Monthly Letter

1. Homozygous receptors for insulin and not IGF-1 accelerate intimal hyperplasia in insulin resistance and diabetes.
Li Q, Fu J, Xia Y, Qi W, Ishikado A, Park K, Yokomizo H, Huang Q, Cai W, Rask-Madsen C, Kahn CR, King GL. Nat Commun. 2019 Sep 27;10(1):4427. doi: 10.1038/s41467-019-12368-2.

2. Urothelial organoids originating from Cd49fhigh mouse stem cells display Notch-dependent differentiation capacity.
Santos CP, Lapi E, Martínez de Villarreal J, Álvaro-Espinosa L, Fernández-Barral A, Barbáchano A, Domínguez O, Laughney AM, Megías D, Muñoz A, Real FX. Nat Commun. 2019 Sep 27;10(1):4407. doi: 10.1038/s41467-019-12307-1.

3. Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas.
Ding X, He M, Chan AWH, Song QX, Sze SC, Chen H, Man MKH, Man K, Chan SL, Lai PBS, Wang X, Wong N. Gastroenterology. 2019 Sep 24. pii: S0016-5085(19)41338-3. doi: 10.1053/j.gastro.2019.09.005.

4. Functional interpretation of single cell similarity maps.
DeTomaso D, Jones MG, Subramaniam M, Ashuach T, Ye CJ, Yosef N. Nat Commun. 2019 Sep 26;10(1):4376. doi: 10.1038/s41467-019-12235-0.

5. Hippo pathway deletion in adult resting cardiac fibroblasts initiates a cell state transition with spontaneous and self-sustaining fibrosis.
Xiao Y, Hill MC, Li L, Deshmukh V, Martin TJ, Wang J, Martin JF. Genes Dev. 2019 Sep 26. doi: 10.1101/gad.329763.119.

6. Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers.
Osmanbeyoglu HU, Shimizu F, Rynne-Vidal A, Alonso-Curbelo D, Chen HA, Wen HY, Yeung TL, Jelinic P, Razavi P, Lowe SW, Mok SC, Chiosis G, Levine DA, Leslie CS. Nat Commun. 2019 Sep 25;10(1):4369. doi: 10.1038/s41467-019-12291-6.

7. Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation.
Price AJ, Collado-Torres L, Ivanov NA, Xia W, Burke EE, Shin JH, Tao R, Ma L, Jia Y, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE. Genome Biol. 2019 Sep 26;20(1):196. doi: 10.1186/s13059-019-1805-1.

8. SSBP1 mutations cause mtDNA depletion underlying a complex optic atrophy disorder.
Del Dotto V, Ullah F, Di Meo I, Magini P, Gusic M, Maresca A, Caporali L, Palombo F, Tagliavini F, Baugh EH, Macao B, Szilagyi Z, Péron C, Gustafson MA, Khan K, La Morgia C, Barboni P, Carbonelli M, Valentino ML, Liguori R, Shashi V, Sullivan JA, Nagaraj S, El-Dairi M, Iannaccone A, Cutcutache I, Bertini E, Carrozzo R, Emma F, Diomedi-Camassei F, Zanna C, Armstrong M, Page MJ, Boesch S, Wortmann SB, Kopajtich R, Stong N, Sperl W, Davis E, Copeland WC, Seri M, Falkenberg M, Prokisch H, Katsanis N, Tiranti V, Pippucci T, Carelli V. J Clin Invest. 2019 Sep 24. pii: 128514. doi: 10.1172/JCI128514.

9. DART-seq: an antibody-free method for global m6A detection.
Meyer KD. Nat Methods. 2019 Sep 23. doi: 10.1038/s41592-019-0570-0.

10. Massively parallel RNA device engineering in mammalian cells with RNA-Seq.
Xiang JS, Kaplan M, Dykstra P, Hinks M, McKeague M, Smolke CD. Nat Commun. 2019 Sep 23;10(1):4327. doi: 10.1038/s41467-019-12334-y.

11. Transcriptional control of lung alveolar type 1 cell development and maintenance by NK homeobox 2-1.
Little DR, Gerner-Mauro KN, Flodby P, Crandall ED, Borok Z, Akiyama H, Kimura S, Ostrin EJ, Chen J. Proc Natl Acad Sci U S A. 2019 Sep 23. pii: 201906663. doi: 10.1073/pnas.1906663116.

