bims-tucedo 2021-10-10 papers

bims-tucedo

Biomed News

on Tumor cell dormancy

Issue of 2021‒10‒10
thirty papers selected by
Isabel Puig Borreil
Vall d’Hebron Institute of Oncology

CEMIP, a novel adaptor protein of OGT, promotes colorectal cancer metastasis through glutamine metabolic reprogramming via reciprocal regulation of β-catenin.
Characterization of peptides targeting metastatic tumor cells as probes for cancer detection and vehicles for therapy delivery.
Prostate cancer dormancy and recurrence.
Lnc00892 competes with c-Jun to block NCL transcription, reducing the stability of RhoA/RhoC mRNA and impairing bladder cancer invasion.
CRISPR screens identify cholesterol biosynthesis as a therapeutic target on stemness and drug resistance of colon cancer.
Decoupling tumor cell metastasis from growth by cellular pilot protein TNFAIP8.
Determinants of renal cell carcinoma invasion and metastatic competence.
Evolving cancer-niche interactions and therapeutic targets during bone metastasis.
ZNF545 loss promotes ribosome biogenesis and protein translation to initiate colorectal tumorigenesis in mice.
Genomic and Transcriptomic Analysis of Relapsed and Refractory Childhood Solid Tumors Reveals a Diverse Molecular Landscape and Mechanisms of Immune Evasion.
IER2-induced senescence drives melanoma invasion through osteopontin.
RNA binding protein RBMS3 is a common EMT effector that modulates triple-negative breast cancer progression via stabilizing PRRX1 mRNA.
Uncovering spatial landscapes in colorectal cancer.
E3 ubiquitin ligase Atrogin-1 mediates adaptive resistance to KIT-targeted inhibition in gastrointestinal stromal tumor.
Anti-PD1 efficacy in metastatic urothelial cancer patients associates with intra-tumoral juxtaposition of T helper-type 1 and CD8+ T-cells.
Targeting AKR1B1 inhibits glutathione de novo synthesis to overcome acquired resistance to EGFR-targeted therapy in lung cancer.
Characterization of the Genomic and Immunological Diversity of Malignant Brain Tumors Through Multi-Sector Analysis.
Eicosanoid regulation of debris-stimulated metastasis.
Petasin potently inhibits mitochondrial complex I-based metabolism that supports tumor growth and metastasis.
USP29 coordinates MYC and HIF1α stabilization to promote tumor metabolism and progression.
Melanoma brain metastases that progress on BRAF-MEK inhibitors demonstrate resistance to ipilimumab-nivolumab that is associated with the Innate PD-1 Resistance Signature (IPRES).
Single-cell RNA sequencing reveals cell heterogeneity and transcriptome profile of breast cancer lymph node metastasis.
Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment.
Transcription Elongation Machinery Is a Druggable Dependency and Potentiates Immunotherapy in Glioblastoma Stem Cells.
Functional drug susceptibility testing using single-cell mass predicts treatment outcome in patient-derived cancer neurosphere models.
Enzymatically Transformable Polymersome-Based Nanotherapeutics to Eliminate Minimal Relapsable Cancer.
Therapeutic targeting of SLC6A8 creatine transporter suppresses colon cancer progression and modulates human creatine levels.
The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the discovery, prediction, and exploration of mutational signatures.
Circulating tumor DNA in stage III colorectal cancer, beyond minimal residual disease detection, towards assessment of adjuvant therapy efficacy and clinical behavior of recurrences.
Next generation of tumor-activating type I IFN enhances anti-tumor immune responses to overcome therapy resistance.

Oncogene. 2021 Oct 04.

CEMIP, a novel adaptor protein of OGT, promotes colorectal cancer metastasis through glutamine metabolic reprogramming via reciprocal regulation of β-catenin.

Qingling Hua, Biying Zhang, Guojie Xu, Lanqing Wang, Haihong Wang, Zhenyu Lin, Dandan Yu, Jinghua Ren, Dejun Zhang, Lei Zhao, Tao Zhang.

Metastasis is the leading cause of colorectal cancer (CRC)-induced death. However, the underlying molecular mechanisms of CRC metastasis are poorly understood. Metabolic reprogramming is an intrinsic feature of cancer, which have complicated effects on cancer metastasis. Here, we find that a novel metastasis-related protein, cell migration-inducing and hyaluronan-binding protein (CEMIP), can act as a novel adaptor protein of O-GlcNAc transferase (OGT) to promote CRC metastasis through glutamine metabolic reprogramming. Mechanistically, CEMIP interacts with OGT and β-catenin, which leads to elevated O-GlcNAcylation of β-catenin and enhanced β-catenin nuclear translocation from cytomembrane. Furthermore, accumulated β-catenin in nucleus enhances the transcription of CEMIP to reciprocally regulate β-catenin and contributes to over-expression of glutaminase 1 and glutamine transporters (SLC1A5 and SLC38A2). Combinational inhibition of CEMIP and glutamine metabolism could dramatically attenuate the metastasis of CRC in vivo. Collectively, this study reveals the importance of glutamine metabolic reprogramming in CEMIP-induced CRC metastasis, indicating the great potential of CEMIP and glutamine metabolism for CRC metastasis prevention.

DOI: https://doi.org/10.1038/s41388-021-02023-w
Cancer Res. 2021 Oct 04. pii: canres.1015.2021. [Epub ahead of print]

Characterization of peptides targeting metastatic tumor cells as probes for cancer detection and vehicles for therapy delivery.

Shraddha Subramanian, Alexes C Daquinag, Solmaz AghaAmiri, Sukhen C Ghosh, Ali Azhdarinia, Mikhail G Kolonin.

Metastasis is the leading cause of cancer-related deaths, and metastatic cancers remain largely incurable due to chemoresistance. Biomarkers of metastatic cells are lacking, and probes that could be used to detect and target metastases would be highly valuable. Here we hypothesize that metastatic cancer cells express cell surface receptors that can be harnessed for identification of molecules homing to metastases. Screening a combinatorial library in a mouse mammary tumor model of spontaneous metastasis identified cyclic peptides with tropism for cancer cells disseminated to the lungs. Two lead peptides, CLRHSSKIC and CRAGVGRGC, bound murine and human cells derived from breast carcinoma and melanoma in culture and were selective for metastatic cells in vivo. In mice, peptide CRAGVGRGC radiolabeled with 67Ga for biodistribution analysis demonstrated selective probe homing to lung metastases. Moreover, systemic administration of 68Ga-labeled CRAGVGRGC enabled non-invasive imaging of lung metastases in mice by positron emission tomography. A CRAGVGRGC-derived peptide induced apoptosis upon cell internalization in vitro and suppressed metastatic burden in vivo. Co-localization of CLRHSSKIC and CRAGVGRGC with N-cadherin+/E-cadherin- cells indicated that both peptides are selective for cancer cells that have undergone the epithelial-to-mesenchymal transition. We conclude that CRAGVGRGC is useful as a probe to facilitate the development of imaging modalities and therapies targeting metastases.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-1015
Cancer Lett. 2021 Oct 05. pii: S0304-3835(21)00498-5. [Epub ahead of print]

Prostate cancer dormancy and recurrence.

