Publications

Highlights

(For a full list see below or go to Google Scholar)

CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer

Cyclin-dependent kinase 7 (CDK7) is a central regulator of the cell cycle and gene transcription. However, little is known about its impact on genomic instability and cancer immunity. Using a selective CDK7 inhibitor, YKL-5-124, we demonstrated that CDK7 inhibition predominately disrupts cell-cycle progression and in- duces DNA replication stress and genome instability in small cell lung cancer (SCLC) while simultaneously triggering immune-response signaling. These tumor-intrinsic events provoke a robust immune surveillance program elicited by T cells, which is further enhanced by the addition of immune-checkpoint blockade. Combining YKL-5-124 with anti-PD-1 offers significant survival benefit in multiple highly aggressive murine models of SCLC, providing a rationale for new combination regimens consisting of CDK7 inhibitors and immunotherapies.

Hua Zhang#, Camilla L. Christensen#, Ruben Dries#, Matthew G. Oser#, Jiehui Deng, Brian Diskin, Fei Li, Yuanwang Pan, Xuzhu Zhang, Yandong Yin, Eleni Papadopoulos, Val Pyon, Cassandra Thakurdin, Nicholas Kwiatkowski, Kandarp Jani, Alexandra R. Rabin, Dayanne M. Castro, Ting Chen, Heather Silver, Qingyuan Huang, Mirna Bulatovic, Catriona M. Dowling, Belen Sundberg, Alan Leggett, Michela Ranieri, Han Han, Shuai Li, Annan Yang, Kristen E. Labbe, Christina Almonte, Vladislav O. Sviderskiy, Max Quinn, Jack Donaghue, Eric S. Wang, Tinghu Zhang, Zhixiang He, Vamsidhar Velcheti, Peter S. Hammerman, Gordon J. Freeman, Richard Bonneau, William G. Kaelin, Jr., Kate D. Sutherland, Ariena Kersbergen, Andrew J. Aguirre, Guo-Cheng Yuan, Eli Rothenberg, George Miller, Nathanael S. Gray and Kwok-Kin Wong.

Zhang H, Camilla C, Dries R et al. 2020. Cancer Cell.

Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors

Cooperative actions of extrinsic signals and cell-intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell-type specific and context-dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system’s actions during development, we selected 95 of its components and investigated their mRNA-expression dynamics, gene-gene interactions, and single-cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA-based perturbation of each individual component and documented the effect on steady-state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene-gene interactions display a marked cell-stage specific behavior. Furthermore, single-cell RNA-profiling at individual stages demonstrated the presence of detailed co-expression modules and subpopulations showing stable co-expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.

Ruben Dries, Agata Stryjewska, Kathleen Coddens, Satoshi Okawa, Tineke Notelaers, Judith Birkhoff, Mike Dekker, Catherine M. Verfaillie, Antonio del Sol, Eskeatnaf Mulugeta, Andrea Conidi, Frank G. Grosveld, Danny Huylebroeck

Dries R et al. 2019. Stem Cell.

BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells.

The CTCF paralogue BORIS is upregulated in transcriptionally reprogrammed neuroblastoma cells rendered resistant to targeted therapy, in which it promotes regulatory chromatin interactions that maintain the resistance phenotype.

David N. Debruyne#, Ruben Dries#, Satyaki Sengupta, Davide Seruggia, Yang Gao, Bandana Sharma, Hao Huang, Lisa Moreau, Michael McLane, Daniel S. Day, Eugenio Marco, Ting Chen, Nathanael S. Gray, Kwok-Kin Wong, Stuart H. Orkin, Guo-Cheng Yuan, Richard A. Young & Rani E. George

Debruyne D, Dries R et al. 2019. Nature.

RESCUE, imputing dropout events in single-cell RNA-sequencing data.

Single-cell RNA-sequencing technologies provide a powerful tool for systematic dissection of cellular heterogeneity. However, the prevalence of dropout events imposes complications during data analysis and, despite numerous efforts from the community, this challenge has yet to be solved.Results; Here we present a computational method, called RESCUE, to mitigate the dropout problem by imputing gene expression levels using information from other cells with similar patterns. Unlike existing methods, we use an ensemble-based approach to minimize the feature selection bias on imputation. By comparative analysis of simulated and real single-cell RNA-seq datasets, we show that RESCUE outperforms existing methods in terms of imputation accuracy which leads to more precise cell-type identification.Conclusions; Taken together, these results suggest that RESCUE is a useful tool for mitigating dropouts in single-cell RNA-seq data. RESCUE is implemented in R and available at https://github.com/seasamgo/rescue.

