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Integrated analysis of molecular atlases unveils modules driving developmental cell subtype specification in the human cortex

Nano et al. introduce a pipeline to generate meta-atlases of the human brain from existing single-cell datasets and extract gene modules linked to cell fate specification. Perturbing these programs in human cortical chimeroids validated their roles in cell type specification.

Patricia R. Nano
Elisa Fazzari
Aparna Bhaduri
ResearchOpen Access21 Apr 2025
Nature Neuroscience

Volume: 28, P: 949-963
Non-muscle myosin II inhibition at the site of axon injury increases axon regeneration

Therapeutic interventions for motor axon regeneration following peripheral nerve injury are currently unavailable. Here authors show local administration of a non-muscle myosin II inhibitor at the injury site increases motor and sensory function recovery in vivo.

Keunjung Heo
Tammy Szu-Yu Ho
Clifford J. Woolf
ResearchOpen Access26 Mar 2025
Nature Communications

Volume: 16, P: 1-15
Cold atmospheric plasma effectively kills chordoma cells through induction of intracellular reactive oxygen species

Sophie Peeters
Peter B. Wu
Anthony C. Wang
ResearchOpen Access01 Jul 2025
Scientific Reports

Volume: 15, P: 1-7
Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia

Eze et al. use single-cell sequencing and immunohistochemical validation to create an atlas of early human brain development. In the telencephalon, they discover a diversity of progenitor subtypes, including two that are enriched in humans.

Ugomma C. Eze
Aparna Bhaduri
Arnold R. Kriegstein
ResearchOpen Access15 Mar 2021
Nature Neuroscience

Volume: 24, P: 584-594
An atlas of cortical arealization identifies dynamic molecular signatures

RNA-sequencing analysis of the prenatal human brain at different stages of development shows that areal transcriptional signatures are dynamic and coexist with developmental and cell-type signatures.

Aparna Bhaduri
Carmen Sandoval-Espinosa
Arnold R. Kriegstein
ResearchOpen Access06 Oct 2021
Nature

Volume: 598, P: 200-204
Chimeric brain organoids capture human genetic diversity

Models of the human brain’s cortex have been made by combining cells from up to five donors. This approach could enable genetic background to be accounted for in studies of brain development and disease.

Aparna Bhaduri
News & Views26 Jun 2024
Nature

Volume: 631, P: 32-33
Cell stress in cortical organoids impairs molecular subtype specification

Single-cell RNA sequencing clarifies the development and specification of neurons in the human cortex and shows that cell stress impairs this process in cortical organoids.

Aparna Bhaduri
Madeline G. Andrews
Arnold R. Kriegstein
Research29 Jan 2020
Nature

Volume: 578, P: 142-148
Functional genomics and systems biology in human neuroscience

Technical developments and large collaborative research networks in neurogenomics promise rapid progress in neuroscience, but translation of results from model systems to human brains is limited by sample availability, technical challenges and ethical issues.

Genevieve Konopka
Aparna Bhaduri
Reviews08 Nov 2023
Nature

Volume: 623, P: 274-282
Single-cell sequencing paints diverse pictures of the brain

A single-cell sequencing study reveals how different types of neuron are distributed in the brain. An analysis then demonstrates how these data can improve our understanding of neuronal functions.

Aparna Bhaduri
Tomasz J. Nowakowski
News & Views31 Oct 2018
Nature

Volume: 563, P: 38-39
The new frontier in understanding human and mammalian brain development

Recent studies integrating multi-omics data with cell atlases across development for brains of humans and model organisms are revealing conserved and divergent patterns of brain development at the molecular and cellular levels, and linking these to complex behavioural and neuropsychiatric phenotypes.

Tomasz J. Nowakowski
Patricia R. Nano
Hongkui Zeng
Reviews05 Nov 2025
Nature

Volume: 647, P: 51-59
K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas

Comprehensive genomic profiling of human H3K27M mutant diffuse midline gliomas, combining single-cell RNA sequencing and ATAC sequencing with bulk ChIP sequencing and other data, proposes distinct oligodendrocyte populations as potential cells of origin.