12. RNA-seq as a tool for evaluating human embryo competence.
Groff AF, Resetkova N, DiDomenico F, Sakkas D, Penzias A, Rinn JL, Eggan K. Genome Res. 2019 Sep 23. doi: 10.1101/gr.252981.119.

13. Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma.
Ooi WF, Nargund AM, Lim KJ, Zhang S, Xing M, Mandoli A, Lim JQ, Ho SWT, Guo Y, Yao X, Lin SJ, Nandi T, Xu C, Ong X, Lee M, Tan AL, Lam YN, Teo JX, Kaneda A, White KP, Lim WK, Rozen SG, Teh BT, Li S, Skanderup AJ, Tan P. Gut. 2019 Sep 21. pii: gutjnl-2018-317612. doi: 10.1136/gutjnl-2018-317612.

14. Tet inactivation disrupts YY1 binding and long-range chromatin interactions during embryonic heart development.
Fang S, Li J, Xiao Y, Lee M, Guo L, Han W, Li T, Hill MC, Hong T, Mo W, Xu R, Zhang P, Wang F, Chang J, Zhou Y, Sun D, Martin JF, Huang Y. Nat Commun. 2019 Sep 20;10(1):4297. doi: 10.1038/s41467-019-12325-z.

15. Structural elucidation of bisulfite adducts to pseudouridine that result in deletion signatures during reverse transcription of RNA.
Fleming AM, Alenko A, Kitt JP, Orendt AM, Flynn PF, Harris JM, Burrows CJ. J Am Chem Soc. 2019 Sep 20. doi: 10.1021/jacs.9b08630.

16. Age-Related Gene Expression Signature in Rats Demonstrate Early, Late, and Linear Transcriptional Changes from Multiple Tissues.
Shavlakadze T, Morris M, Fang J, Wang SX, Zhu J, Zhou W, Tse HW, Mondragon-Gonzalez R, Roma G, Glass DJ. Cell Rep. 2019 Sep 17;28(12):3263-3273.e3. doi: 10.1016/j.celrep.2019.08.043.

17. TCR and Inflammatory Signals Tune Human MAIT Cells to Exert Specific Tissue Repair and Effector Functions.
Leng T, Akther HD, Hackstein CP, Powell K, King T, Friedrich M, Christoforidou Z, McCuaig S, Neyazi M, Arancibia-Cárcamo CV, Hagel J, Powrie F; Oxford IBD Investigators, Peres RS, Millar V, Ebner D, Lamichhane R, Ussher J, Hinks TSC, Marchi E, Willberg C, Klenerman P. Cell Rep. 2019 Sep 17;28(12):3077-3091.e5. doi: 10.1016/j.celrep.2019.08.050.

18. Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants.
He Y, Luo X, Zhou B, Hu T, Meng X, Audano PA, Kronenberg ZN, Eichler EE, Jin J, Guo Y, Yang Y, Qi X, Su B. Nat Commun. 2019 Sep 17;10(1):4233. doi: 10.1038/s41467-019-12174-w.

19. The Integrator complex cleaves nascent mRNAs to attenuate transcription.
Tatomer DC, Elrod ND, Liang D, Xiao MS, Jiang JZ, Jonathan M, Huang KL, Wagner EJ, Cherry S, Wilusz JE. Genes Dev. 2019 Sep 17. doi: 10.1101/gad.330167.119.

20. cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes.
DePasquale EAK, Schnell D, Dexheimer P, Ferchen K, Hay S, Chetal K, Valiente-Alandí Í, Blaxall BC, Grimes HL, Salomonis N. Nucleic Acids Res. 2019 Sep 16. pii: gkz789. doi: 10.1093/nar/gkz789.

21. Recurrent GNAQ mutation encoding T96S in natural killer/T cell lymphoma.
Li Z, Zhang X, Xue W, Zhang Y, Li C, Song Y, Mei M, Lu L, Wang Y, Zhou Z, Jin M, Bian Y, Zhang L, Wang X, Li L, Li X, Fu X, Sun Z, Wu J, Nan F, Chang Y, Yan J, Yu H, Feng X, Wang G, Zhang D, Fu X, Zhang Y, Young KH, Li W, Zhang M. Nat Commun. 2019 Sep 16;10(1):4209. doi: 10.1038/s41467-019-12032-9.

