New & Noteworthy Publications

The CVG is committed to increasing awareness of current genomics research in our community. Listed below are the latest noteworthy publications from CVG member labs. We hope this will be a helpful way to stay informed of the exciting genomics work that is happening on our campus.

To help keep this page up-to-date, please email Charlotte Williams ( a citation or link to your new paper as soon as it is available online.

Director's Highlights Spring 2020

Developmental Cell Volume 53 Issue 2

Metabolic reprogramming promotes neural crest migration via Yap/Tead signaling.

Bhattacharya D (CVG Scholar 2018), Azambuja AP, Simoes-Costa M.
Developmental Cell. 2020 Apr 2.

In this study, the Simoes-Costa lab shows that metabolic reprogramming, specifically enhanced dependence on anaerobic glycolysis termed the Warburg effect, drives neural crest development. Although the Warburg effect is best studied in the context of cancer, the broader implication of this exciting work is that the Warburg effect is likely an important developmental mechanism that is aberrantly reactivated during tumor development and metastasis. The lead author on this work is Deb Bhattacharya, a CVG Scholar in 2018.

Marcos Simoes-Costa
Nature Communications cover

Gastric squamous-columnar junction contains a large pool of cancer-prone immature osteopontin responsive Lgr5− CD44+ cells.

Fu DJ, Wang L, Chouairi FK, Rose IM (CVG T32 Scholar 2017), Abetov DA, Miller AD, Yamulla RJ, Schimenti JC, Flesken-Nikitin A, Nikitin AY.
Nature Communications. 2020 Jan 3;11(1):1-3. PMID: 31901081

This study from the Nikitin lab explores gastric cancer, particularly tumors arising from the gastro-esophageal junction, for which the prognosis is extremely poor for unknown reasons. The authors identify a unique population of cancer prone cells only at the gastro-esophageal junction, which appear to be responsible for the initiation and progression of gastric cancer in this area. Co-author Ian Rose is a Vertebrate Developmental Genomics T32 fellow (2017) and Andrea Flesken-Nikitin is a CVG seed grant awardee (2019).

John Schimenti
Andrea Flesken-Nikitin
Alexander Nikitin
Cell Reports Volume 31 Issue 2

Hotspots of Aberrant Enhancer Activity in Fibrolamellar Carcinoma Reveal Candidate Oncogenic Pathways and Therapeutic Vulnerabilities.

Dinh TA, Sritharan R, Smith FD, Francisco AB, Ma RK, Bunaciu RP, Kanke M, Danko CG, Massa AP, Scott JD, Sethupathy P.
Cell Reports. 2020 Apr 14;31(2):107509.

In this study, the Sethupathy lab leverages ChRO-seq technology, pioneered in the Danko laboratory at Cornell, to define the chromatin landscape of a rare but devastating early-onset liver cancer called fibolamellar carcinoma (FLC). The authors reveal key signaling pathways that are aberrant in FLC and identify previously unsuspected genes that maintain FLC tumor cell survival. Studies in cell models suggest that combination therapy with inhibitors of these genes may offer a new therapeutic approach for this cancer for which there is currently no effective treatment.

Charles Danko
Praveen Sethupathy
FASEB Journal Volume 34 Issue 1

Hepatocyte p53 ablation induces metabolic dysregulation that is corrected by food restriction and vertical sleeve gastrectomy in mice.

Holter MM (CVG Scholar 2018), Garibay D, Lee SA, Saikia M, McGavigan AK (CVG Scholar 2015), Ngyuen L, Moore ES, Daugherity E, Cohen P, Kelly K, Weiss RS, Cummings BP.
FASEB J. 2020 Jan;34(1):1846-1858. PMID: 31914635

Although p53 is widely appreciated as a tumor suppressor, this study from the Cummings lab explores its role in energy metabolism. Specifically, the authors find that loss of p53 only in the liver leads to metabolic dysfunction. Moreover, they show that a specific type of bariatric surgery referred to as vertical sleeve gastrectomy can rescue the effects of liver-specific p53 loss to restore systemic energy balance. The lead author, Marlena Holter, is a CVG scholar (2018), and the study represents a collaboration with other CVG labs (Kelly and Weiss).

Bethany Cummings
Kathleen Kelly
Robert Weiss
Nature Communications cover

Thermal cues drive plasticity in resistance to desiccation in a montane salamander with implications for responses to climate change.

Riddell EA, Roback EY, Wells CE, Zamudio KR, Sears MW.
Nature communications. 2019 Sep 9;10(1):1-2.

