bims-tucedo 2021-07-11 papers

bims-tucedo

Biomed News

on Tumor cell dormancy

Issue of 2021–07–11
seventeen papers selected by
Isabel Puig Borreil, Vall d’Hebron Institute of Oncology

A SNAI2-PEAK1-INHBA stromal axis drives progression and lapatinib resistance in HER2-positive breast cancer by supporting subpopulations of tumor cells positive for antiapoptotic and stress signaling markers.
The ratio of toxic-to-nontoxic microRNAs predicts platinum sensitivity in ovarian cancer.
CCM3 is a gatekeeper in focal adhesions regulating mechanotransduction and YAP/TAZ signalling.
MIR21-induced loss of junctional adhesion molecule A promotes activation of oncogenic pathways, progression and metastasis in colorectal cancer.
Long non-coding RNA ANRIL promotes homologous recombination-mediated DNA repair by maintaining ATR protein stability to enhance cancer resistance.
The Emerging Roles of RNA m6A Methylation and Demethylation as Critical Regulators of Tumorigenesis, Drug Sensitivity, and Resistance.
Acid-base transporters and pH dynamics in human breast carcinomas predict proliferative activity, metastasis, and survival.
Patterns of Resistance Differ in Patients with Acute Myeloid Leukemia Treated with Type I versus Type II FLT3 Inhibitors.
A Therapeutic Strategy for Preferential Targeting of TET2-Mutant and TET Dioxygenase-Deficient Cells in Myeloid Neoplasms.
FTO downregulation mediated by hypoxia facilitates colorectal cancer metastasis.
Targeting HIF-activated collagen prolyl 4-hydroxylase expression disrupts collagen deposition and blocks primary and metastatic uveal melanoma growth.
Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness.
The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile.
Prognostic role and biologic features of Musashi-2 expression in colon polyps and during colorectal cancer progression.
The role of endolysosomal trafficking in anticancer drug resistance.
Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy.
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.

Oncogene. 2021 Jul 08.

A SNAI2-PEAK1-INHBA stromal axis drives progression and lapatinib resistance in HER2-positive breast cancer by supporting subpopulations of tumor cells positive for antiapoptotic and stress signaling markers.

Sarkis Hamalian, Robert Güth, Farhana Runa, Francesca Sanchez, Eric Vickers, Megan Agajanian, Justin Molnar, Tuan Nguyen, Joshua Gamez, Jonathan D Humphries, Anupma Nayak, Martin J Humphries, Julia Tchou, Ioannis K Zervantonakis, Jonathan A Kelber.

Intercellular mechanisms by which the stromal microenvironment contributes to solid tumor progression and targeted therapy resistance remain poorly understood, presenting significant clinical hurdles. PEAK1 (Pseudopodium-Enriched Atypical Kinase One) is an actin cytoskeleton- and focal adhesion-associated pseudokinase that promotes cell state plasticity and cancer metastasis by mediating growth factor-integrin signaling crosstalk. Here, we determined that stromal PEAK1 expression predicts poor outcomes in HER2-positive breast cancers high in SNAI2 expression and enriched for MSC content. Specifically, we identified that the fibroblastic stroma in HER2-positive breast cancer patient tissue stains positive for both nuclear SNAI2 and cytoplasmic PEAK1. Furthermore, mesenchymal stem cells (MSCs) and cancer-associated fibroblasts (CAFs) express high PEAK1 protein levels and potentiate tumorigenesis, lapatinib resistance and metastasis of HER2-positive breast cancer cells in a PEAK1-dependent manner. Analysis of PEAK1-dependent secreted factors from MSCs revealed INHBA/activin-A as a necessary factor in the conditioned media of PEAK1-expressing MSCs that promotes lapatinib resistance. Single-cell CycIF analysis of MSC-breast cancer cell co-cultures identified enrichment of p-Akthigh/p-gH2AXlow, MCL1high/p-gH2AXlow and GRP78high/VIMhigh breast cancer cell subpopulations by the presence of PEAK1-expressing MSCs and lapatinib treatment. Bioinformatic analyses on a PEAK1-centric stroma-tumor cell gene set and follow-up immunostaining of co-cultures predict targeting antiapoptotic and stress pathways as a means to improve targeted therapy responses and patient outcomes in HER2-positive breast cancer and other stroma-rich malignancies. These data provide the first evidence that PEAK1 promotes tumorigenic phenotypes through a previously unrecognized SNAI2-PEAK1-INHBA stromal cell axis.