22. Genetic characterization of B-cell prolymphocytic leukemia: a prognostic model involving MYC and TP53.
Chapiro E, Pramil E, Diop M, Roos-Weil D, Dillard C, Gabillaud C, Maloum K, Settegrana C, Baseggio L, Lesesve JF, Yon M, Jondreville L, Lesty C, Davi FB, Le Garff-Tavernier M, Droin NM, Dessen P, Algrin C, Leblond V, Gabarre J, Bouzy S, Eclache V, Gaillard B, Callet-Bauchu E, Muller M, Lefebvre C, Nadal N, Ittel A, Struski S, Collonge-Rame MA, Quilichini B, Fert-Ferrer S, Auger N, Radford-Weiss I, Wagner L, Scheinost S, Zenz T, Susin SA, Bernard OA, Nguyen-Khac F. Blood. 2019 Sep 16. pii: blood.2019001187. doi: 10.1182/blood.2019001187.

23. Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells.
Tan L, Lacko LA, Zhou T, Tomoiaga D, Hurtado R, Zhang T, Sevilla A, Zhong A, Mason CE, Noggle S, Evans T, Stuhlmann H, Schwartz RE, Chen S. Nat Commun. 2019 Sep 13;10(1):4155. doi: 10.1038/s41467-019-12063-2.

24. Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction.
Bhattacherjee A, Djekidel MN, Chen R, Chen W, Tuesta LM, Zhang Y. Nat Commun. 2019 Sep 13;10(1):4169. doi: 10.1038/s41467-019-12054-3.

25. Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ.
Foley JW, Zhu C, Jolivet P, Zhu SX, Lu P, Meaney MJ, West RB. Genome Res. 2019 Sep 13. pii: gr.234807.118. doi: 10.1101/gr.234807.118.

26. CDK12 inhibition mediates DNA damage and is synergistic with sorafenib treatment in hepatocellular carcinoma.
Wang C, Wang H, Lieftink C, du Chatinier A, Gao D, Jin G, Jin H, Beijersbergen RL, Qin W, Bernards R. Gut. 2019 Sep 13. pii: gutjnl-2019-318506. doi: 10.1136/gutjnl-2019-318506.

27. Skin colonization by circulating neoplastic clones in cutaneous T-cell lymphoma.
Iyer A, Hennessey D, O'Keefe S, Patterson J, Wang W, Wong GK, Gniadecki R. Blood. 2019 Sep 12. pii: blood.2019002516. doi: 10.1182/blood.2019002516.

28. Tracing Tumor Evolution in Sarcoma Reveals Clonal Origin of Advanced Metastasis.
Tang YJ, Huang J, Tsushima H, Ban GI, Zhang H, Oristian KM, Puviindran V, Williams N, Ding X, Ou J, Jung SH, Lee CL, Jiao Y, Chen BJ, Kirsch DG, Alman BA. Cell Rep. 2019 Sep 10;28(11):2837-2850.e5. doi: 10.1016/j.celrep.2019.08.029.

29. The single-cell transcriptomic landscape of early human diabetic nephropathy.
Wilson PC, Wu H, Kirita Y, Uchimura K, Ledru N, Rennke HG, Welling PA, Waikar SS, Humphreys BD. Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19619-19625. doi: 10.1073/pnas.1908706116. Epub 2019 Sep 10.

30. A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures.
Zhang N, Shi S, Jia TZ, Ziegler A, Yoo B, Yuan X, Li W, Zhang S. Nucleic Acids Res. 2019 Sep 3. pii: gkz731. doi: 10.1093/nar/gkz731.

31. Assessment of kinship detection using RNA-seq data.
Blay N, Casas E, Galván-Femenía I, Graffelman J, de Cid R, Vavouri T. Nucleic Acids Res. 2019 Sep 10. pii: gkz776. doi: 10.1093/nar/gkz776.

32. Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data.
Shulman ED, Elkon R. Nucleic Acids Res. 2019 Sep 10. pii: gkz781. doi: 10.1093/nar/gkz781.

33. Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers.
Parikh AR, Leshchiner I, Elagina L, Goyal L, Levovitz C, Siravegna G, Livitz D, Rhrissorrakrai K, Martin EE, Van Seventer EE, Hanna M, Slowik K, Utro F, Pinto CJ, Wong A, Danysh BP, de la Cruz FF, Fetter IJ, Nadres B, Shahzade HA, Allen JN, Blaszkowsky LS, Clark JW, Giantonio B, Murphy JE, Nipp RD, Roeland E, Ryan DP, Weekes CD, Kwak EL, Faris JE, Wo JY, Aguet F, Dey-Guha I, Hazar-Rethinam M, Dias-Santagata D, Ting DT, Zhu AX, Hong TS, Golub TR, Iafrate AJ, Adalsteinsson VA, Bardelli A, Parida L, Juric D, Getz G, Corcoran RB. Nat Med. 2019 Sep;25(9):1415-1421. doi: 10.1038/s41591-019-0561-9. Epub 2019 Sep 9.

34. Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.
Zhang AW, O'Flanagan C, Chavez EA, Lim JLP, Ceglia N, McPherson A, Wiens M, Walters P, Chan T, Hewitson B, Lai D, Mottok A, Sarkozy C, Chong L, Aoki T, Wang X, Weng AP, McAlpine JN, Aparicio S, Steidl C, Campbell KR, Shah SP. Nat Methods. 2019 Oct;16(10):1007-1015. doi: 10.1038/s41592-019-0529-1. Epub 2019 Sep 9.

35. Genetic Variants Implicate Dual Oxidase-2 (DUOX2) in Familial and Sporadic Non-Medullary Thyroid Cancer.
Bann DV, Jin Q, Sheldon KE, Houser KR, Nguyen L, Warrick JI, Baker MJ, Broach J, Gerhard GS, Goldenberg D. Cancer Res. 2019 Sep 9. pii: canres.0721.2019. doi: 10.1158/0008-5472.CAN-19-0721.

36. A comparison of automatic cell identification methods for single-cell RNA sequencing data.
Abdelaal T, Michielsen L, Cats D, Hoogduin D, Mei H, Reinders MJT, Mahfouz A. Genome Biol. 2019 Sep 9;20(1):194. doi: 10.1186/s13059-019-1795-z.

37. Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in the dsRNA Response.
Rath S, Prangley E, Donovan J, Demarest K, Wingreen NS, Meir Y, Korennykh A. Mol Cell. 2019 Sep 19;75(6):1218-1228.e6. doi: 10.1016/j.molcel.2019.07.027. Epub 2019 Sep 4.

38. RNA editing alterations define manifestation of prion diseases.
Kanata E, Llorens F, Dafou D, Dimitriadis A, Thüne K, Xanthopoulos K, Bekas N, Espinosa JC, Schmitz M, Marín-Moreno A, Capece V, Shormoni O, Andréoletti O, Bonn S, Torres JM, Ferrer I, Zerr I, Sklaviadis T. Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19727-19735. doi: 10.1073/pnas.1803521116. Epub 2019 Sep 6.

39. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.
Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. Cell. 2019 Sep 5;178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018.

40. Homozygous NLRP1 gain-of-function mutation in siblings with a syndromic form of recurrent respiratory papillomatosis.
Drutman SB, Haerynck F, Zhong FL, Hum D, Hernandez NJ, Belkaya S, Rapaport F, de Jong SJ, Creytens D, Tavernier SJ, Bonte K, De Schepper S, van der Werff Ten Bosch J, Lorenzo-Diaz L, Wullaert A, Bossuyt X, Orth G, Bonagura VR, Béziat V, Abel L, Jouanguy E, Reversade B, Casanova JL. Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):19055-19063. doi: 10.1073/pnas.1906184116. Epub 2019 Sep 4.