Tracy S, Yuan GC and Dries R

Tracy et al. 2019. BMC Bioinformatics.

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation.

Cyclin-dependent kinase 12 (CDK12) modulates transcription elongation by phosphorylating the carboxy-terminal domain of RNA polymerase II and selectively affects the expression of genes involved in the DNA damage response (DDR) and mRNA processing. Yet, the mechanisms underlying such selectivity remain unclear. Here we show that CDK12 inhibition in cancer cells lacking CDK12 mutations results in gene length-dependent elongation defects, inducing premature cleavage and polyadenylation (PCPA) and loss of expression of long (greater than 45 kb) genes, a substantial proportion of which participate in the DDR. This early termination phenotype correlates with an increased number of intronic polyadenylation sites, a feature especially prominent among DDR genes. Phosphoproteomic analysis indicated that CDK12 directly phosphorylates pre-mRNA processing factors, including those regulating PCPA. These results support a model in which DDR genes are uniquely susceptible to CDK12 inhibition primarily due to their relatively longer lengths and lower ratios of U1 snRNP binding to intronic polyadenylation sites.

Krajewska M#, Dries R#, Grassetti AV, Dust S, Gao Y, Huang H, Sharma B, Day DS, Kwiatkowski N, Pomaville M, Dodd O, Chipumuro E, Zhang T, Greenleaf AL, Yuan GC, Gray NS, Young RA, Geyer M, Gerber SA, George RE

Krajewska M, Dries R et al. 2019. Nature Communications.

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+.

Imaging the transcriptome in situ with high accuracy has been a major challenge in single-cell biology, which is particularly hindered by the limits of optical resolution and the density of transcripts in single cells. Here we demonstrate an evolution of sequential fluorescence in situ hybridization (seqFISH+). We show that seqFISH+ can image mRNAs for 10,000 genes in single cells with high accuracy and sub-diffraction-limit resolution in the cortex, subventricular zone and olfactory bulb of mouse brain, using a standard confocal microscope. The transcriptome-level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand-receptor pairs across neighbouring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery- driven studies of biological processes in situ.

Chee-Huat Linus eng, Michael Lawson, Qian Zhu, Ruben Dries, Noushin Koulena, Yodai takei, Jina Yun, Christopher Cronin, Christoph Karp, Guo-Cheng Yuan & Long Cai

Eng C.H. L et al. 2019. Nature.

Identification of spatially associated subpopulations by combining scrNAseq and sequential fluorescence in situ hybridization data.

How intrinsic gene-regulatory networks interact with a cells spatial environment to define its identity remains poorly understood. We developed an approach to distinguish between intrinsic and extrinsic effects on global gene expression by integrating analysis of sequencing-based and imaging-based single-cell transcriptomic profiles, using cross-platform cell type mapping combined with a hidden Markov random field model. We applied this approach to dissect the cell-type- and spatial-domain-associated heterogeneity in the mouse visual cortex region. Our analysis identified distinct spatially associated, cell-type-independent signatures in the glutamatergic and astrocyte cell compartments. Using these signatures to analyze single-cell RNA sequencing data, we identified previously unknown spatially associated subpopulations, which were validated by comparison with anatomical structures and Allen Brain Atlas images.

Qian Zhu, Sheel Shah, Ruben Dries, Long Cai & Guo-Cheng Yuan

Zhu Q et al. 2019. Nature Biotechnology.

Genomic and functional fidelity of small cell lung cancer patient-derived xenografts.

Small cell lung cancer (SCLC) patient-derived xenografts (PDXs) can be generated from biopsies or circulating tumor cells (CTCs), though scarcity of tissue and low efficiency of tumor growth have previously limited these approaches. Applying an established clinical-translational pipeline for tissue collection and an automated microfluidic platform for CTC-enrichment, we generated 17 biopsy-derived PDXs and 17 CTC-derived PDXs in a two-year timeframe, at 89% and 38% efficiency, respectively. Whole exome sequencing showed that somatic alterations are stably maintained between patient tumors and PDXs. Early-passage PDXs maintain the genomic and transcriptional profiles of the founder PDX. In vivo treatment with etoposide and cisplatin (EP) in 30 PDX models demonstrated greater sensitivity in PDXs from EP naïve patients, and resistance to EP corresponded to increased expression of a MYC gene signature. Finally, serial CTC-derived PDXs generated from an individual patient at multiple time points accurately recapitulated the evolving drug sensitivities of that patient’s disease. Collectively, this work highlights the translational potential of this strategy.