Frank C Cackowski, Elisabeth I Heath.

  Prostate cancer can progress rapidly after diagnosis, but can also become undetectable after curative intent radiation or surgery, only to recur years or decades later. This capacity to lie dormant and recur long after a patient was thought to be cured, is relatively unique to prostate cancer, with estrogen receptor positive breast cancer being the other common and well-studied example. Most investigators agree that the bone marrow is an important site for dormant tumor cells, given the frequency of bone metastases and that multiple studies have reported disseminated tumor cells in patients with localized disease. However, while more difficult to study, lymph nodes and the prostate bed are likely to be important reservoirs as well. Dormant tumor cells may be truly quiescent and in the G0 phase of the cell cycle, which is commonly called cellular dormancy. However, tumor growth may also be held in check through a balance of proliferation and cell death (tumor mass dormancy). For induction of cellular dormancy, prostate cancer cells respond to signals from their microenvironment, including TGF-β2, BMP-7, GAS6, and Wnt-5a, which result in signals transduced in part through p38 MAPK and pluripotency associated transcription factors including SOX2 and NANOG, which likely affect the epi-genome through histone modification. Clinical use of adjuvant radiation or androgen deprivation has been modestly successful to prevent recurrence. With the rapid pace of discovery in this field, systemic adjuvant therapy is likely to continue to improve in the future.

Keywords:  Adjuvant therapy; Dormancy; Metastasis; Prostate cancer; Quiescence; Recurrence

DOI:  https://doi.org/10.1016/j.canlet.2021.09.037
Oncogene. 2021 Oct 06.

Lnc00892 competes with c-Jun to block NCL transcription, reducing the stability of RhoA/RhoC mRNA and impairing bladder cancer invasion.

Shuwei Ren, Ning Zhang, Liping Shen, Yongyong Lu, Yixin Chang, Zhenni Lin, Ning Sun, Yuanmei Zhang, Jiheng Xu, Haishan Huang, Honglei Jin.

Metastasis of bladder cancer is a complex process and has been associated with poor clinical outcomes. However, the mechanisms of bladder cancer metastasis remain largely unknown. The present study found that the long noncoding RNA lnc00892 was significantly downregulated in bladder cancer tissues, with low lnc00892 expression associated with poor prognosis of bladder cancer patients. Lnc00892 significantly inhibited the migration, invasion, and metastasis of bladder cancer cells in vitro and in vivo. In-depth analysis showed that RhoA/C acted downstream of lnc00892 to inhibit bladder cancer metastasis. Mechanistically, lnc00892 reduces nucleolin gene transcription by competitively binding the promoter of nucleolin with c-Jun, thereby inhibiting nucleolin-mediated stabilization of RhoA/RhoC mRNA. Taken together, these findings provide novel insights into understanding the mechanisms of bladder cancer metastasis and suggest that lnc00892 can serve as a potential therapeutic target in patients with invasive bladder cancer.

DOI: https://doi.org/10.1038/s41388-021-02033-8
Oncogene. 2021 Oct 07.

CRISPR screens identify cholesterol biosynthesis as a therapeutic target on stemness and drug resistance of colon cancer.

Shanshan Gao, Fraser Soares, Shiyan Wang, Chi Chun Wong, Huarong Chen, Zhenjie Yang, Weixin Liu, Minnie Y Y Go, Musaddeque Ahmed, Yong Zeng, Catherine Adell O'Brien, Joseph J Y Sung, Housheng Hansen He, Jun Yu.

Cancer stem cells (CSCs) are responsible for tumor progression, recurrence, and drug resistance. To identify genetic vulnerabilities of colon cancer, we performed targeted CRISPR dropout screens comprising 657 Drugbank targets and 317 epigenetic regulators on two patient-derived colon CSC-enriched spheroids. Next-generation sequencing of pooled genomic DNAs isolated from surviving cells yielded therapeutic candidates. We unraveled 44 essential genes for colon CSC-enriched spheroids propagation, including key cholesterol biosynthetic genes (HMGCR, FDPS, and GGPS1). Cholesterol biosynthesis was induced in colon cancer tissues, especially CSC-enriched spheroids. The genetic and pharmacological inhibition of HMGCR/FDPS impaired self-renewal capacity and tumorigenic potential of the spheroid models in vitro and in vivo. Mechanistically, HMGCR or FDPS depletion impaired cancer stemness characteristics by activating TGF-β signaling, which in turn downregulated expression of inhibitors of differentiation (ID) proteins, key regulators of cancer stemness. Cholesterol and geranylgeranyl diphosphate (GGPP) rescued the growth inhibitory and signaling effect of HMGCR/FDPS blockade, implying a direct role of these metabolites in modulating stemness. Finally, cholesterol biosynthesis inhibitors and 5-FU demonstrated antitumor synergy in colon CSC-enriched spheroids, tumor organoids, and xenografts. Taken together, our study unravels novel genetic vulnerabilities of colon CSC-enriched spheroids and suggests cholesterol biosynthesis as a potential target in conjunction with traditional chemotherapy for colon cancer treatment.

DOI: https://doi.org/10.1038/s41388-021-01882-7
Oncogene. 2021 Oct 04.

Decoupling tumor cell metastasis from growth by cellular pilot protein TNFAIP8.

Mingyue Li, Xinyuan Li, Jason R Goldsmith, Songlin Shi, Li Zhang, Ali Zamani, Lin Wan, Honghong Sun, Ting Li, Jiyeon Yu, Zienab Etwebi, Mayassa J Bou-Dargham, Youhai H Chen.

Cancer metastasis accounts for nearly 90% of all cancer deaths. Metastatic cancer progression requires both cancer cell migration to the site of the metastasis and subsequent proliferation after colonization. However, it has long been recognized that cancer cell migration and proliferation can be uncoupled; but the mechanism underlying this paradox is not well understood. Here we report that TNFAIP8 (tumor necrosis factor-α-induced protein 8), a "professional" transfer protein of phosphoinositide second messengers, promotes cancer cell migration or metastasis but inhibits its proliferation or cancer growth. TNFAIP8-deficient mice developed larger tumors, but TNFAIP8-deficient tumor cells completely lost their ability to migrate toward chemoattractants and were defective in colonizing lung tissues as compared to wild-type counterparts. Mechanistically, TNFAIP8 served as a cellular "pilot" of tumor cell migration by locally amplifying PI3K-AKT and Rac signals on the cell membrane facing chemoattractant; at the same time, TNFAIP8 also acted as a global inhibitor of tumor cell growth and proliferation by regulating Hippo signaling pathway. These findings help explain the migration-proliferation paradox of cancer cells that characterizes many cancers.

DOI: https://doi.org/10.1038/s41388-021-02035-6
Nat Commun. 2021 Oct 04. 12(1): 5760

Determinants of renal cell carcinoma invasion and metastatic competence.