Rapid water loss is a universal threat for animals, but the cues and responsive mechanisms that regulate resistance to water loss are poorly defined. Using gene expression network analyses and careful phenotypic assessments, Kelly Zamudio and collaborators demonstrate that the risk of water loss for salamanders rises exponentially with temperature. They also find that salamanders regulate water loss through regeneration of capillary beds in the skin, indicating that tissue renewal may be used for physiological purposes beyond replacing lost limbs.

Kelly Zamudio
Scientific Reports logo

Genome Diversity and the Origin of the Arabian Horse

Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M, Prabhu A, Bucca S, Bugno-Poniewierska M, Wallner B, Malek J, Miller DC, Clark AG, Antczak DF, and Brooks SA.
Scientific Reports. 2020 Jun 16;10(1):1-3.

The Arabian horse is one of the oldest breeds of any domesticated animal. This study from CVG members Doug Antczak and Andy Clark, in collaboration with colleagues across the world, leverages genomics to study the origin of the Arabian horse. The results point to a Middle Eastern origin, indicate unique genetic adaptations for physiology and morphology, and importantly dispel the popular belief that thoroughbred race horses were founded by Arabian stallions. The findings have attracted attention from the lay press; a prominent recent article can be found here.

Doug Antczak
Andrew Clark

Winter 2019 and Spring 2020

Exploring physiological and genetic variation of digital cushion thickness of Holstein and Jersey cows and bulls.

Stambuk CR, Staiger EA, Nazari-Ghadikolaei A, Heins BJ, Huson HJ
Journal of Dairy Sciences, accepted May 2020

Time- and population dependent genetic patterns underlie bovine milk somatic cell count.

Miles AM, Huson HJ
Journal of Dairy Science, accepted April 2020

Dextran-coated iron oxide nanoparticle-induced nanotoxicity in neuron cultures.

Badman RP, Moore SL, Killian JL, Feng T, Cleland TA, Hu F, Wang MD
Scientific Reports 2020, in press.

High variability in infection mechanisms and host responses: A review of functional genomic studies of amphibian chytridiomycosis.

Zamudio KR, McDonald CA, Belasen A.
Herpetologica 2020 (in press).

Show me you care: female mate choice based on egg attendance rather than male or territorial traits.

Valencia-Aguilar A, Zamudio KR, Haddad CFB, Bogdanowicz SM, Prado CPA.
Behavioral Ecology May 31 2020, araa051

Context-dependent odor learning requires the anterior olfactory nucleus.

Levinson M, Kolenda JP, Alexandrou GJ, Escanilla O, Smith DM, Cleland TA, Linster C
Behavioral Neuroscience 2020 May 7 doi: 10.1037/bne0000371. Online ahead of print. PMID: 32378908

Depleting Interferon Regulatory Factor‐1 (IRF‐1) with CRISPR/Cas9 attenuates inducible oxidative metabolism without affecting RA‐induced differentiation in HL‐60 human AML cells.

Zhu K, Yue J, Yen A.
FASEB BioAdvances 23 April 2020

Incapacitating effects of fungal coinfection in a novel pathogen system.

McDonald CA, Longo AV, Lips KR, Zamudio KR.
Molecular Ecology 20 April 2020

Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance.

Mason NA, Fletcher NK (CVG Scholar 2014), Gill BA, Funk WC, Zamudio KR.
Systematics and Biodiversity. 2020 Apr 3:1-2.

A Genetic Investigation of Island Jersey Cattle, the Foundation of the Jersey Breed: Comparing Population Structure and Selection to Guernsey, Holstein, and United States Jersey Cattle.

Huson HJ, Sonstegard TS, Godfrey J, Hambrook D, Wolfe C, Wiggans G, Blackburn H, VanTassell CP.
Frontiers in Genetics. 2020 Apr 17;11:366.

Dissecting the novel partners of nuclear c-Raf and its role in all-trans retinoic acid (ATRA)-induced myeloblastic leukemia cells differentiation.

Rashid A, Wang R, Zhang L, Yue J, Yang M, Yen A.
Experimental Cell Research. 2020 Apr 10:111989.

Network architecture and regulatory logic in neural crest development.

Hovland AS (CVG T32 Trainee 2019), Rothstein M (CVG Scholar 2017), Simoes-Costa M.
Wiley Interdiscip Rev Syst Biol Med. 2020. Mar;12(2):e1468. doi: 10.1002/wsbm.1468

Roscovitine enhances all-trans retinoic acid (ATRA)-induced nuclear enrichment of an ensemble of activated signaling molecules and augments ATRA-induced myeloid cell differentiation.

Rashid A, Duan X, Gao F, Yang M, Yen A.
Oncotarget. 2020 Mar 24;11(12):1017.