Drapkin BJ, George J, Christensen CL, Mino-Kenudson M, Dries R, Sundaresan T, Phat S, Myers DT, Zhong J, Igo P, Hazar-Rethinam MH, LiCausi JA, Gomez-Caraballo M, Kem M, Jani KN, Azimi R, Abedpour N, Menon R, Lakis S, Heist RS, BÃŒttner R, Haas S, Sequist LV, Shaw AT, Wong KK, Hata AN, Toner M, Maheswaran S, Haber DA, Peifer M, Dyson N, Thomas RK, Farago AF

Drapkin B et al. 2019. Cancer Discovery.

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells.

In human embryonic stem cells (ESCs) the transcription factor Zeb2 regulates neuroectoderm versus mesendoderm formation, but it is unclear how Zeb2 affects the global transcriptional regulatory network in these cell-fate decisions. We generated Zeb2 knockout (KO) mouse ESCs, subjected them as embryoid bodies (EBs) to neural and general differentiation and carried out temporal RNA-sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS) analysis in neural differentiation. This shows that Zeb2 acts preferentially as a transcriptional repressor associated with developmental progression and that Zeb2 KO ESCs can exit from their naïve state. However, most cells in these EBs stall in an early epiblast-like state and are impaired in both neural and mesendodermal differentiation. Genes involved in pluripotency, epithelial-to-mesenchymal transition (EMT), and DNA-(de)methylation, including Tet1, are deregulated in the absence of Zeb2. The observed elevated Tet1 levels in the mutant cells and the knowledge of previously mapped Tet1-binding sites correlate with loss-of-methylation in neural-stimulating conditions, however, after the cells initially acquired the correct DNA-methyl marks. Interestingly, cells from such Zeb2 KO EBs maintain the ability to re-adapt to 2i+LIF conditions even after prolonged differentiation, while knockdown of Tet1 partially rescues their impaired differentiation. Hence, in addition to its role in EMT, Zeb2 is critical in ESCs for exit from the epiblast state, and links the pluripotency network and DNA-methylation with irreversible commitment to differentiation.

Stryjewska A#, Dries R#, Pieters T, Verstappen G, Conidi A, Coddens K, Francis A, Umans L, van IJcken WF, Berx G, van Grunsven LA, Grosveld FG, Goossens S, Haigh JJ, Huylebroeck D.

Styjewska A, Dries R et al. 2017. Stem Cells.

BMP-SMAD Signaling Regulates Lineage Priming, but Is Dispensable for Self-Renewal in Mouse Embryonic Stem Cells

Naive mouse embryonic stem cells (mESCs) are in a metastable state and fluctuate between inner cell mass- and epiblast-like phenotypes. Here, we show transient activation of the BMP-SMAD signaling pathway in mESCs containing a BMP-SMAD responsive reporter transgene. Activation of the BMP-SMAD reporter transgene in naive mESCs correlated with lower levels of genomic DNA methylation, high expression of 5-methylcytosine hydroxylases Tet1/2 and low levels of DNA methyltransferases Dnmt3a/b. Moreover, naive mESCs, in which the BMP-SMAD reporter transgene was activated, showed higher resistance to differentiation. Using double Smad1;Smad5 knockout mESCs, we showed that BMP-SMAD signaling is dispensable for self-renewal in both naive and ground state. These mutant mESCs were still pluripotent, but they exhibited higher levels of DNA methylation than their wild-type counterparts and had a higher propensity to differentiate. We showed that BMP-SMAD signaling modulates lineage priming in mESCs, by transiently regulating the enzymatic machinery responsible for DNA methylation.

Gomes Fernandes M, Dries R, Roost MS, Semrau S, de Melo Bernardo A, Davis RP, Ramakrishnan R, Szuhai K, Maas E, Umans L, Abon Escalona V, Salvatori D, Deforce D, Van Criekinge W, Huylebroeck D, Mummery C, Zwijsen A, de Sousa Lopes SM.

Fernandes G et al. 2016. Stem Cell Reports.

 

Full List

Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb
Astrid Deryckere, Elke Stappers, Ruben Dries, Elise Peyre, Veronique van den Berghe, Andrea Conidi, F. Isabella Zampeta, Annick Francis, Marjolein Bresseleers, Agata Stryjewska, Ria Vanlaer, Elke Maas, Ihor V. Smal, Wilfred F. J. van IJcken, Frank G. Grosveld, Laurent Nguyen, Danny Huylebroeck, Eve Seuntjens
Deryckere A et al. 2020. Development.

CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer
Hua Zhang#, Camilla L. Christensen#, Ruben Dries#, Matthew G. Oser#, Jiehui Deng, Brian Diskin, Fei Li, Yuanwang Pan, Xuzhu Zhang, Yandong Yin, Eleni Papadopoulos, Val Pyon, Cassandra Thakurdin, Nicholas Kwiatkowski, Kandarp Jani, Alexandra R. Rabin, Dayanne M. Castro, Ting Chen, Heather Silver, Qingyuan Huang, Mirna Bulatovic, Catriona M. Dowling, Belen Sundberg, Alan Leggett, Michela Ranieri, Han Han, Shuai Li, Annan Yang, Kristen E. Labbe, Christina Almonte, Vladislav O. Sviderskiy, Max Quinn, Jack Donaghue, Eric S. Wang, Tinghu Zhang, Zhixiang He, Vamsidhar Velcheti, Peter S. Hammerman, Gordon J. Freeman, Richard Bonneau, William G. Kaelin, Jr., Kate D. Sutherland, Ariena Kersbergen, Andrew J. Aguirre, Guo-Cheng Yuan, Eli Rothenberg, George Miller, Nathanael S. Gray and Kwok-Kin Wong.
Zhang H, Camilla C, Dries R et al. 2020. Cancer Cell.

Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors
Ruben Dries, Agata Stryjewska, Kathleen Coddens, Satoshi Okawa, Tineke Notelaers, Judith Birkhoff, Mike Dekker, Catherine M. Verfaillie, Antonio del Sol, Eskeatnaf Mulugeta, Andrea Conidi, Frank G. Grosveld, Danny Huylebroeck
Dries R et al. 2019. Stem Cell.

BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells.
David N. Debruyne#, Ruben Dries#, Satyaki Sengupta, Davide Seruggia, Yang Gao, Bandana Sharma, Hao Huang, Lisa Moreau, Michael McLane, Daniel S. Day, Eugenio Marco, Ting Chen, Nathanael S. Gray, Kwok-Kin Wong, Stuart H. Orkin, Guo-Cheng Yuan, Richard A. Young & Rani E. George
Debruyne D, Dries R et al. 2019. Nature.

RESCUE, imputing dropout events in single-cell RNA-sequencing data.
Tracy S, Yuan GC and Dries R
Tracy et al. 2019. BMC Bioinformatics.

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation.
Krajewska M#, Dries R#, Grassetti AV, Dust S, Gao Y, Huang H, Sharma B, Day DS, Kwiatkowski N, Pomaville M, Dodd O, Chipumuro E, Zhang T, Greenleaf AL, Yuan GC, Gray NS, Young RA, Geyer M, Gerber SA, George RE
Krajewska M, Dries R et al. 2019. Nature Communications.

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+.
Chee-Huat Linus eng, Michael Lawson, Qian Zhu, Ruben Dries, Noushin Koulena, Yodai takei, Jina Yun, Christopher Cronin, Christoph Karp, Guo-Cheng Yuan & Long Cai
Eng C.H. L et al. 2019. Nature.

Identification of spatially associated subpopulations by combining scrNAseq and sequential fluorescence in situ hybridization data.
Qian Zhu, Sheel Shah, Ruben Dries, Long Cai & Guo-Cheng Yuan
Zhu Q et al. 2019. Nature Biotechnology.

NK cells mediate synergistic antitumor effects of combined inhibition of HDAC6 and BET in a SCLC preclinical model.
Liu Y, Li Y, Liu S, Adeegbe DO, Christensen CL, Quinn MM, Dries R, Han S, Buczkowski K, Wang X, Chen T, Gao P, Zhang H, Li F, Hammerman PS, Bradner JE, Quayle SN, Wong KK
Liu Y et al. 2019. Cancer Research.

Genomic and functional fidelity of small cell lung cancer patient-derived xenografts.
Drapkin BJ, George J, Christensen CL, Mino-Kenudson M, Dries R, Sundaresan T, Phat S, Myers DT, Zhong J, Igo P, Hazar-Rethinam MH, LiCausi JA, Gomez-Caraballo M, Kem M, Jani KN, Azimi R, Abedpour N, Menon R, Lakis S, Heist RS, BÃŒttner R, Haas S, Sequist LV, Shaw AT, Wong KK, Hata AN, Toner M, Maheswaran S, Haber DA, Peifer M, Dyson N, Thomas RK, Farago AF
Drapkin B et al. 2019. Cancer Discovery.