DOI: https://doi.org/10.1038/s41388-021-01906-2
Cancer Res. 2021 Jun 15. pii: canres.0953.2021. [Epub ahead of print]

The ratio of toxic-to-nontoxic microRNAs predicts platinum sensitivity in ovarian cancer.

Monal Patel, Yinu Wang, Elizabeth T Bartom, Rohin Dhir, Kenneth P Nephew, Daniela Matei, Andrea E Murmann, Ernst Lengyel, Marcus E Peter.

Ovarian cancer remains one of the deadliest gynecologic malignancies affecting women, and development of resistance to platinum remains a major barrier to achieving a cure. Multiple mechanisms have been identified to confer platinum resistance. Numerous microRNAs (miRNAs) have been linked to platinum sensitivity and resistance in ovarian cancer. miRNA activity occurs mainly when the guide strand of the miRNA, with its seed sequence at position 2-7/8, is loaded into the RNA-induced silencing (RISC) complex and targets complementary short seed matches in the 3' untranslated region of mRNAs. Toxic 6mer seeds, which target genes critical for cancer cell survival, have been found in tumor suppressive miRNAs. Many small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) can also kill cancer cells via toxic seeds, the most toxic of which carry G-rich 6mer seed sequences. We showed here that treatment of ovarian cancer cells with platinum led to increased RISC-bound miRNAs carrying toxic 6mer seeds and decreased miRNAs with nontoxic seeds. Platinum-tolerant cells did not exhibit this toxicity shift but retained sensitivity to cell death mediated by siRNAs carrying toxic 6mer seeds. Analysis of RISC-bound miRNAs in ovarian cancer patients revealed that the ratio between miRNAs with toxic versus nontoxic seeds was predictive of treatment outcome. Application of the 6mer seed toxicity concept to cancer relevant miRNAs provides a new framework for understanding and predicting cancer therapy responses.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-0953
Nat Cell Biol. 2021 Jul 05.

CCM3 is a gatekeeper in focal adhesions regulating mechanotransduction and YAP/TAZ signalling.

Shan Wang, Emelie Englund, Pontus Kjellman, Zhen Li, Johannes Kumra Ahnlide, Carmen Rodriguez-Cupello, Mattia Saggioro, Ryu Kanzaki, Kristian Pietras, David Lindgren, Håkan Axelson, Christelle N Prinz, Vinay Swaminathan, Chris D Madsen.

The YAP/TAZ transcriptional programme is not only a well-established driver of cancer progression and metastasis but also an important stimulator of tissue regeneration. Here we identified Cerebral cavernous malformations 3 (CCM3) as a regulator of mechanical cue-driven YAP/TAZ signalling, controlling both tumour progression and stem cell differentiation. We demonstrate that CCM3 localizes to focal adhesion sites in cancer-associated fibroblasts, where it regulates mechanotransduction and YAP/TAZ activation. Mechanistically, CCM3 and focal adhesion kinase (FAK) mutually compete for binding to paxillin to fine-tune FAK/Src/paxillin-driven mechanotransduction and YAP/TAZ activation. In mouse models of breast cancer, specific loss of CCM3 in cancer-associated fibroblasts leads to exacerbated tissue remodelling and force transmission to the matrix, resulting in reciprocal YAP/TAZ activation in the neighbouring tumour cells and dissemination of metastasis to distant organs. Similarly, CCM3 regulates the differentiation of mesenchymal stromal/stem cells. In conclusion, CCM3 is a gatekeeper in focal adhesions that controls mechanotransduction and YAP/TAZ signalling.

DOI: https://doi.org/10.1038/s41556-021-00702-0
Cell Death Differ. 2021 Jul 05.

MIR21-induced loss of junctional adhesion molecule A promotes activation of oncogenic pathways, progression and metastasis in colorectal cancer.

Andrea Lampis, Jens C Hahne, Pierluigi Gasparini, Luciano Cascione, Somaieh Hedayat, Georgios Vlachogiannis, Claudio Murgia, Elisa Fontana, Joanne Edwards, Paul G Horgan, Luigi Terracciano, Owen J Sansom, Carlos D Martins, Gabriela Kramer-Marek, Carlo M Croce, Chiara Braconi, Matteo Fassan, Nicola Valeri.