Kangsan Kim, Qinbo Zhou, Alana Christie, Christina Stevens, Yuanqing Ma, Oreoluwa Onabolu, Suneetha Chintalapati, Tiffani Mckenzie, Vanina Toffessi Tcheuyap, Layton Woolford, He Zhang, Nirmish Singla, Pravat Kumar Parida, Mauricio Marquez-Palencia, Ivan Pedrosa, Vitaly Margulis, Arthur Sagalowsky, Zhiqun Xie, Tao Wang, Steffen Durinck, Zora Modrusan, Somasekar Seshagiri, Payal Kapur, James Brugarolas, Srinivas Malladi.

Metastasis is the principal cause of cancer related deaths. Tumor invasion is essential for metastatic spread. However, determinants of invasion are poorly understood. We addressed this knowledge gap by leveraging a unique attribute of kidney cancer. Renal tumors invade into large vessels forming tumor thrombi (TT) that migrate extending sometimes into the heart. Over a decade, we prospectively enrolled 83 ethnically-diverse patients undergoing surgical resection for grossly invasive tumors at UT Southwestern Kidney Cancer Program. In this study, we perform comprehensive histological analyses, integrate multi-region genomic studies, generate in vivo models, and execute functional studies to define tumor invasion and metastatic competence. We find that invasion is not always associated with the most aggressive clone. Driven by immediate early genes, invasion appears to be an opportunistic trait attained by subclones with diverse oncogenomic status in geospatial proximity to vasculature. We show that not all invasive tumors metastasize and identify determinants of metastatic competency. TT associated with metastases are characterized by higher grade, mTOR activation and a particular immune contexture. Moreover, TT grade is a better predictor of metastasis than overall tumor grade, which may have implications for clinical practice.

DOI: https://doi.org/10.1038/s41467-021-25918-4
Nat Rev Cancer. 2021 Oct 05.

Evolving cancer-niche interactions and therapeutic targets during bone metastasis.

Robert L Satcher, Xiang H-F Zhang.

Many cancer types metastasize to bone. This propensity may be a product of genetic traits of the primary tumour in some cancers. Upon arrival, cancer cells establish interactions with various bone-resident cells during the process of colonization. These interactions, to a large degree, dictate cancer cell fates at multiple steps of the metastatic cascade, from single cells to overt metastases. The bone microenvironment may even influence cancer cells to subsequently spread to multiple other organs. Therefore, it is imperative to spatiotemporally delineate the evolving cancer-bone crosstalk during bone colonization. In this Review, we provide a summary of the bone microenvironment and its impact on bone metastasis. On the basis of the microscopic anatomy, we tentatively define a roadmap of the journey of cancer cells through bone relative to various microenvironment components, including the potential of bone to function as a launch pad for secondary metastasis. Finally, we examine common and distinct features of bone metastasis from various cancer types. Our goal is to stimulate future studies leading to the development of a broader scope of potent therapies.

DOI: https://doi.org/10.1038/s41568-021-00406-5
Oncogene. 2021 Oct 06.

ZNF545 loss promotes ribosome biogenesis and protein translation to initiate colorectal tumorigenesis in mice.

Shiyan Wang, Chi Chun Wong, Yanquan Zhang, Junzhe Huang, Chuangen Li, Jianning Zhai, Guoping Wang, Hong Wei, Xueji Zhang, Housheng Hansen He, Jun Yu.

Ribosome biogenesis plays a pivotal role in tumorigenesis by supporting robust protein translation. We investigate the functional and molecular mechanism of Zinc finger protein 545 (ZNF545), a transcriptional repressor for ribosomal RNA (rRNA), in colorectal cancer (CRC). ZNF545 was silenced in CRC compared to adjacent normal tissues (P < 0.0001), implying a tumor-suppressive role. Colon-specific Znf545 knockout in mice accelerated CRC in ApcMin/+ and azoxymethane/dextran sulfate sodium-induced CRC. Mechanistically, we demonstrated that ZNF545 uses its two zinc finger clusters to bind to minimal rDNA promoter, where it assembled transcriptional repressor complex by interacting with KAP1. Znf545 deletion in mouse embryonic fibroblasts not only increased rRNA transcription rate and the nucleolar size and number but also altered the nucleolar composition and architecture with an increased number of fibrillar centers surrounded by net-like dense fibrillar components. Consequently, Znf545 deletion promoted the gene expression of translation machinery, protein translation, and cell growth. Consistent with its tumor-suppressive role, ZNF545 overexpression in CRC cells induced growth arrest and apoptosis. Finally, administration of rRNA synthesis inhibitor, CX-5461, inhibited CRC development in Znf545Δ/ΔApcMin/+ mice. In conclusion, ZNF545 suppresses CRC through repressing rRNA transcription and protein translation. Targeting rRNA biosynthesis in ZNF545-silenced tumors is a potential therapeutic strategy for CRC.

DOI: https://doi.org/10.1038/s41388-021-01938-8
Cancer Res. 2021 Oct 05. pii: canres.CAN-21-1033-E.2021. [Epub ahead of print]

Genomic and Transcriptomic Analysis of Relapsed and Refractory Childhood Solid Tumors Reveals a Diverse Molecular Landscape and Mechanisms of Immune Evasion.

Sara A Byron, William P D Hendricks, Abhinav B Nagulapally, Jacqueline M Kraveka, William S Ferguson, Valerie I Brown, Don E Eslin, Deanna Mitchell, Albert Cornelius, William Roberts, Michael S Isakoff, Javier E Oesterheld, Randal K Wada, Jawhar Rawwas, Kathleen Neville, Peter E Zage, Virginia L Harrod, Genevieve Bergendahl, Elizabeth VanSickle, Karl Dykema, Jeffrey Bond, Hsien-Chao Chou, Jun S Wei, Xinyu Wen, Hue V Reardon, Alison Roos, Sara Nasser, Tyler Izatt, Daniel Enriquez, Apurva M Hegde, Faith Cisneros, Austin Christofferson, Bryce Turner, Szabolcs Szelinger, Jonathan J Keats, Rebecca F Halperin, Javed Khan, Giselle L Saulnier Sholler, Jeffrey M Trent.

Children with treatment-refractory or relapsed (R/R) tumors face poor prognoses. As the genomic underpinnings driving R/R disease are not well defined, we describe here the genomic and transcriptomic landscapes of R/R solid tumors from 202 patients enrolled in Beat Childhood Cancer Consortium clinical trials. Tumor mutational burden (TMB) was elevated relative to untreated tumors at diagnosis, with one-third of tumors classified as having a pediatric high TMB. Prior chemotherapy exposure influenced the mutational landscape of these R/R tumors, with more than 40% of tumors demonstrating mutational signatures associated with platinum or temozolomide chemotherapy and two tumors showing treatment-associated hypermutation. Immunogenomic profiling found a heterogenous pattern of neoantigen and MHC class I expression and a general absence of immune infiltration. Transcriptional analysis and functional gene set enrichment analysis identified cross-pathology clusters associated with development, immune signaling, and cellular signaling pathways. While the landscapes of these R/R tumors reflected those of their corresponding untreated tumors at diagnosis, important exceptions were observed suggestive of tumor evolution, treatment resistance mechanisms, and mutagenic etiologies of treatment.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-1033
Oncogene. 2021 Oct 05.

