Berto Laboratory

Our lab has focused on understanding the gene regulatory mechanisms that contribute to neuropsychiatric and neurodevelopmental disorders and how these complex regulatory mechanisms have evolved in the human lineage at the cell-type level. In addition to the neuro-evolutionary genomic interests, I am involved in the neuroimaging genomic field. Combining the techniques of gene expression profiling and advanced signal processing of brain oscillations recorded during mnemonic tasks and fMRI in a resting state is an innovative way to link brain activity with molecular mechanisms. With this cross-disciplinary and innovative plan, I uncovered novel gene signatures that may be important for brain pathophysiology.

Our Research
Neurogenomics
Using postnatal to adult post-mortem human brain tissue from healthy individuals, we will assess the developmental trajectories of the gray/white matter in multiple region of interests. Our group will take advantage of scRNA-seq, scATAC-seq, and histone marks H3K27ac/H3K4me3 ChIP-seq to uncover the contribution of transcriptomic, epigenomics, and active/poised enhancers at cell type specific level. Computational methods will be used to define developmental trajectories and to integrate the multi-omics data processed with the aim to refine and prioritize coding and non-coding regions important for the brain development. By integrating GWAS risk-loci and common variants associated with disorders and complex traits, we will provide the association of neurogenomics of the human brain with neuropsychiatric disorders at coding and non-coding level.
Image

Evolutionary Genomics
Our group will take advantage of cells and tissues from human and non-human primates to characterize the molecular mechanisms under evolution on the human lineage. Our group will take advantage of induced pluripotent stem cells (iPSC) from multiple great apes. Combining RNA-seq and ATAC-seq, we will uncover the human-specific evolutionary trajectories relevant for the maturation and proliferation of neuronal and glia derived cells. We will further take advantage of this in-vitro system as a platform for gene modeling. Integration with GWAS-risk loci will be performed to assess whether human-specific trajectories are affected by loci that put at risk for specific neuropsychiatric disorders.
Image

Imaging Genomics
Imaging genomics is an emerging field that want to connect brain function with genomics and genetics. Our group will work on evolutionary neuroimaging genomics comparing human with non-human primates imaging data and associate human-specific brain activity with human specific genomics and risk-loci associated with neuropsychiatric disorders. We will also include disorders such as autism and schizophrenia. Our group will apply and develop new imaging genomic tools to reconstruct these evolutionary trajectories and to link human-specific phenotypes from medical imaging with genomics and genetics.
Image


Team:
Director
Stefano Berto, PhD
Assistant Professor
Education: Ph.D. Leipzig University 2016
Research Interests: Neurogenomics, Evolutionary Genomics, Neuroimaging Genomics, Neuropsychiatric Disorders

Staff and Students
L. Dailey Nettles, PhD
Postdoctoral Scholar
Dailey is a postdoctoral scholar at the Medical University of South Carolina in the lab of Stefano Berto, PhD. Dailey received her PhD in Neuroscience from the University of Colorado Anschutz Medical Campus where she studied the role of myelin in motor cortex circuit function under the co-mentorship of Cristin Welle, PhD and Ethan Hughes, PhD. She received her BS in Neuroscience from the University of Alabama at Birmingham, where she trained in the lab of Gwendalyn King, PhD. Dailey joined the Berto Lab in 2022 and is excited to continue her research career in neuroscience with an emphasis on the interactions between neurons and glia in neurological diseases. Outside of lab, Dailey is an avid knitter, quilter, and baker. She enjoys craft beer and good food, exploring the Lowcountry, and spending time with her husband, son, and dog.

Christina Stanton, BS
Research Technician
Christina is a recent graduate from the University of South Carolina. She received her BS in Biochemistry and Molecular Biology in May of 2022. During her time at the University of South Carolina, she conducted research concerning the neurotoxin BMAA, and its correlation to neurodegenerative disorders, under the direction of John Ferry, PhD. Christina joined the Berto Lab in September of 2022 while taking a gap year, with plans to return to academia in pursuit of a PhD in Neuroscience, or a related field. In her free time, she can often be found learning chess openings, surfing on Folly Beach, or practicing Mandarin Chinese.