Junctional adhesion molecules (JAMs) play a critical role in cell permeability, polarity and migration. JAM-A, a key protein of the JAM family, is altered in a number of conditions including cancer; however, consequences of JAM-A dysregulation on carcinogenesis appear to be tissue dependent and organ dependent with significant implications for the use of JAM-A as a biomarker or therapeutic target. Here, we test the expression and prognostic role of JAM-A downregulation in primary and metastatic colorectal cancer (CRC) (n = 947). We show that JAM-A downregulation is observed in ~60% of CRC and correlates with poor outcome in four cohorts of stages II and III CRC (n = 1098). Using JAM-A knockdown, re-expression and rescue experiments in cell line monolayers, 3D spheroids, patient-derived organoids and xenotransplants, we demonstrate that JAM-A silencing promotes proliferation and migration in 2D and 3D cell models and increases tumour volume and metastases in vivo. Using gene-expression and proteomic analyses, we show that JAM-A downregulation results in the activation of ERK, AKT and ROCK pathways and leads to decreased bone morphogenetic protein 7 expression. We identify MIR21 upregulation as the cause of JAM-A downregulation and show that JAM-A rescue mitigates the effects of MIR21 overexpression on cancer phenotype. Our results identify a novel molecular loop involving MIR21 dysregulation, JAM-A silencing and activation of multiple oncogenic pathways in promoting invasiveness and metastasis in CRC.

DOI: https://doi.org/10.1038/s41418-021-00820-0
Mol Cancer. 2021 Jul 05. 20(1): 94

Long non-coding RNA ANRIL promotes homologous recombination-mediated DNA repair by maintaining ATR protein stability to enhance cancer resistance.

Lei Liu, Yuanyuan Chen, Yijuan Huang, Kun Cao, Tingting Liu, Hui Shen, Jianguo Cui, Bailong Li, Jianming Cai, Fu Gao, Yanyong Yang.



Keywords:  ATR; Cancer resistance; DNA damage repair; Long non-coding RNA

DOI:  https://doi.org/10.1186/s12943-021-01382-y
Cancer Res. 2021 Jul 01. 81(13): 3431-3440

The Emerging Roles of RNA m6A Methylation and Demethylation as Critical Regulators of Tumorigenesis, Drug Sensitivity, and Resistance.

Qing Lan, Pei Y Liu, Jessica L Bell, Jenny Y Wang, Stefan Hüttelmaier, Xu Dong Zhang, Lirong Zhang, Tao Liu.

RNA N6 -methyladenosine (m6A) modification occurs in approximately 25% of mRNAs at the transcriptome-wide level. RNA m6A is regulated by the RNA m6A methyltransferases methyltransferase-like 3 (METTL3), METTL14, and METTL16 (writers), demethylases FTO and ALKBH5 (erasers), and binding proteins YTHDC1-2, YTHDF1-3, IGF2BP1-3, and SND1 (readers). These RNA m6A modification proteins are frequently upregulated or downregulated in human cancer tissues and are often associated with poor patient prognosis. By modulating pre-mRNA splicing, mRNA nuclear export, decay, stability, and translation of oncogenic and tumor suppressive transcripts, RNA m6A modification proteins regulate cancer cell proliferation, survival, migration, invasion, tumor initiation, progression, metastasis, and sensitivity to anticancer therapies. Importantly, small-molecule activators of METTL3, as well as inhibitors of METTL3, FTO, ALKBH5, and IGF2BP1 have recently been identified and have shown considerable anticancer effects when administered alone or in combination with other anticancer agents, both in vitro and in mouse models of human cancers. Future compound screening and design of more potent and selective RNA m6A modification protein inhibitors and activators are expected to provide novel anticancer agents, appropriate for clinical trials in patients with cancer tissues harboring aberrant RNA m6A modification protein expression or RNA m6A modification protein-induced resistance to cancer therapy.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-4107
Elife. 2021 Jul 05. pii: e68447. [Epub ahead of print]10

Acid-base transporters and pH dynamics in human breast carcinomas predict proliferative activity, metastasis, and survival.