IER2-induced senescence drives melanoma invasion through osteopontin.

Lenka Kyjacova, Rafael Saup, Kerstin Rönsch, Sabine Wallbaum, Stefanie Dukowic-Schulze, Amelia Foss, Sandra D Scherer, Melanie Rothley, Antje Neeb, Nicole Grau, Wilko Thiele, Sonja Thaler, Natascha Cremers, Carsten Sticht, Norbert Gretz, Boyan K Garvalov, Jochen Utikal, Jonathan P Sleeman.

Expression of the immediate-early response gene IER2 has been associated with the progression of several types of cancer, but its functional role is poorly understood. We found that increased IER2 expression in human melanoma is associated with shorter overall survival, and subsequently investigated the mechanisms through which IER2 exerts this effect. In experimental melanoma models, sustained expression of IER2 induced senescence in a subset of melanoma cells in a p53/MAPK/AKT-dependent manner. The senescent cells produced a characteristic secretome that included high levels of the extracellular phosphoglycoprotein osteopontin. Nuclear localization of the IER2 protein was critical for both the induction of senescence and osteopontin secretion. Osteopontin secreted by IER2-expressing senescent cells strongly stimulated the migration and invasion of non-senescent melanoma cells. Consistently, we observed coordinate expression of IER2, p53/p21, and osteopontin in primary human melanomas and metastases, highlighting the pathophysiological relevance of IER2-mediated senescence in melanoma progression. Together, our study reveals that sustained IER2 expression drives melanoma invasion and progression through stimulating osteopontin secretion via the stochastic induction of senescence.

DOI: https://doi.org/10.1038/s41388-021-02027-6
Oncogene. 2021 Oct 04.

RNA binding protein RBMS3 is a common EMT effector that modulates triple-negative breast cancer progression via stabilizing PRRX1 mRNA.

C James Block, Allison V Mitchell, Ling Wu, James Glassbrook, Douglas Craig, Wei Chen, Gregory Dyson, Donald DeGracia, Lisa Polin, Manohar Ratnam, Heather Gibson, Guojun Wu.

The epithelial-to-mesenchymal transition (EMT) has been recognized as a driving force for tumor progression in breast cancer. Recently, our group identified the RNA Binding Motif Single Stranded Interacting Protein 3 (RBMS3) to be significantly associated with an EMT transcriptional program in breast cancer. Additional expression profiling demonstrated that RBMS3 was consistently upregulated by multiple EMT transcription factors and correlated with mesenchymal gene expression in breast cancer cell lines. Functionally, RBMS3 was sufficient to induce EMT in two immortalized mammary epithelial cell lines. In triple-negative breast cancer (TNBC) models, RBMS3 was necessary for maintaining the mesenchymal phenotype and invasion and migration in vitro. Loss of RBMS3 significantly impaired both tumor progression and spontaneous metastasis in vivo. Using a genome-wide approach to interrogate mRNA stability, we found that ectopic expression of RBMS3 upregulates many genes that are resistant to degradation following transcriptional blockade by actinomycin D (ACTD). Specifically, RBMS3 was shown to interact with the mRNA of EMT transcription factor PRRX1 and promote PRRX1 mRNA stability. PRRX1 is required for RBMS3-mediated EMT and is partially sufficient to rescue the effect of RBMS3 knockdown in TNBC cell lines. Together, this study identifies RBMS3 as a novel and common effector of EMT, which could be a promising therapeutic target for TNBC treatment.

DOI: https://doi.org/10.1038/s41388-021-02030-x
Nat Cell Biol. 2021 Oct 06.

Uncovering spatial landscapes in colorectal cancer.

Zhe Wang.

DOI: https://doi.org/10.1038/s41556-021-00773-z
Oncogene. 2021 Oct 07.

E3 ubiquitin ligase Atrogin-1 mediates adaptive resistance to KIT-targeted inhibition in gastrointestinal stromal tumor.

Alfonso García-Valverde, Jordi Rosell, Sergi Sayols, David Gómez-Peregrina, Daniel F Pilco-Janeta, Iván Olivares-Rivas, Enrique de Álava, Joan Maurel, Jordi Rubió-Casadevall, Anna Esteve, Marta Gut, Claudia Valverde, Jordi Barretina, Joan Carles, George D Demetri, Jonathan A Fletcher, Joaquín Arribas, César Serrano.

KIT/PDGFRA oncogenic tyrosine kinase signaling is the central oncogenic event in most gastrointestinal stromal tumors (GIST), which are human malignant mesenchymal neoplasms that often feature myogenic differentiation. Although targeted inhibition of KIT/PDGFRA provides substantial clinical benefit, GIST cells adapt to KIT/PDGFRA driver suppression and eventually develop resistance. The specific molecular events leading to adaptive resistance in GIST remain unclear. By using clinically representative in vitro and in vivo GIST models and GIST patients' samples, we found that the E3 ubiquitin ligase Atrogin-1 (FBXO32)-the main effector of muscular atrophy in cachexia-resulted in the most critical gene derepressed in response to KIT inhibition, regardless the type of KIT primary or secondary mutation. Atrogin-1 in GISTs is transcriptionally controlled by the KIT-FOXO3a axis, thus indicating overlap with Atrogin-1 regulation mechanisms in nonneoplastic muscle cells. Further, Atrogin-1 overexpression was a GIST-cell-specific pro-survival mechanism that enabled the adaptation to KIT-targeted inhibition by apoptosis evasion through cell quiescence. Buttressed on these findings, we established in vitro and in vivo the preclinical proof-of-concept for co-targeting KIT and the ubiquitin pathway to maximize the therapeutic response to first-line imatinib treatment.

DOI: https://doi.org/10.1038/s41388-021-02049-0
Clin Cancer Res. 2021 Oct 06. pii: clincanres.3319.2020. [Epub ahead of print]

Anti-PD1 efficacy in metastatic urothelial cancer patients associates with intra-tumoral juxtaposition of T helper-type 1 and CD8+ T-cells.

Maud Rijnders, Hayri E Balcioglu, Debbie G J Robbrecht, Astrid A M Oostvogels, Rebecca Wijers, Maureen J B Aarts, Paul Hamberg, Geert J L H van Leenders, J Alberto Nakauma-González, Jens Voortman, Hans M Westgeest, Joost L Boormans, Ronald de Wit, Martijn Lolkema, Astrid A M van der Veldt, Reno Debets.