CDK4/6 Inhibition Augments Anti-Tumor Immunity by Enhancing T Cell Activation.
Deng J, Wang ES, Jenkins RW, Li S, Dries R, Yates K, Chhabra S, Huang W, Liu H, Aref AR, Ivanova E, Paweletz CP, Bowden M, Zhou CW, Herter-Sprie GS, Sorrentino JA, Bisi JE, Lizotte PH, Merlino AA, Quinn MM, Bufe LE, Yang A, Zhang Y, Zhang H, Gao P, Chen T, Cavanaugh ME, Rode AJ, Haines E, Roberts PJ, Strum JC, Richards WG, Lorch JH, Parangi S, Gunda V, Boland GM, Bueno R, Palakurthi S, Freeman GJ, Ritz J, Haining WN, Sharpless NE, Arthanari H, Shapiro GI, Barbie DA, Gray NS, Wong KK
Deng J et al. 2018. Nature Discovery.

Interleukin-17A Promotes Lung Tumor Progression through Neutrophil Attraction to Tumor Sites and Mediating Resistance to PD-1 Blockade.
Akbay EA, Koyama S, Liu Y, Dries R, Bufe LE, Silkes M, Alam MM, Magee DM, Jones R, Jinushi M, Kulkarni M, Carretero J, Wang X, Warner-Hatten T, Cavanaugh JD, Osa A, Kumanogoh A, Freeman GJ, Awad MM, Christiani DC, Bueno R, Hammerman PS, Dranoff G, Wong KK.
Akbay EA et al. 2017. Journal Thoracic Oncology.

Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-Small Cell Lung Cancer.
Adeegbe DO, Liu Y, Lizotte PH, Kamihara Y, Aref AR, Almonte C, Dries R, Li Y, Liu S, Wang X, Warner-Hatten T, Castrillon J, Yuan GC, Poudel-Neupane N, Zhang H, Guerriero JL, Han S, Awad MM, Barbie DA, Ritz J, Jones SS, Hammerman PS, Bradner J, Quayle SN, Wong KK.
Adeegbe DO et al. 2017. Cancer Discovery.

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells.
Stryjewska A#, Dries R#, Pieters T, Verstappen G, Conidi A, Coddens K, Francis A, Umans L, van IJcken WF, Berx G, van Grunsven LA, Grosveld FG, Goossens S, Haigh JJ, Huylebroeck D.
Styjewska A, Dries R et al. 2017. Stem Cells.

Multiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypes.
Lizotte PH, Ivanova EV, Awad MM, Jones RE, Keogh L, Liu H, Dries R, Almonte C, Herter-Sprie GS, Santos A, Feeney NB, Paweletz CP, Kulkarni MM, Bass AJ, Rustgi AK, Yuan GC, Kufe DW, JÀnne PA, Hammerman PS, Sholl LM, Hodi FS, Richards WG, Bueno R, English JM, Bittinger MA, Wong KK.
Lizotte PH et al. 2016. JCI Insight.

BMP-SMAD Signaling Regulates Lineage Priming, but Is Dispensable for Self-Renewal in Mouse Embryonic Stem Cells
Gomes Fernandes M, Dries R, Roost MS, Semrau S, de Melo Bernardo A, Davis RP, Ramakrishnan R, Szuhai K, Maas E, Umans L, Abon Escalona V, Salvatori D, Deforce D, Van Criekinge W, Huylebroeck D, Mummery C, Zwijsen A, de Sousa Lopes SM.
Fernandes G et al. 2016. Stem Cell Reports.

Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1.
van den Berghe V, Stappers E, Vandesande B, Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, Goossens S, Haigh JJ, Fishell G, Goffinet A, Aerts S, Huylebroeck D, Seuntjens E.
van den Berghe et al. 2013. Neuron.

Few Smad proteins and many Smad-interacting proteins yield multiple functions and action modes in TGFβ/BMP signaling in vivo
Conidi A, Cazzola S, Beets K, Coddens K, Collart C, Cornelis F, Cox L, Joke D, Dobreva MP, Dries R, Esguerra C, Francis A, Ibrahimi A, Kroes R, Lesage F, Maas E, Moya I, Pereira PN, Stappers E, Stryjewska A, van den Berghe V, Vermeire L, Verstappen G, Seuntjens E, Umans L, Zwijsen A, Huylebroeck D.
Conidi A et al. 2011. Cytokine & Growth Factor Reviews.