Berto Laboratory Recent Publications (2020-present) 
Targeting de novo lipogenesis and the Lands cycle induces ferroptosis in KRAS-mutant lung cancer
Caterina Bartolacci, Cristina Andreani, Goncalo Dias do Vale, Stefano Berto, Margherita Melegari, Anna Coleen Crouch, Dodge L Baluya, George Kemble, Kurt Hodges, Jaqueline Starrett, Katerina Politi, Sandra Lynne Starnes, Daniele Lorenzini, Maria Gabriela Raso, Luisa Solis Soto, Carmen Behrens, Humam Kadara, Boning Gao, David Gerber, Ignacio I Wistuba, John Minna, Jeffrey McDonald, Pier Paolo Scaglioni

Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder
Stefano Berto, Alex H Treacher, Emre Caglayan, Danni Luo, Jillian R Haney, Michael J Gandal, Daniel H Geschwind, Albert A Montillo, Genevieve Konopka

Carbon Monoxide Activates PERK-Regulated Autophagy to Induce Immunometabolic Reprogramming and Boost Antitumor T-cell Function
Paramita Chakraborty, Rasesh Y Parikh, Seungho Choi, Danh Tran, Monika Gooz, Zachariah T Hedley, Do-Sung Kim, Dariusz Pytel, Inhong Kang, Satish N Nadig, Gyda C Beeson, Lauren Ball, Meenal Mehrotra, Hongjun Wang, Stefano Berto, Viswanathan Palanisamy, Hong Li, Shilpak Chatterjee, Paulo C Rodriguez, Eduardo N Maldonado, J Alan Diehl, Vamsi K Gangaraju, Shikhar Mehrotra

Decoding Brain Function Through Genetics
Kazuya Toriumi, Guang-Zhong Wang, Stefano Berto, Noriyoshi Usui

NPAS4 supports drug-cue associations and relapse-like behavior through regulation of the cell type-specific activation balance in the nucleus accumbens
Brandon W Hughes, Evgeny Tsvetkov, Benjamin M Siemsen, Kirsten K Snyder, Rose Marie Akiki, Daniel J Wood, Rachel D Penrod, Michael D Scofield, Stefano Berto, Makoto Taniguchi, Christopher W Cowan

Non-coding enhancer RNA regulates NPAS4 in the mPFC to control chronic stress-induced anhedonia-like behavior
Brandon W Hughes, Benjamin M Siemsen, Stefano Berto, Jaswinder Kumar, Rebecca G Cornbrooks, Rose Marie Akiki, Jordan S Carter, Emma C Brase, Nobuya Koike, Michael D Scofield, Christopher W Cowan, Makoto Taniguchi

Early Life Stress Alters Gene Expression and Cytoarchitecture in the Prefrontal Cortex Leading to Social Impairment and Increased Anxiety
Noriyoshi Usui, Yuta Ono, Ryoko Aramaki, Stefano Berto, Genevieve Konopka, Hideo Matsuzaki, Shoichi Shimada

NPAS4 regulates the transcriptional response of the suprachiasmatic nucleus to light and circadian behavior
Pin Xu, Stefano Berto, Ashwinikumar Kulkarni, Byeongha Jeong, Chryshanthi Joseph, Kimberly H Cox, Michael E Greenberg, Tae-Kyung Kim, Genevieve Konopka, Joseph S Takahashi

Combined glyoxalase 1 dysfunction and vitamin B6 deficiency in a schizophrenia model system causes mitochondrial dysfunction in the prefrontal cortex
Kazuya Toriumi, Stefano Berto, Shin Koike, Noriyoshi Usui, Takashi Dan, Kazuhiro Suzuki, Mitsuhiro Miyashita, Yasue Horiuchi, Akane Yoshikawa, Mai Asakura, Kenichiro Nagahama, Hsiao-Chun Lin, Yuki Sugaya, Takaki Watanabe, Masanobu Kano, Yuki Ogasawara, Toshio Miyata, Masanari Itokawa, Genevieve Konopka, Makoto Arai

Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans
Fatma Ayhan, Ashwinikumar Kulkarni, Stefano Berto, Karthigayini Sivaprakasam, Connor Douglas, Bradley C Lega, Genevieve Konopka

Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder
Stefano Berto, Alex Treacher, Emre Caglayan, Danni Luo, Jillian R Haney, Michael J Gandal, Daniel H Geschwind, Albert Montillo, Genevieve Konopka

Zbtb16 regulates social cognitive behaviors and neocortical development
Noriyoshi Usui, Stefano Berto, Ami Konishi, Makoto Kondo, Genevieve Konopka, Hideo Matsuzaki, Shoichi Shimada

Evolution of DNA methylation in the human brain
Hyeonsoo Jeong, Isabel Mendizabal, Stefano Berto, Paramita Chatterjee, Thomas Layman, Noriyoshi Usui, Kazuya Toriumi, Connor Douglas, Devika Singh, Iksoo Huh, Todd M. Preuss, Genevieve Konopka & Soojin V. Yi

Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding
Stefano Berto, Miles R Fontenot, Sarah Seger, Fatma Ayhan, Emre Caglayan, Ashwinikumar Kulkarni, Connor Douglas, Carol A Tamminga, Bradley C Lega, Genevieve Konopka

Hippocampal subfield transcriptome analysis in schizophrenia psychosis
Jessica Marie Perez, Stefano Berto, Kelly Gleason, Subroto Ghose, Chunfeng Tan, Tae-Kyung Kim, Genevieve Konopka, Carol A Tamminga

Reduction of MEF2C in Microglia Leads to Structural and Transcriptomic Changes in Mouse Models of MEF2C Haploinsufficiency Syndrome
Stefano Berto, Miles Fontenot, Sarah Seger, Fatma Ayhan, Emre Caglayan, Ashwinikumar Kulkarni, Connor Douglas, Carol A. Tamminga, Bradley C. Lega, Genevieve Konopka.

Genomics at cellular resolution: insights into cognitive disorders and their evolution
Stefano Berto, Yuxiang Liu, Genevieve Konopka
MEF2C Hypofunction in Neuronal and Neuroimmune Populations Produces MEF2C Haploinsufficiency Syndrome–like Behaviors in Mice
Adam J Harrington, Catherine M Bridges, Stefano Berto, Kayla Blankenship, Jennifer Y Cho, Ahlem Assali, Benjamin M Siemsen, Hannah W Moore, Evgeny Tsvetkov, Acadia Thielking, Genevieve Konopka, David B Everman, Michael D Scofield, Steven A Skinner, Christopher W Cowan

Epigenetic inheritance of circadian period in clonal cells
Yan Li, Yongli Shan, Gokhul Krishna Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly H Cox, Seung-Hee Yoo, Shuzhang Yang, Genevieve Konopka, Joseph S Takahashi

Neuronal and neuroimmune dysfunction underlies behavioral and synaptic phenotypes in a mouse model of MEF2C Haploinsufficiency Syndrome
Catherine Bridges, Adam Harrington, Kayla Blankenship, Ahlem Assali, Hannah Warren Moore, Stefano Berto, Yongjoo Jennifer Cho, Evgeny Tsvetkov, Steven Skinner, Christopher Cowan

Cell-Type Specific Epigenetic Links to Schizophrenia Risk in Control and Patients
Hyeonsoo Jeong, Isabel Mendizabal, Stefano Berto, Paramita Chatterjee, Thomas Layman, Noriyoshi Usui, Kazuya Toriumi, Connor Douglas, Devika Singh, Iksoo Huh, Todd M. Preuss, Genevieve Konopka & Soojin V. Yi

For more information on the work we do in our lab, please visit https://bertolab.org/