PURPOSE: PD1 inhibition results in durable anti-tumor responses in a proportion of metastatic urothelial cancer (mUC) patients. The majority of patients, however, does not experience clinical benefit. In this study, we aimed to identify early changes in T-cell subsets that underlie anti-PD1 efficacy in mUC patients.EXPERIMENTAL DESIGN: Paired samples were collected from peripheral blood, plasma, and metastatic lesions of 56 mUC patients at baseline and weeks 6 and 12 after initiating pembrolizumab treatment (200mg intravenously, q3w). Samples were analyzed using multiplex flow cytometry, ELISA and in situ stainings, including cellular network analysis. Treatment response was evaluated as best overall response according to RECIST v1.1, and patients were classified as responder (complete or partial response) or non-responder (progressive disease).
RESULTS: In responders, baseline fractions of CD4+ T-cells expressing co-signaling receptors were higher compared to non-responders. The fraction of circulating PD1+ CD4+ T-cells decreased at week 6 and 12, whereas the fraction of 4-1BB+ CD28+ CD4+ T-cells increased at week 12. In metastatic lesions of responders, the baseline density of T helper-type 1 (Th1) cells, defined as T-bet+ CD4+ T-cells, was higher as compared to non-responders. Upon treatment, Th1 cells became localized in close proximity to CD8+ T-cells, CD11b+ myeloid cells, and tumor cells.
CONCLUSIONS: A decrease in the fraction of circulating PD1+ CD4+ T-cells, and juxtaposition of Th1, CD8+, and myeloid cells was associated with response to anti-PD1 treatment in mUC patients.

DOI: https://doi.org/10.1158/1078-0432.CCR-20-3319
Sci Transl Med. 2021 Oct 06. 13(614): eabg6428

Targeting AKR1B1 inhibits glutathione de novo synthesis to overcome acquired resistance to EGFR-targeted therapy in lung cancer.

Ke-Ren Zhang, Yu-Fei Zhang, Hui-Min Lei, Ya-Bin Tang, Chun-Shuang Ma, Qian-Ming Lv, Shi-Yi Wang, Li-Ming Lu, Ying Shen, Hong-Zhuan Chen, Liang Zhu.

[Figure: see text].

DOI: https://doi.org/10.1126/scitranslmed.abg6428
Cancer Discov. 2021 Oct 05. pii: candisc.0291.2021. [Epub ahead of print]

Characterization of the Genomic and Immunological Diversity of Malignant Brain Tumors Through Multi-Sector Analysis.

Maximilian O Schaettler, Megan M Richters, Anthony Z Wang, Zachary L Skidmore, Bryan Fisk, Katherine E Miller, Tammi L Vickery, Albert H Kim, Michael R Chicoine, Joshua W Osbun, Eric C Leuthardt, Joshua L Dowling, Gregory J Zipfel, Ralph G Dacey, Hsiang-Chih Lu, Tanner M Johanns, Obi L Griffith, Elaine R Mardis, Malachi Griffith, Gavin P Dunn.

Despite some success in secondary brain metastases, targeted or immune-based therapies have shown limited efficacy against primary brain malignancies such as glioblastoma (GBM). While the intratumoral heterogeneity of GBM is implicated in treatment resistance, it remains unclear whether this diversity is observed within brain metastases and to what extent cancer-cell intrinsic heterogeneity sculpts the local immune microenvironment. Here, we profiled the immunogenomic state of 93 spatially distinct regions from 30 malignant brain tumors through whole exome, RNA, and TCR-sequencing. Our analyses identified differences between primary and secondary malignancies with gliomas displaying more spatial heterogeneity at the genomic and neoantigen level. Additionally, this spatial diversity was recapitulated in the distribution of T cell clones where some gliomas harbored highly expanded but spatially restricted clonotypes. This study defines the immunogenomic landscape across a cohort of malignant brain tumors and contains implications for the design of targeted and immune-based therapies against intracranial malignancies.

DOI: https://doi.org/10.1158/2159-8290.CD-21-0291
Proc Natl Acad Sci U S A. 2021 Oct 12. pii: e2107771118. [Epub ahead of print]118(41):

Eicosanoid regulation of debris-stimulated metastasis.

Jianjun Deng, Haixia Yang, Victoria M Haak, Jun Yang, Franciele C Kipper, Chantal Barksdale, Sung Hee Hwang, Allison Gartung, Diane R Bielenberg, Selvakumar Subbian, Koc-Kan Ho, Xiang Ye, Daidi Fan, Yongkui Sun, Bruce D Hammock, Dipak Panigrahy.

  Cancer therapy reduces tumor burden via tumor cell death ("debris"), which can accelerate tumor progression via the failure of inflammation resolution. Thus, there is an urgent need to develop treatment modalities that stimulate the clearance or resolution of inflammation-associated debris. Here, we demonstrate that chemotherapy-generated debris stimulates metastasis by up-regulating soluble epoxide hydrolase (sEH) and the prostaglandin E2 receptor 4 (EP4). Therapy-induced tumor cell debris triggers a storm of proinflammatory and proangiogenic eicosanoid-driven cytokines. Thus, targeting a single eicosanoid or cytokine is unlikely to prevent chemotherapy-induced metastasis. Pharmacological abrogation of both sEH and EP4 eicosanoid pathways prevents hepato-pancreatic tumor growth and liver metastasis by promoting macrophage phagocytosis of debris and counterregulating a protumorigenic eicosanoid and cytokine storm. Therefore, stimulating the clearance of tumor cell debris via combined sEH and EP4 inhibition is an approach to prevent debris-stimulated metastasis and tumor growth.

Keywords:  autacoid; debris; inflammation resolution; prostaglandin E2 receptor 4; soluble epoxide hydrolase

DOI:  https://doi.org/10.1073/pnas.2107771118
J Clin Invest. 2021 Sep 01. pii: e139933. [Epub ahead of print]131(17):

Petasin potently inhibits mitochondrial complex I-based metabolism that supports tumor growth and metastasis.

Kazuki Heishima, Nobuhiko Sugito, Tomoyoshi Soga, Masashi Nishikawa, Yuko Ito, Ryo Honda, Yuki Kuranaga, Hiroki Sakai, Ryo Ito, Takayuki Nakagawa, Hiroshi Ueda, Yukihiro Akao.

  Mitochondrial electron transport chain complex I (ETCC1) is the essential core of cancer metabolism, yet potent ETCC1 inhibitors capable of safely suppressing tumor growth and metastasis in vivo are limited. From a plant extract screening, we identified petasin (PT) as a highly potent ETCC1 inhibitor with a chemical structure distinct from conventional inhibitors. PT had at least 1700 times higher activity than that of metformin or phenformin and induced cytotoxicity against a broad spectrum of tumor types. PT administration also induced prominent growth inhibition in multiple syngeneic and xenograft mouse models in vivo. Despite its higher potency, it showed no apparent toxicity toward nontumor cells and normal organs. Also, treatment with PT attenuated cellular motility and focal adhesion in vitro as well as lung metastasis in vivo. Metabolome and proteome analyses revealed that PT severely depleted the level of aspartate, disrupted tumor-associated metabolism of nucleotide synthesis and glycosylation, and downregulated major oncoproteins associated with proliferation and metastasis. These findings indicate the promising potential of PT as a potent ETCC1 inhibitor to target the metabolic vulnerability of tumor cells.

