodeling TME and treating recurrent OS.

Keywords:  Cancer associated fibroblasts; Osteosarcoma; Single-cell transcriptomics; Tumor immune microenvironment

DOI:  https://doi.org/10.7150/thno.73714
Mol Cancer. 2022 Aug 19. 21(1): 167

Circular RNA circFIRRE drives osteosarcoma progression and metastasis through tumorigenic-angiogenic coupling.

Lingfeng Yu, Hao Zhu, Zhen Wang, Jianhao Huang, Yan Zhu, Gentao Fan, Yicun Wang, Xi Chen, Guangxin Zhou.

  BACKGROUND: Disappointing clinical efficacy of standard treatment has been proven in refractory metastatic osteosarcoma, and the emerging anti-angiogenic regimens are still in the infantile stage. Thus, there is an urgent need to develop novel therapeutic approach for osteosarcoma lung metastasis.METHODS: circFIRRE was selected from RNA-sequencing of 4 matched osteosarcoma and adjacent samples. The expression of circFIRRE was verified in clinical osteosarcoma samples and cell lines via quantitative real-time polymerase chain reaction (RT-qPCR). The effect of circFIRRE was investigated in cell lines in vitro models, ex vivo models and in vivo xenograft tumor models, including proliferation, invasion, migration, metastasis and angiogenesis. Signaling regulatory mechanism was evaluated by RT-qPCR, Western blot, RNA pull-down and dual-luciferase reporter assays.
RESULTS: In this article, a novel circular RNA, circFIRRE (hsa_circ_0001944) was screened out and identified from RNA-sequencing, and was upregulated in both osteosarcoma cell lines and tissues. Clinically, aberrantly upregulated circFIRRE portended higher metastatic risk and worse prognosis in osteosarcoma patients. Functionally, in vitro, ex vivo and in vivo experiments demonstrated that circFIRRE could drive primary osteosarcoma progression and lung metastasis by inducing both tumor cells and blood vessels, we call as "tumorigenic-angiogenic coupling". Mechanistically, upregulated circFIRRE was induced by transcription factor YY1, and partially boosted the mRNA and protein level of LUZP1 by sponging miR-486-3p and miR-1225-5p.
CONCLUSIONS: We identified circFIRRE as a master regulator in the tumorigenesis and angiogenesis of osteosarcoma, which could be purposed as a novel prognostic biomarker and therapeutic target for refractory osteosarcoma.

Keywords:  Angiogenesis; LUZP1; Osteosarcoma; YY1; circFIRRE; miR-1225-5p; miR-486-3p

DOI:  https://doi.org/10.1186/s12943-022-01624-7
Nat Med. 2022 Aug;28(8): 1646-1655

Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer.

Walid K Chatila, Jin K Kim, Henry Walch, Michael R Marco, Chin-Tung Chen, Fan Wu, Dana M Omer, Danny N Khalil, Karuna Ganesh, Xuan Qu, Anisha Luthra, Seo-Hyun Choi, Yu-Jui Ho, Ritika Kundra, Katharine I Groves, Oliver S Chow, Andrea Cercek, Martin R Weiser, Maria Widmar, Iris H Wei, Emmanouil P Pappou, Garrett M Nash, Philip B Paty, Qian Shi, Efsevia Vakiani, S Duygu Selcuklu, Mark T A Donoghue, David B Solit, Michael F Berger, Jinru Shia, Raphael Pelossof, Paul B Romesser, Rona Yaeger, J Joshua Smith, Nikolaus Schultz, Francisco Sanchez-Vega, Julio Garcia-Aguilar.