Nicolai J Toft, Trine V Axelsen, Helene L Pedersen, Marco Mele, Mark Burton, Eva Balling, Tonje Johansen, Mads Thomassen, Peer M Christiansen, Ebbe Boedtkjer.

  Breast cancer heterogeneity in histology and molecular subtype influences metabolic and proliferative activity and hence the acid load on cancer cells. We hypothesized that acid-base transporters and intracellular pH (pHi) dynamics contribute inter-individual variability in breast cancer aggressiveness and prognosis. We show that Na+,HCO3--cotransport and Na+/H+-exchange dominate cellular net acid extrusion in human breast carcinomas. Na+/H+-exchange elevates pHi preferentially in estrogen receptor-negative breast carcinomas, whereas Na+,HCO3--cotransport raises pHi more in invasive lobular than ductal breast carcinomas and in higher malignancy grade breast cancer. HER2-positive breast carcinomas have elevated protein expression of Na+/H+-exchanger NHE1/SLC9A1 and Na+,HCO3--cotransporter NBCn1/SLC4A7. Increased dependency on Na+,HCO3--cotransport associates with severe breast cancer: enlarged CO2/HCO3--dependent rises in pHi predict accelerated cell proliferation; whereas enhanced CO2/HCO3--dependent net acid extrusion, elevated NBCn1 protein expression, and reduced NHE1 protein expression predict lymph node metastasis. Accordingly, we observe reduced survival for patients suffering from Luminal A or Basal-like/triple-negative breast cancer with high SLC4A7 and/or low SLC9A1 mRNA expression. We conclude that the molecular mechanisms of acid-base regulation depend on clinicopathological characteristics of breast cancer patients. NBCn1 expression and dependency on Na+,HCO3--cotransport for pHi regulation, measured in biopsies of human primary breast carcinomas, independently predict proliferative activity, lymph node metastasis, and patient survival.

Keywords:  cancer biology; human

DOI:  https://doi.org/10.7554/eLife.68447
Cancer Discov. 2021 Mar;2(2): 125-134

Patterns of Resistance Differ in Patients with Acute Myeloid Leukemia Treated with Type I versus Type II FLT3 Inhibitors.

Ahmad S Alotaibi, Musa Yilmaz, Rashmi Kanagal-Shamanna, Sanam Loghavi, Tapan M Kadia, Courtney D DiNardo, Gautam Borthakur, Marina Konopleva, Sherry A Pierce, Sa A Wang, Guilin Tang, Veronica Guerra, Bachar Samra, Naveen Pemmaraju, Elias Jabbour, Nicholas J Short, Ghayas C Issa, Maro Ohanian, Guillermo Garcia-Manero, Kapil N Bhalla, Keyur P Patel, Koichi Takahashi, Michael Andreeff, Jorge E Cortes, Hagop M Kantarjian, Farhad Ravandi, Naval Daver.

Despite promising results with FLT3 inhibitors (FLT3i), response durations remain short. We studied pretreatment and relapse bone marrow samples from patients with FLT3-mutated acute myeloid leukemia (AML) treated with FLT3i-based therapies (secondary resistance cohort), and pretreatment bone marrow samples from patients with no response to FLT3i-based therapies (primary resistance cohort). Targeted next-generation sequencing (NGS) at relapse identified emergent mutations involving on-target FLT3, epigenetic modifiers, RAS/MAPK pathway, and less frequently WT1 and TP53. RAS/MAPK and FLT3-D835 mutations emerged most commonly following type I and II FLT3i-based therapies, respectively. Patients with emergent mutations at relapse had inferior overall survival compared with those without emergent mutations. Among pretreatment RAS-mutated patients, pretreatment cohort-level variant allelic frequencies for RAS were higher in nonresponders, particularly with type I FLT3i-based therapies, suggesting a potential role in primary resistance as well. These data demonstrate distinct pathways of resistance in FLT3-mutated AML treated with type I versus II FLT3i. SIGNIFICANCE: Sequential NGS-based mutational analysis at relapse after FLT3i-based therapies showed distinct pathways of secondary resistance between type I and II FLT3i. FLT3 mutations may be lost at relapse after FLT3i-based therapies. Pretreatment RAS/MAPK mutations may also be associated with primary resistance in patients treated with type I FLT3i.See related commentary by Shastri et al., p. 113.