Keywords:  Amino acid metabolism; Cancer; Metabolism; Mitochondria; Oncology

DOI:  https://doi.org/10.1172/JCI139933
Oncogene. 2021 Oct 02.

USP29 coordinates MYC and HIF1α stabilization to promote tumor metabolism and progression.

Rongfu Tu, Wenqian Kang, Mengjie Yang, Liyuan Wang, Qing Bao, Zhi Chen, Yang Dong, Jingchao Wang, Jue Jiang, Hudan Liu, Guoliang Qing.

Tumor cells must rewire cellular metabolism to satisfy the demands of unbridled growth and proliferation. How these metabolic processes are integrated to fuel cancer cell growth remains largely unknown. Deciphering the regulatory mechanisms is vital to develop targeted strategies for tumor-selective therapies. We herein performed an unbiased and functional siRNA screen against 96 deubiquitinases, which play indispensable roles in cancer and are emerging as therapeutic targets, and identified USP29 as a top candidate essential for metabolic reprogramming that support biosynthesis and survival in tumor cells. Integrated metabolic flux analysis and molecular investigation reveal that USP29 directly deubiquitinates and stabilizes MYC and HIF1α, two master regulators of metabolic reprogramming, enabling adaptive response of tumor cells in both normoxia and hypoxia. Systemic knockout of Usp29 depleted MYC and HIF1α in MYC-driven neuroblastoma and B cell lymphoma, inhibited critical metabolic targets and significantly prolonged survival of tumor-bearing mice. Strikingly, mice homozygous null for the Usp29 gene are viable, fertile, and display no gross phenotypic abnormalities. Altogether, these results demonstrate that USP29 selectively coordinates MYC and HIF1α to integrate metabolic processes critical for cancer cell growth, and therapeutic targeting of USP29, a potentially targetable enzyme, could create a unique vulnerability given deregulation of MYC and HIF1α frequently occurs in human cancers.

DOI: https://doi.org/10.1038/s41388-021-02031-w
J Immunother Cancer. 2021 Oct;pii: e002995. [Epub ahead of print]9(10):

Melanoma brain metastases that progress on BRAF-MEK inhibitors demonstrate resistance to ipilimumab-nivolumab that is associated with the Innate PD-1 Resistance Signature (IPRES).

Peter Kar Han Lau, Breon Feran, Lorey Smith, Arian Lasocki, Ramyar Molania, Kortnye Smith, Alison Weppler, Christopher Angel, Damien Kee, Prachi Bhave, Belinda Lee, Richard J Young, Amir Iravani, Hanxian Aw Yeang, Ismael A Vergara, David Kok, Kate Drummond, Paul Joseph Neeson, Karen E Sheppard, Tony Papenfuss, Benjamin J Solomon, Shahneen Sandhu, Grant A McArthur.

  BACKGROUND: Melanoma brain metastases (MBMs) are a challenging clinical problem with high morbidity and mortality. Although first-line dabrafenib-trametinib and ipilimumab-nivolumab have similar intracranial response rates (50%-55%), central nervous system (CNS) resistance to BRAF-MEK inhibitors (BRAF-MEKi) usually occurs around 6 months, and durable responses are only seen with combination immunotherapy. We sought to investigate the utility of ipilimumab-nivolumab after MBM progression on BRAF-MEKi and identify mechanisms of resistance.METHODS: Patients who received first-line ipilimumab-nivolumab for MBMs or second/third line ipilimumab-nivolumab for intracranial metastases with BRAFV600 mutations with prior progression on BRAF-MEKi and MRI brain staging from March 1, 2015 to June 30, 2018 were included. Modified intracranial RECIST was used to assess response. Formalin-fixed paraffin-embedded samples of BRAFV600 mutant MBMs that were naïve to systemic treatment (n=18) or excised after progression on BRAF-MEKi (n=14) underwent whole transcriptome sequencing. Comparative analyses of MBMs naïve to systemic treatment versus BRAF-MEKi progression were performed.
RESULTS: Twenty-five and 30 patients who received first and second/third line ipilimumab-nivolumab, were included respectively. Median sum of MBM diameters was 13 and 20.5 mm for the first and second/third line ipilimumab-nivolumab groups, respectively. Intracranial response rate was 75.0% (12/16), and median progression-free survival (PFS) was 41.6 months for first-line ipilimumab-nivolumab. Efficacy of second/third line ipilimumab-nivolumab after BRAF-MEKi progression was poor with an intracranial response rate of 4.8% (1/21) and median PFS of 1.3 months. Given the poor activity of ipilimumab-nivolumab after BRAF-MEKi MBM progression, we performed whole transcriptome sequencing to identify mechanisms of drug resistance. We identified a set of 178 differentially expressed genes (DEGs) between naïve and MBMs with progression on BRAF-MEKi treatment (p value <0.05, false discovery rate (FDR) <0.1). No distinct pathways were identified from gene set enrichment analyses using Kyoto Encyclopedia of Genes and Genomes, Gene Ontogeny or Hallmark libraries; however, enrichment of DEG from the Innate Anti-PD1 Resistance Signature (IPRES) was identified (p value=0.007, FDR=0.03).
CONCLUSIONS: Second-line ipilimumab-nivolumab for MBMs after BRAF-MEKi progression has poor activity. MBMs that are resistant to BRAF-MEKi that also conferred resistance to second-line ipilimumab-nivolumab showed enrichment of the IPRES gene signature.

Keywords:  central nervous system neoplasms; immunotherapy; melanoma; tumor microenvironment

DOI:  https://doi.org/10.1136/jitc-2021-002995
Oncogenesis. 2021 Oct 05. 10(10): 66

Single-cell RNA sequencing reveals cell heterogeneity and transcriptome profile of breast cancer lymph node metastasis.

Kun Xu, Runtian Wang, Hui Xie, Longfei Hu, Cong Wang, Jiali Xu, Chengjun Zhu, Yiqiu Liu, Fangyan Gao, Xintong Li, Cenzhu Wang, Jinyi Huang, Wenbin Zhou, Guohua Zhou, Yongqian Shu, Xiaoxiang Guan.

Molecular mechanisms underlying breast cancer lymph node metastasis remain unclear. Using single-cell sequencing, we investigated the transcriptome profile of 96,796 single cells from 15 paired samples of primary tumors and axillary lymph nodes. We identified nine cancer cell subclusters including CD44 + / ALDH2 + /ALDH6A1 + breast cancer stem cells (BCSCs), which had a copy-number variants profile similar to that of normal breast tissue. Importantly, BCSCs existed only in primary tumors and evolved into metastatic clusters infiltrating into lymph nodes. Furthermore, transcriptome data suggested that NECTIN2-TIGIT-mediated interactions between metastatic breast cancer cells and tumor microenvironment (TME) cells, which promoted immune escape and lymph node metastasis. This study is the first to delineate the transcriptome profile of breast cancer lymph node metastasis using single-cell RNA sequencing. Our findings offer novel insights into the mechanisms underlying breast cancer metastasis and have implications in developing novel therapies to inhibit the initiation of breast cancer metastasis.