The incidence of rectal cancer is increasing in patients younger than 50 years. Locally advanced rectal cancer is still treated with neoadjuvant radiation, chemotherapy and surgery, but recent evidence suggests that patients with a complete response can avoid surgery permanently. To define correlates of response to neoadjuvant therapy, we analyzed genomic and transcriptomic profiles of 738 untreated rectal cancers. APC mutations were less frequent in the lower than in the middle and upper rectum, which could explain the more aggressive behavior of distal tumors. No somatic alterations had significant associations with response to neoadjuvant therapy in a treatment-agnostic manner, but KRAS mutations were associated with faster relapse in patients treated with neoadjuvant chemoradiation followed by consolidative chemotherapy. Overexpression of IGF2 and L1CAM was associated with decreased response to neoadjuvant therapy. RNA-sequencing estimates of immune infiltration identified a subset of microsatellite-stable immune hot tumors with increased response and prolonged disease-free survival.

DOI: https://doi.org/10.1038/s41591-022-01930-z
Oncogene. 2022 Aug 16.

PACT promotes the metastasis of basal-like breast cancer through Rac1 SUMOylation and activation.

Luyao Wei, Wantao Wang, Junxia Yao, Zhengyu Cui, Zihang Xu, Hanqing Ding, Xiaojun Wu, Deheng Wang, Jia Luo, Zun-Ji Ke.

Most basal-like breast cancers (BLBCs) are triple-negative breast cancers (TNBCs), which is associated with high malignancy, high rate of recurrence and distant metastasis, and poor prognosis among all types of breast cancer. However, there are currently no effective therapies for BLBC. Furthermore, chemoresistance limits the therapeutic options for BLBC treatment. In this study, we screen out protein activator of the interferon-induced protein kinase (PACT) as an essential gene in BLBC metastasis. We find that high PACT expression level was associated with poor prognosis among BLBC patients. In vivo and in vitro investigations indicated that PACT could regulate BLBC metastasis by interacting with SUMO-conjugating enzyme Ubc9 to stimulate the SUMOylation and thus consequently the activation of Rac1. BLBC patients receiving chemotherapy presents poorer prognosis with PACT high expression, and PACT disruption sensitizes experimental mammary tumor metastases to chemotherapy, thus providing insights to consider PACT as a potential therapeutic target to overcome acquired chemoresistance in BLBC.

DOI: https://doi.org/10.1038/s41388-022-02431-6
Cell Rep Med. 2022 Aug 16. pii: S2666-3791(22)00260-9. [Epub ahead of print]3(8): 100717

hiPSC-derived bone marrow milieu identifies a clinically actionable driver of niche-mediated treatment resistance in leukemia.

Deepali Pal, Helen Blair, Jessica Parker, Sean Hockney, Melanie Beckett, Mankaran Singh, Ricky Tirtakusuma, Ryan Nelson, Hesta McNeill, Sharon H Angel, Aaron Wilson, Salem Nizami, Sirintra Nakjang, Peixun Zhou, Claire Schwab, Paul Sinclair, Lisa J Russell, Jonathan Coxhead, Christina Halsey, James M Allan, Christine J Harrison, Anthony V Moorman, Olaf Heidenreich, Josef Vormoor.

  Leukemia cells re-program their microenvironment to augment blast proliferation and enhance treatment resistance. Means of clinically targeting such niche-driven treatment resistance remain ambiguous. We develop human induced pluripotent stem cell (hiPSC)-engineered niches to reveal druggable cancer-niche dependencies. We reveal that mesenchymal (iMSC) and vascular niche-like (iANG) hiPSC-derived cells support ex vivo proliferation of patient-derived leukemia cells, affect dormancy, and mediate treatment resistance. iMSCs protect dormant and cycling blasts against dexamethasone, while iANGs protect only dormant blasts. Leukemia proliferation and protection from dexamethasone-induced apoptosis is dependent on cancer-niche interactions mediated by CDH2. Consequently, we test CDH2 antagonist ADH-1 (previously in Phase I/II trials for solid tumors) in a very aggressive patient-derived xenograft leukemia mouse model. ADH-1 shows high in vivo efficacy; ADH-1/dexamethasone combination is superior to dexamethasone alone, with no ADH-1-conferred additional toxicity. These findings provide a proof-of-concept starting point to develop improved, potentially safer therapeutics targeting niche-mediated cancer dependencies in blood cancers.