DOI: https://doi.org/10.1158/2643-3230.BCD-20-0143
Cancer Discov. 2021 Mar;2(2): 146-161

A Therapeutic Strategy for Preferential Targeting of TET2-Mutant and TET Dioxygenase-Deficient Cells in Myeloid Neoplasms.

Yihong Guan, Anand D Tiwari, James G Phillips, Metis Hasipek, Dale R Grabowski, Simona Pagliuca, Priyanka Gopal, Cassandra M Kerr, Vera Adema, Tomas Radivoyevitch, Yvonne Parker, Daniel J Lindner, Manja Meggendorfer, Mohamed Abazeed, Mikkeal A Sekeres, Omar Y Mian, Torsten Haferlach, Jaroslaw P Maciejewski, Babal K Jha.

TET2 is frequently mutated in myeloid neoplasms. Genetic TET2 deficiency leads to skewed myeloid differentiation and clonal expansion, but minimal residual TET activity is critical for survival of neoplastic progenitor and stem cells. Consistent with mutual exclusivity of TET2 and neomorphic IDH1/2 mutations, here we report that IDH1/2 mutant-derived 2-hydroxyglutarate is synthetically lethal to TET dioxygenase-deficient cells. In addition, a TET-selective small-molecule inhibitor decreases cytosine hydroxymethylation and restricted clonal outgrowth of TET2 mutant but not normal hematopoietic precursor cells in vitro and in vivo. Although TET inhibitor phenocopied somatic TET2 mutations, its pharmacologic effects on normal stem cells are, unlike mutations, reversible. Treatment with TET inhibitor suppresses the clonal evolution of TET2-mutant cells in murine models and TET2-mutated human leukemia xenografts. These results suggest that TET inhibitors may constitute a new class of targeted agents in TET2-mutant neoplasia. SIGNIFICANCE: Loss-of-function somatic TET2 mutations are among the most frequent lesions in myeloid neoplasms and associated disorders. Here we report a strategy for selective targeting of residual TET dioxygenase activity in TET-deficient clones that results in restriction of clonal evolution in vitro and in vivo.

DOI: https://doi.org/10.1158/2643-3230.BCD-20-0173
Oncogene. 2021 Jul 03.

FTO downregulation mediated by hypoxia facilitates colorectal cancer metastasis.

Dan-Yun Ruan, Ting Li, Ying-Nan Wang, Qi Meng, Yang Li, Kai Yu, Min Wang, Jin-Fei Lin, Li-Zhi Luo, De-Shen Wang, Jun-Zhong Lin, Long Bai, Ze-Xian Liu, Qi Zhao, Xiang-Yuan Wu, Huai-Qiang Ju, Rui-Hua Xu.

Fat mass and obesity-associated protein (FTO), an N6-methyladenosine (m6A) demethylase, participates in tumor progression and metastasis in many malignancies, but its role in colorectal cancer (CRC) is still unclear. Here, we found that FTO protein levels, but not RNA levels, were downregulated in CRC tissues. Reduced FTO protein expression was correlated with a high recurrence rate and poor prognosis in resectable CRC patients. Moreover, we demonstrated that hypoxia restrained FTO protein expression, mainly due to an increase in ubiquitin-mediated protein degradation. The serine/threonine kinase receptor associated protein (STRAP) might served as the E3 ligase and K216 was the major ubiquitination site responsible for hypoxia-induced FTO degradation. FTO inhibited CRC metastasis both in vitro and in vivo. Mechanistically, FTO exerted a tumor suppressive role by inhibiting metastasis-associated protein 1 (MTA1) expression in an m6A-dependent manner. Methylated MTA1 transcripts were recognized by an m6A "reader", insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2), which then stabilized its mRNA. Together, our findings highlight the critical role of FTO in CRC metastasis and reveal a novel epigenetic mechanism by which the hypoxic tumor microenvironment promotes CRC metastasis.

DOI: https://doi.org/10.1038/s41388-021-01916-0
Oncogene. 2021 Jul 03.

Targeting HIF-activated collagen prolyl 4-hydroxylase expression disrupts collagen deposition and blocks primary and metastatic uveal melanoma growth.