DOI: https://doi.org/10.1038/s41389-021-00355-6
Cell. 2021 Oct 04. pii: S0092-8674(21)01066-7. [Epub ahead of print]

Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment.

Khiem C Lam, Romina E Araya, April Huang, Quanyi Chen, Martina Di Modica, Richard R Rodrigues, Amélie Lopès, Sarah B Johnson, Benjamin Schwarz, Eric Bohrnsen, Alexandria P Cogdill, Catharine M Bosio, Jennifer A Wargo, Maxwell P Lee, Romina S Goldszmid.

  The tumor microenvironment (TME) influences cancer progression and therapy response. Therefore, understanding what regulates the TME immune compartment is vital. Here we show that microbiota signals program mononuclear phagocytes in the TME toward immunostimulatory monocytes and dendritic cells (DCs). Single-cell RNA sequencing revealed that absence of microbiota skews the TME toward pro-tumorigenic macrophages. Mechanistically, we show that microbiota-derived stimulator of interferon genes (STING) agonists induce type I interferon (IFN-I) production by intratumoral monocytes to regulate macrophage polarization and natural killer (NK) cell-DC crosstalk. Microbiota modulation with a high-fiber diet triggered the intratumoral IFN-I-NK cell-DC axis and improved the efficacy of immune checkpoint blockade (ICB). We validated our findings in individuals with melanoma treated with ICB and showed that the predicted intratumoral IFN-I and immune compositional differences between responder and non-responder individuals can be transferred by fecal microbiota transplantation. Our study uncovers a mechanistic link between the microbiota and the innate TME that can be harnessed to improve cancer therapies.

Keywords:  STING; cancer immunology; dendritic cells; immune checkpoint blockade immunotherapy; innate immunity; interferon; macrophages; microbiota; monocytes; tumor microenvironment

DOI:  https://doi.org/10.1016/j.cell.2021.09.019
Cancer Discov. 2021 Oct 06. pii: candisc.1848.2020. [Epub ahead of print]

Transcription Elongation Machinery Is a Druggable Dependency and Potentiates Immunotherapy in Glioblastoma Stem Cells.

Zhixin Qiu, Linjie Zhao, Jia Z Shen, Zhengyu Liang, Qiulian Wu, Kailin Yang, Lihua Min, Ryan C Gimple, Qiyuan Yang, Shruti Bhargava, Chunyu Jin, Cheryl Kim, Denise Hinz, Deobrat Dixit, Jean A Bernatchez, Briana C Prager, Guoxin Zhang, Zhen Dong, Deguan Lv, Xujun Wang, Leo J Y Kim, Zhe Zhu, Katherine A Jones, Ye Zheng, Xiuxing Wang, Jair L Siqueira-Neto, Lukas Chavez, Xiang-Dong Fu, Charles Spruck, Jeremy N Rich.

Glioblastoma (GBM) is the most lethal primary brain cancer characterized by therapeutic resistance, which is promoted by GBM stem cells (GSCs). Here, we interrogated gene expression and whole genome CRISPR/Cas9 screening in a large panel of patient-derived GSCs, differentiated glioblastoma cells (DGCs), and neural stem cells (NSCs) to identify master regulators of GSC stemness, revealing an essential transcription state with increased RNA polymerase II-mediated transcription. The YY1 and transcriptional CDK9 complex was essential for GSC survival and maintenance in vitro and in vivo. YY1 interacted with CDK9 to regulate transcription elongation in GSCs. Genetic or pharmacological targeting of YY1-CDK9 complex elicited RNA m6A modification-dependent interferon responses, reduced regulatory T cell infiltration, and augmented efficacy of immune checkpoint therapy in glioblastoma. Collectively, these results suggest that YY1-CDK9 transcription elongation complex defines a targetable cell state with active transcription, suppressed interferon responses, and immunotherapy resistance in glioblastoma.

DOI: https://doi.org/10.1158/2159-8290.CD-20-1848
Cell Rep. 2021 Oct 05. pii: S2211-1247(21)01247-X. [Epub ahead of print]37(1): 109788

Functional drug susceptibility testing using single-cell mass predicts treatment outcome in patient-derived cancer neurosphere models.

Max A Stockslager, Seth Malinowski, Mehdi Touat, Jennifer C Yoon, Jack Geduldig, Mahnoor Mirza, Annette S Kim, Patrick Y Wen, Kin-Hoe Chow, Keith L Ligon, Scott R Manalis.

  Functional precision medicine aims to match individual cancer patients to optimal treatment through ex vivo drug susceptibility testing on patient-derived cells. However, few functional diagnostic assays have been validated against patient outcomes at scale because of limitations of such assays. Here, we describe a high-throughput assay that detects subtle changes in the mass of individual drug-treated cancer cells as a surrogate biomarker for patient treatment response. To validate this approach, we determined ex vivo response to temozolomide in a retrospective cohort of 69 glioblastoma patient-derived neurosphere models with matched patient survival and genomics. Temozolomide-induced changes in cell mass distributions predict patient overall survival similarly to O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation and may aid in predictions in gliomas with mismatch-repair variants of unknown significance, where MGMT is not predictive. Our findings suggest cell mass is a promising functional biomarker for cancers and drugs that lack genomic biomarkers.

Keywords:  cancer; cell mass; cell size; functional drug susceptibility testing; glioblastoma

DOI:  https://doi.org/10.1016/j.celrep.2021.109788
Adv Mater. 2021 Oct 07. e2105254

Enzymatically Transformable Polymersome-Based Nanotherapeutics to Eliminate Minimal Relapsable Cancer.

Junjie Li, Zhishen Ge, Kazuko Toh, Xueying Liu, Anjaneyulu Dirisala, Wendong Ke, Panyue Wen, Hang Zhou, Zheng Wang, Shiyan Xiao, Joachim F R Van Guyse, Theofilus A Tockary, Jinbing Xie, Daniel Gonzalez-Carter, Hiroaki Kinoh, Satoshi Uchida, Yasutaka Anraku, Kazunori Kataoka.

  Prevention of metastatic and local-regional recurrence of cancer after surgery remains difficult. Targeting postsurgical premetastatic niche and microresiduals presents an excellent prospective opportunity but is often challenged by poor therapeutic delivery into minimal residual tumors. Here, an enzymatically transformable polymer-based nanotherapeutic approach is presented that exploits matrix metalloproteinase (MMP) overactivation in tumor-associated tissues to guide the codelivery of colchicine (microtubule-disrupting and anti-inflammatory agent) and marimastat (MMP inhibitor). The dePEGylation of polymersomes catalyzed by MMPs not only exposes the guanidine moiety to improve tissue/cell-targeting/retention to increase bioavailability, but also differentially releases marimastat and colchicine to engage their extracellular (MMPs) and intracellular (microtubules) targets of action, respectively. In primary tumors/overt metastases, the vasculature-specific targeting of nanotherapeutics can function synchronously with the enhanced permeability and retention effect to deter malignant progression of metastatic breast cancer. After the surgical removal of large primary tumors, nanotherapeutic agents are localized in the premetastatic niche and at the site of the postsurgical wound, disrupting the premetastatic microenvironment and eliminating microresiduals, which radically reduces metastatic and local-regional recurrence. The findings suggest that nanotherapeutics can safely widen the therapeutic window to resuscitate colchicine and MMP inhibitors for other inflammatory disorders.