Membrane metalloendopeptidase suppresses prostate carcinogenesis by attenuating effects of gastrin-releasing peptide on stem/progenitor cells.

Cheng CY, Zhou Z, Stone M, Lu B, Flesken-Nikitin A, Nanus DM, Nikitin AY.
Oncogenesis. 2020 Mar 23;9(3):1-4.

Performance analysis of novel toxin-antidote CRISPR gene drive systems.

Champer J, Kim IK, Champer SE, Clark AG, Messer PW.
BMC Biol. 2020 Mar 12;18(1):27. doi: 10.1186/s12915-020-0761-2. PubMed PMID: 32164660

Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs.

Champer SE, Oh SY, Liu C, Wen Z, Clark AG, Messer PW, Champer J.
Sci Adv. 2020 Mar 4;6(10):eaaz0525. doi: 10.1126/sciadv.aaz0525. PubMed PMID: 32181354

Rapid online learning and robust recall in a neuromorphic olfactory circuit.

Imam N, Cleland TA.
Nature Machine Intelligence. 2020 Mar;2(3):181-91.

A toxin-antidote CRISPR gene drive system for regional population modification.

Champer J, Lee E, Yang E, Liu C, Clark AG, Messer PW.
Nat Commun. 2020 Feb 27;11(1):1082. doi: 10.1038/s41467-020-14960-3. PubMed PMID: 32109227

Roscovitine enhances All-trans retinoic acid (ATRA)-induced leukemia cell differentiation: Novel effects on signaling molecules for a putative Cdk2 inhibitor.

Rashid A, Duan X, Gao F, Yang M, Yen A.
Cellular Signalling. 2020 Feb 4:109555.

Phenotypic characterization and genome-wide association studies of digital cushion thickness in Holstein cows.

Stambuk CR, Staiger EA, Nazari-Ghadikolaei A, Heins BJ, Huson HJ.
Journal of Dairy Science. 2020 Feb 7.

Genetic diversity, population structure and runs of homozygosity in Ethiopian short fat-tailed and Awassi sheep breeds using genome-wide 50k SNP markers.

Getachew T, Haile A, Mészáros G, Rischkowsky B, *Huson HJ, Gizaw S, Wurzinger M, Mwai AO, Sölkner J
Livestock Science. 2020 Feb 1;232:103899. *Contributed to experimental design and sample collection.

Temperature‐mediated shifts in salamander transcriptomic responses to the amphibian‐killing fungus.

Ellison A, Zamudio K, Lips K, Muletz‐Wolz C.
Molecular Ecology. 2020 Jan;29(2):325-43.

Gene expression varies within and between enzootic and epizootic lineages of Batrachochytrium dendrobatidis (Bd) in the Americas.

McDonald CA, Ellison AR, Toledo LF, James TY, Zamudio KR.
Fungal biology. 2020 Jan 1;124(1):34-43.

Enteroendocrine Progenitor Cell–Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner.

Singh AP*, Hung YH*, Bonfini A, Kanke M, Shanahan MT, Dame MK, Biraud M, Peck BCE, Freund JM, Cubitt RL, Curry EG, Gonzalez LM, Dekaney CM, Bewick GA, Kurpios NA, S. Ding S, Spence JR, Buchon N, and Sethupathy P.
Cellular and Molecular Gastroenterology and Hepatology. 2020 Jan 1;9(3):447-64.
Selected for journal cover (pdf).

Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification.

Rothstein M (CVG Scholar 2017), Simoes-Costa M.
Genome Research. 2020 Jan 1;30(1):35-48.

Glacial cycles drive rapid divergence of cryptic field vole species.

Fletcher NK (CVG Scholar 2014), Acevedo P, Herman JS, Paupério J, Alves PC, Searle JB.
Ecology and Evolution. 2019 Dec;9(24):14101-13.

Special Issue: Repetitive DNA Sequences.

Lower SE, Dion-Côté AM, Clark AG, Barbash DA.
Genes 2019 Nov 6;10(11), 896 doi: 10.3390/genes10110896. PMID: 31698818;

Evolution of placental invasion and cancer metastasis are causally linked.

Kshitiz, Afzal J, Maziarz JD, Hamidzadeh A, Liang C, Erkenbrack EM, Kim HN, Haeger JD, Pfarrer C, Hoang T, Ott T, Spencer T, Pavličev M, Antczak DF, Levchenko A, Wagner GP.
Nat Ecol Evol. 2019 Dec;3(12):1743-1753. doi: 10.1038/s41559-019-1046-4. PMID: 31768023

Bull efficiency using dairy genetic traits.

Whitt CE, Tauer L, Huson HJ
PLOS ONE Nov 11, 2019; 14:11 e0223436

Publications 2019