Stefan Kaluz, Qing Zhang, Yuki Kuranaga, Hua Yang, Satoru Osuka, Debanjan Bhattacharya, Narra S Devi, Jiyoung Mun, Wei Wang, Ruiwen Zhang, Mark M Goodman, Hans E Grossniklaus, Erwin G Van Meir.

Uveal melanoma (UM) is the most prevalent primary intraocular malignancy in adults, and patients that develop metastases (~50%) survive <1 year, highlighting the urgent need for new therapies. TCGA has recently revealed that a hypoxia gene signature is associated with poor UM patient prognosis. Here we show that expression of hypoxia-regulated collagen prolyl-4-hydroxylase genes P4HA1 and P4HA2 is significantly upregulated in UM patients with metastatic disease and correlates with poor prognosis, suggesting these enzymes might be key tumor drivers. We targeted hypoxia-induced expression of P4HA1/2 in UM with KCN1, a hypoxia inducible factor-1 (HIF-1) pathway inhibitor and found potent inhibition of primary and metastatic disease and extension of animal survival, without overt side effects. At the molecular level, KCN1 antagonized hypoxia-induced expression of P4HA1 and P4HA2, which regulate collagen maturation and deposition in the extracellular matrix. The treatment decreased prolyl hydroxylation, induced proteolytic cleavage and rendered a disordered structure to collagen VI, the main collagen produced by UM, and reduced UM cell invasion. Together, these data demonstrate that extracellular collagen matrix formation can be targeted in UM by inhibiting hypoxia-induced P4HA1 and P4HA2 expression, warranting further development of this strategy in patients with uveal melanoma.

DOI: https://doi.org/10.1038/s41388-021-01919-x
Elife. 2021 Jul 08. pii: e64212. [Epub ahead of print]10

Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness.

Haritha Mathsyaraja, Jonathen Catchpole, Brian Freie, Emily Eastwood, Ekaterina Babaeva, Michael Geuenich, Pei Feng Cheng, Jessica Ayers, Ming Yu, Nan Wu, Sitapriya Moorthi, Kumud R Poudel, Amanda Koehne, William Grady, A McGarry Houghton, Alice H Berger, Yuzuru Shiio, David MacPherson, Robert N Eisenman.

  MGA, a transcription factor and member of the MYC network, is mutated or deleted in a broad spectrum of malignancies. As a critical test of a tumor suppressive role, we inactivated Mga in two mouse models of non-small cell lung cancer using a CRISPR-based approach. MGA loss significantly accelerated tumor growth in both models and led to de-repression of non-canonical Polycomb ncPRC1.6 targets, including genes involved in metastasis and meiosis. Moreover, MGA deletion in human lung adenocarcinoma lines augmented invasive capabilities. We further show that MGA-MAX, E2F6, and L3MBTL2 co-occupy thousands of promoters and that MGA stabilizes these ncPRC1.6 subunits. Lastly, we report that MGA loss also induces a pro-growth effect in human colon organoids. Our studies establish MGA as a bona fide tumor suppressor in vivo and suggest a tumor suppressive mechanism in adenocarcinomas resulting from widespread transcriptional attenuation of MYC and E2F target genes mediated by MGA-MAX associated with a non-canonical Polycomb complex.

Keywords:  MAX; MGA; cancer biology; colon organoids; lung adenocarcinoma; mouse; non-canonical polycomb; tumor suppressor

DOI:  https://doi.org/10.7554/eLife.64212
Sci Adv. 2021 Jul;pii: eabf4408. [Epub ahead of print]7(28):

The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile.

Jean Berthelet, Verena C Wimmer, Holly J Whitfield, Antonin Serrano, Thomas Boudier, Stefano Mangiola, Michal Merdas, Farrah El-Saafin, David Baloyan, Jordan Wilcox, Steven Wilcox, Adam C Parslow, Anthony T Papenfuss, Belinda Yeo, Matthias Ernst, Bhupinder Pal, Robin L Anderson, Melissa J Davis, Kelly L Rogers, Frédéric Hollande, Delphine Merino.