Keywords:  bioavailability and toxicity; inflammatory microenvironment; minimal residual diseases; postsurgical wounds; premetastatic niche; stimuli-responsive nanotherapeutics

DOI:  https://doi.org/10.1002/adma.202105254
Sci Adv. 2021 Oct 08. 7(41): eabi7511

Therapeutic targeting of SLC6A8 creatine transporter suppresses colon cancer progression and modulates human creatine levels.

Isabel Kurth, Norihiro Yamaguchi, Celia Andreu-Agullo, Helen S Tian, Subhasree Sridhar, Shugaku Takeda, Foster C Gonsalves, Jia Min Loo, Afsar Barlas, Katia Manova-Todorova, Robert Busby, Johanna C Bendell, James Strauss, Marwan Fakih, Autumn J McRee, Andrew E Hendifar, Lee S Rosen, Andrea Cercek, Robert Wasserman, Michael Szarek, Scott L Spector, Syed Raza, Masoud F Tavazoie, Sohail F Tavazoie.

[Figure: see text].

DOI: https://doi.org/10.1126/sciadv.abi7511
Cancer Res. 2021 Oct 08. pii: canres.0899.2021. [Epub ahead of print]

The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the discovery, prediction, and exploration of mutational signatures.

Aaron Chevalier, Shiyi Yang, Zainab Khurshid, Nathan Sahelijo, Tong Tong, Jonathan H Huggins, Masanao Yajima, Joshua D Campbell.

Mutational signatures are patterns of somatic alterations in the genome caused by carcinogenic exposures or aberrant cellular processes. To provide a comprehensive workflow for preprocessing, analysis, and visualization of mutational signatures, we created the Mutational Signature Comprehensive Analysis Toolkit (musicatk) package. musicatk enables users to select different schemas for counting mutation types and easily combine count tables from different schemas. Multiple distinct methods are available to deconvolute signatures and exposures or to predict exposures in individual samples given a pre-existing set of signatures. Additional exploratory features include the ability to compare signatures to the COSMIC database, embed tumors in two dimensions with UMAP, cluster tumors into subgroups based on exposure frequencies, identify differentially active exposures between tumor subgroups, and plot exposure distributions across user-defined annotations such as tumor type. Overall, musicatk will enable users to gain novel insights into the patterns of mutational signatures observed in cancer cohorts.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-0899
Clin Cancer Res. 2021 Oct 08. pii: clincanres.2404.2021. [Epub ahead of print]

Circulating tumor DNA in stage III colorectal cancer, beyond minimal residual disease detection, towards assessment of adjuvant therapy efficacy and clinical behavior of recurrences.

Tenna Vesterman Henriksen, Noelia Tarazona, Amanda Frydendahl, Thomas Reinert, Francisco Gimeno-Valiente, Juan Antonio Carbonell-Asins, Shruti Sharma, Derrick Renner, Dina Hafez, Desamparados Roda, Marisol Huerta, Susana Roselló, Anders Husted Madsen, Uffe S Løve, Per Vadgaard Andersen, Ole Thorlacius-Ussing, Lene Hjerrild Iversen, Kåre Andersson Gotschalck, Himanshu Sethi, Alexey Aleshin, Andres Cervantes, Claus Lindbjerg Andersen.

PURPOSE: Sensitive methods for risk stratification, monitoring therapeutic efficacy, and early relapse detection may have a major impact on treatment decisions and patient management for stage III colorectal cancer patients. Beyond assessing the predictive power of postoperative ctDNA detection, we explored the added benefits of serial analysis: assessing adjuvant chemotherapy (ACT) efficacy, early relapse detection, and ctDNA growth rates.EXPERIMENTAL DESIGN: We recruited 168 stage III colorectal cancer patients treated with curative intent at Danish and Spanish hospitals between 2014-2019. To quantify ctDNA in plasma samples (n=1204), 16 patient-specific somatic single nucleotide variants were profiled using multiplex-PCR, next generation sequencing.
RESULTS: Detection of ctDNA was a strong recurrence predictor postoperatively (HR=7.0; 95%CI 3.7-13.5, P<0.001) and directly after ACT (HR=50.76; 95%CI 15.4-167, P<0.001). The recurrence rate of postoperative ctDNA-positive patients treated with ACT was 80% (16/20). Only patients who cleared ctDNA permanently during ACT did not relapse. Serial ctDNA assessment after the end of treatment was similarly predictive of recurrence (HR=50.80; 95%CI 14.9-172; P<0.001), and revealed two distinct rates of exponential ctDNA growth, slow (27% ctDNA-increase/month) and fast (137% ctDNA-increase/month) (p<0.001). The ctDNA growth rate was prognostic of survival (HR=2.7, 95%CI 1.1-6.7, p=0.039). Serial ctDNA analysis every three months detected recurrence with a median lead-time of 9.8 months compared to standard-of-care computed tomography.
CONCLUSIONS: Serial postoperative ctDNA analysis has a strong prognostic value and enables tumor growth rate assessment. The novel combination of ctDNA detection and growth rate assessment provides unique opportunities for guiding decision-making.

DOI: https://doi.org/10.1158/1078-0432.CCR-21-2404
Nat Commun. 2021 Oct 07. 12(1): 5866

Next generation of tumor-activating type I IFN enhances anti-tumor immune responses to overcome therapy resistance.

Xuezhi Cao, Yong Liang, Zhenxiang Hu, Huiyu Li, Jiaming Yang, Eric J Hsu, Jiankun Zhu, Jin Zhou, Yang-Xin Fu.

Type I interferon is promising in treating different kinds of tumors, but has been limited by its toxicity, lack of tumor targeting, and very short half-life. To target tumors, reduce systemic toxicity, and increase half-life, here we engineer a masked type I IFN-Fc (ProIFN) with its natural receptor connected by a cleavable linker that can be targeted by tumor-associated proteases. ProIFN has a prolonged serum half-life and shows an improved tumor-targeting effect. Interestingly, ProIFN-treated mice show enhanced DC cross-priming and significant increased CD8+ infiltration and effector function in the tumor microenvironment. ProIFN is able to improve checkpoint blockade efficacy in established tumors, as well as radiation efficacy for both primary and metastatic tumors. ProIFN exhibits superior long-term pharmacokinetics with minimal toxicity in monkeys. Therefore, this study demonstrates an effective tumor-activating IFN that can increase targeted immunity against primary tumor or metastasis and reduce periphery toxicity to the host.

DOI: https://doi.org/10.1038/s41467-021-26112-2