Keywords:  cancer microenvironment; dormancy; drugging cancer niche; iPSC-niche; treatment resistance

DOI:  https://doi.org/10.1016/j.xcrm.2022.100717
Proc Natl Acad Sci U S A. 2022 Aug 23. 119(34): e2206824119

Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma.

Altaf A Dar, Vladimir Bezrookove, Mehdi Nosrati, Ryan Ice, John M Patino, Edith M Vaquero, Brian Parrett, Stanley P Leong, Kevin B Kim, Robert J Debs, Liliana Soroceanu, James R Miller, Pierre-Yves Desprez, James E Cleaver, Nathan Salomonis, Sean McAllister, Mohammed Kashani-Sabet.

  Therapy of BRAF-mutant melanoma with selective inhibitors of BRAF (BRAFi) and MEK (MEKi) represents a major clinical advance but acquired resistance to therapy has emerged as a key obstacle. To date, no clinical approaches successfully resensitize to BRAF/MEK inhibition. Here, we develop a therapeutic strategy for melanoma using bromosporine, a bromodomain inhibitor. Bromosporine (bromo) monotherapy produced significant anti-tumor effects against established melanoma cell lines and patient-derived xenografts (PDXs). Combinatorial therapy involving bromosporine and cobimetinib (bromo/cobi) showed synergistic anti-tumor effects in multiple BRAFi-resistant PDX models. The bromo/cobi combination was superior in vivo to standard BRAFi/MEKi therapy in the treatment-naive BRAF-mutant setting and to MEKi alone in the setting of immunotherapy-resistant NRAS- and NF1-mutant melanoma. RNA sequencing of xenografts treated with bromo/cobi revealed profound down-regulation of genes critical to cell division and mitotic progression. Bromo/cobi treatment resulted in marked DNA damage and cell-cycle arrest, resulting in induction of apoptosis. These studies introduce bromodomain inhibition, alone or combined with agents targeting the mitogen activated protein kinase pathway, as a rational therapeutic approach for melanoma refractory to standard targeted or immunotherapeutic approaches.

Keywords:  bromodomain inhibition; drug resistance; melanoma; targeted therapy

DOI:  https://doi.org/10.1073/pnas.2206824119
Nat Commun. 2022 Aug 18. 13(1): 4851

Predicting response to immunotherapy in gastric cancer via multi-dimensional analyses of the tumour immune microenvironment.

Yang Chen, Keren Jia, Yu Sun, Cheng Zhang, Yilin Li, Li Zhang, Zifan Chen, Jiangdong Zhang, Yajie Hu, Jiajia Yuan, Xingwang Zhao, Yanyan Li, Jifang Gong, Bin Dong, Xiaotian Zhang, Jian Li, Lin Shen.

A single biomarker is not adequate to identify patients with gastric cancer (GC) who have the potential to benefit from anti-PD-1/PD-L1 therapy, presumably owing to the complexity of the tumour microenvironment. The predictive value of tumour-infiltrating immune cells (TIICs) has not been definitively established with regard to their density and spatial organisation. Here, multiplex immunohistochemistry is used to quantify in situ biomarkers at sub-cellular resolution in 80 patients with GC. To predict the response to immunotherapy, we establish a multi-dimensional TIIC signature by considering the density of CD4+FoxP3-PD-L1+, CD8+PD-1-LAG3-, and CD68+STING+ cells and the spatial organisation of CD8+PD-1+LAG3- T cells. The TIIC signature enables prediction of the response of patients with GC to anti-PD-1/PD-L1 immunotherapy and patient survival. Our findings demonstrate that a multi-dimensional TIIC signature may be relevant for the selection of patients who could benefit the most from anti-PD-1/PD-L1 immunotherapy.

DOI: https://doi.org/10.1038/s41467-022-32570-z