Intratumoral heterogeneity is a driver of breast cancer progression, but the nature of the clonal interactive network involved in this process remains unclear. Here, we optimized the use of optical barcoding to visualize and characterize 31 cancer subclones in vivo. By mapping the clonal composition of thousands of metastases in two clinically relevant sites, the lungs and liver, we found that metastases were highly polyclonal in lungs but not in the liver. Furthermore, the transcriptome of the subclones varied according to their metastatic niche. We also identified a reversible niche-driven signature that was conserved in lung and liver metastases collected during patient autopsies. Among this signature, we found that the tumor necrosis factor-α pathway was up-regulated in lung compared to liver metastases, and inhibition of this pathway affected metastasis diversity. These results highlight that the cellular and molecular heterogeneity observed in metastases is largely dictated by the tumor microenvironment.

DOI: https://doi.org/10.1126/sciadv.abf4408
PLoS One. 2021 ;16(7): e0252132

Prognostic role and biologic features of Musashi-2 expression in colon polyps and during colorectal cancer progression.

Leonid Kharin, Igor Bychkov, Nikolay Karnaukhov, Mark Voloshin, Rushaniya Fazliyeva, Alexander Deneka, Elena Frantsiyants, Oleg Kit, Erica Golemis, Yanis Boumber.

BACKGROUND: The RNA-binding protein Musashi-2 (MSI2) controls the translation of proteins that support stem cell identity and lineage determination and is associated with progression in some cancers. We assessed MSI2 as potential clinical biomarker in colorectal cancer (CRC) and tubulovillous adenoma (TA) of colon mucosa.
METHODS: We assessed 125 patients, of whom 20 had polyps of the colon (TAs), and 105 had CRC. Among 105 patients with CRC, 45 had stages I-III; among metastatic CRC (mCRC) patients, 31 had synchronous and 29 metachronous liver metastases. We used immunohistochemistry to measure MSI2 expression in matching specimens of normal tissue versus TAs, primary CRC tumors, and metastases, correlating expression to clinical outcomes. We analyzed the biological effects of depleting MSI2 expression in human CRC cells.
RESULTS: MSI2 expression was significantly elevated in polyps versus primary tissue, and further significantly elevated in primary tumors and metastases. MSI2 expression correlated with decreased progression free survival (PFS) and overall survival (OS), higher tumor grade, and right-side localization (p = 0.004) of tumors. In metastases, high MSI2 expression correlated with E-cadherin expression. Knockdown of MSI2 in CRC cells suppressed proliferation, survival and clonogenic capacity, and decreased expression of TGFβ1, E-cadherin, and ZO1.
CONCLUSION: Elevated expression of MSI2 is associated with pre-cancerous TAs in the colonic mucosa, suggesting it is an early event in transformation. MSI2 expression is further elevated during CRC progression, and associated with poor prognosis. Depletion of MSI2 reduces CRC cell growth. These data imply a causative role of MSI2 overexpression at multiple stages of CRC formation and progression.

DOI: https://doi.org/10.1371/journal.pone.0252132
Drug Resist Updat. 2021 Jul;pii: S1368-7646(21)00027-3. [Epub ahead of print]57 100769

The role of endolysosomal trafficking in anticancer drug resistance.

Noor A Hussein, Saloni Malla, Mariah A Pasternak, David Terrero, Noah G Brown, Charles R Ashby, Yehuda G Assaraf, Zhe-Sheng Chen, Amit K Tiwari.

  Multidrug resistance (MDR) remains a major obstacle towards curative treatment of cancer. Despite considerable progress in delineating the basis of intrinsic and acquired MDR, the underlying molecular mechanisms remain to be elucidated. Emerging evidences suggest that dysregulation in endolysosomal compartments is involved in mediating MDR through multiple mechanisms, such as alterations in endosomes, lysosomes and autophagosomes, that traffic and biodegrade the molecular cargo through macropinocytosis, autophagy and endocytosis. For example, altered lysosomal pH, in combination with transcription factor EB (TFEB)-mediated lysosomal biogenesis, increases the sequestration of hydrophobic anti-cancer drugs that are weak bases, thereby producing an insufficient and off-target accumulation of anti-cancer drugs in MDR cancer cells. Thus, the use of well-tolerated, alkalinizing compounds that selectively block Vacuolar H⁺-ATPase (V-ATPase) may be an important strategy to overcome MDR in cancer cells and increase chemotherapeutic efficacy. Other mechanisms of endolysosomal-mediated drug resistance include increases in the expression of lysosomal proteases and cathepsins that are involved in mediating carcinogenesis and chemoresistance. Therefore, blocking the trafficking and maturation of lysosomal proteases or direct inhibition of cathepsin activity in the cytosol may represent novel therapeutic modalities to overcome MDR. Furthermore, endolysosomal compartments involved in catabolic pathways, such as macropinocytosis and autophagy, are also shown to be involved in the development of MDR. Here, we review the role of endolysosomal trafficking in MDR development and discuss how targeting endolysosomal pathways could emerge as a new therapeutic strategy to overcome chemoresistance in cancer.