41. Clonal Mutations Activate the NF-κB Pathway to Promote Recurrence of Nasopharyngeal Carcinoma.
You R, Liu YP, Lin DC, Li Q, Yu T, Zou X, Lin M, Zhang XL, He GP, Yang Q, Zhang YN, Xie YL, Jiang R, Wu CY, Zhang C, Cui C, Wang JQ, Wang Y, Zhuang AH, Guo GF, Hua YJ, Sun R, Yun JP, Zuo ZX, Liu ZX, Zhu XF, Kang TB, Qian CN, Mai HQ, Sun Y, Zeng MS, Feng L, Zeng YX, Chen MY. Cancer Res. 2019 Sep 4. pii: canres.3845.2018. doi: 10.1158/0008-5472.CAN-18-3845.

42. A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage.
Sharir A, Marangoni P, Zilionis R, Wan M, Wald T, Hu JK, Kawaguchi K, Castillo-Azofeifa D, Epstein L, Harrington K, Pagella P, Mitsiadis T, Siebel CW, Klein AM, Klein OD. Nat Cell Biol. 2019 Sep;21(9):1102-1112. doi: 10.1038/s41556-019-0378-2. Epub 2019 Sep 2.

43. Non-classical tissue monocytes and two functionally distinct populations of interstitial macrophages populate the mouse lung.
Schyns J, Bai Q, Ruscitti C, Radermecker C, De Schepper S, Chakarov S, Farnir F, Pirottin D, Ginhoux F, Boeckxstaens G, Bureau F, Marichal T. Nat Commun. 2019 Sep 3;10(1):3964. doi: 10.1038/s41467-019-11843-0.

44. Extracellular RNA in a single droplet of human serum reflects physiologic and disease states.
Zhou Z, Wu Q, Yan Z, Zheng H, Chen CJ, Liu Y, Qi Z, Calandrelli R, Chen Z, Chien S, Su HI, Zhong S. Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):19200-19208. doi: 10.1073/pnas.1908252116. Epub 2019 Sep 3.

45. Single-cell transcriptional analyses of spasmolytic polypeptide-expressing metaplasia arising from acute drug injury and chronic inflammation in the stomach.
Bockerstett KA, Lewis SA, Wolf KJ, Noto CN, Jackson NM, Ford EL, Ahn TH, DiPaolo RJ. Gut. 2019 Sep 3. pii: gutjnl-2019-318930. doi: 10.1136/gutjnl-2019-318930.

46. Serine-phosphorylated STAT3 promotes tumorigenesis via modulation of RNA polymerase transcriptional activity.
Balic J, Garama DJ, Saad M, Yu L, West A, West AJ, Livis T, Bhathal PS, Gough DJ, Jenkins BJ. Cancer Res. 2019 Sep 3. pii: canres.0974.2019. doi: 10.1158/0008-5472.CAN-19-0974.

47. Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency.
Zhao T, Huan Q, Sun J, Liu C, Hou X, Yu X, Silverman IM, Zhang Y, Gregory BD, Liu CM, Qian W, Cao X. Genome Biol. 2019 Sep 3;20(1):189. doi: 10.1186/s13059-019-1799-8.

48. Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders.
Rao X, Thapa KS, Chen AB, Lin H, Gao H, Reiter JL, Hargreaves KA, Ipe J, Lai D, Xuei X, Wang Y, Gu H, Kapoor M, Farris SP, Tischfield J, Foroud T, Goate AM, Skaar TC, Mayfield RD, Edenberg HJ, Liu Y. Mol Psychiatry. 2019 Sep 2. doi: 10.1038/s41380-019-0508-z.

49. Tumour-infiltrating CD8+ lymphocytes and colorectal cancer recurrence by tumour and nodal stage.
Glaire MA, Domingo E, Sveen A, Bruun J, Nesbakken A, Nicholson G, Novelli M, Lawson K, Oukrif D, Kildal W, Danielsen HE, Kerr R, Kerr D, Tomlinson I, Lothe RA, Church DN. Br J Cancer. 2019 Sep;121(6):474-482. doi: 10.1038/s41416-019-0540-4. Epub 2019 Aug 7. Erratum in: Br J Cancer. 2019 Sep 23;:.

50. APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data.
Leonard S, Meyer S, Lacour S, Nasser W, Hommais F, Reverchon S. Nucleic Acids Res. 2019 Sep 5;47(15):e88. doi: 10.1093/nar/gkz485.