Keywords:  Autophagy; Cancer; Cathepsins; Endolysosomal trafficking; Lysosomes; Macropinocytosis; Multidrug resistance

DOI:  https://doi.org/10.1016/j.drup.2021.100769
Cancer Discov. 2021 Jan;2(1): 54-69

Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy.

Helene Kretzmer, Anat Biran, Noelia Purroy, Camilla K Lemvigh, Kendell Clement, Michaela Gruber, Hongcang Gu, Laura Rassenti, Arman W Mohammad, Connie Lesnick, Susan L Slager, Esteban Braggio, Tait D Shanafelt, Neil E Kay, Stacey M Fernandes, Jennifer R Brown, Lili Wang, Shuqiang Li, Kenneth J Livak, Donna S Neuberg, Sven Klages, Bernd Timmermann, Thomas J Kipps, Elias Campo, Andreas Gnirke, Catherine J Wu, Alexander Meissner.

Most human cancers converge to a deregulated methylome with reduced global levels and elevated methylation at select CpG islands. To investigate the emergence and dynamics of the cancer methylome, we characterized genome-wide DNA methylation in preneoplastic monoclonal B-cell lymphocytosis (MBL) and chronic lymphocytic leukemia (CLL), including serial samples collected across disease course. We detected the aberrant tumor-associated methylation landscape at CLL diagnosis and found no significant differentially methylated regions in the high-count MBL-to-CLL transition. Patient methylomes showed remarkable stability with natural disease and posttherapy progression. Single CLL cells were consistently aberrantly methylated, indicating a homogeneous transition to the altered epigenetic state and a distinct expression profile together with MBL cells compared with normal B cells. Our longitudinal analysis reveals the cancer methylome to emerge early, which may provide a platform for subsequent genetically driven growth dynamics, and, together with its persistent presence, suggests a central role in disease onset. SIGNIFICANCE: DNA methylation data from a large cohort of patients with MBL and CLL show that epigenetic transformation emerges early and persists throughout disease stages with limited subsequent changes. Our results indicate an early role for this aberrant landscape in the normal-to-preneoplastic transition that may reflect a pan-cancer mechanism.See related commentary by Rossi, p. 6.This article is highlighted in the In This Issue feature, p. 1.

DOI: https://doi.org/10.1158/2643-3230.BCD-19-0058
Mol Cell. 2021 Jun 29. pii: S1097-2765(21)00493-7. [Epub ahead of print]

Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.

Jaclyn M Einstein, Mark Perelis, Isaac A Chaim, Jitendra K Meena, Julia K Nussbacher, Alexandra T Tankka, Brian A Yee, Heyuan Li, Assael A Madrigal, Nicholas J Neill, Archana Shankar, Siddhartha Tyagi, Thomas F Westbrook, Gene W Yeo.

  RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in supporting MYC-driven oncogenic pathways. We find that disrupting YTHDF2-dependent mRNA degradation triggers apoptosis in triple-negative breast cancer (TNBC) cells and tumors. eCLIP and m6A sequencing reveal that YTHDF2 interacts with mRNAs encoding proteins in the MAPK pathway that, when stabilized, induce epithelial-to-mesenchymal transition and increase global translation rates. scRibo-STAMP profiling of translating mRNAs reveals unique alterations in the translatome of single cells within YTHDF2-depleted solid tumors, which selectively contribute to endoplasmic reticulum stress-induced apoptosis in TNBC cells. Thus, our work highlights the therapeutic potential of RBPs by uncovering a critical role for YTHDF2 in counteracting the global increase of mRNA synthesis in MYC-driven breast cancers.

Keywords:  CRISPR screening; MYC-driven cancer; N6-methyladenosine; RNA-binding protein; STAMP; YTHDF2; scRNA-seq

DOI:  https://doi.org/10.1016/j.molcel.2021.06.014