Selin Jessa
Abdulshakour Mohammadnia
Claudia L. Kleinman
Research05 Dec 2022
Nature Genetics

Volume: 54, P: 1865-1880
Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma

Paul Khavari and colleagues identify recurrent mutations concentrated at an ultraviolet signature hotspot in the KNSTRN gene in 19% of cutaneous squamous cell carcinomas. KNSTRN encodes a kinetochore protein.

Carolyn S Lee
Aparna Bhaduri
Paul A Khavari
Research07 Sept 2014
Nature Genetics

Volume: 46, P: 1060-1062
Retinoblastoma outcomes in Europe: a prospective analysis of 483 patients from 40 countries

Richard Bowman
Mattan Arazi
Richard Bowman
Research17 Dec 2025
Eye

P: 1-9
Neuronal vulnerability and multilineage diversity in multiple sclerosis

Single-cell RNA sequencing was used to construct a map of gene expression in lesions from brains of patients with multiple sclerosis, revealing distinct lineage- and region-specific transcriptomic changes associated with selective cortical neuron damage and glial activation.

Lucas Schirmer
Dmitry Velmeshev
David H. Rowitch
Research17 Jul 2019
Nature

Volume: 573, P: 75-82
Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2

Paul Khavari and colleagues report genomic analyses of cutaneous T cell lymphomas. They identify recurrent point mutations and genomic gains of TNFRSF1B, encoding the tumor necrosis factor receptor TNFR2, in 18% of tumors and show that expression of a recurrent TNFR2 mutant in T cells leads to enhanced non-canonical NF-κB signaling that is sensitive to the proteasome inhibitor bortezomib.

Alexander Ungewickell
Aparna Bhaduri
Paul A Khavari
Research10 Aug 2015
Nature Genetics

Volume: 47, P: 1056-1060
Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system

This Review provides insights for construction of molecular cell atlases and outlines key study design considerations. The authors emphasize the power of single-cell and single-nucleus genomics in revealing cellular transitions during nervous system development and disease.

Igor Adameyko
Trygve Bakken
Tomasz J. Nowakowski
Reviews03 Dec 2024
Nature Neuroscience

Volume: 27, P: 2278-2291
The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer

Paul Khavari and colleagues analyze tumor genomes to identify snoRNAs showing frequent copy number loss of adjacently encoded snoRNAs SNORD50A and SNORD50B. These snoRNAs directly bound K-Ras and their loss leads to increased activity of both wild-type and oncogenic K-Ras and is associated with reduced survival.

Zurab Siprashvili
Dan E Webster
Paul A Khavari
Research23 Nov 2015
Nature Genetics

Volume: 48, P: 53-58
Profiling human brain vascular cells using single-cell transcriptomics and organoids

A protocol extension describing the purification of prenatal human brain endothelial and mural cells with FACS and their utilization in downstream applications, including cell culture, organoid transplantation and single-cell transcriptomics.

Elizabeth E. Crouch
Loukas N. Diafos
Eric J. Huang
Protocols15 Dec 2023
Nature Protocols

Volume: 19, P: 603-628
A study of the mutational landscape of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma

Michael G Ozawa
Aparna Bhaduri
Robert S Ohgami
ResearchOpen Access24 Jun 2016
Modern Pathology

Volume: 29, P: 1212-1220

Search

Integrated analysis of molecular atlases unveils modules driving developmental cell subtype specification in the human cortex

Non-muscle myosin II inhibition at the site of axon injury increases axon regeneration

Cold atmospheric plasma effectively kills chordoma cells through induction of intracellular reactive oxygen species

Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia

An atlas of cortical arealization identifies dynamic molecular signatures

Chimeric brain organoids capture human genetic diversity

Cell stress in cortical organoids impairs molecular subtype specification

Functional genomics and systems biology in human neuroscience

Single-cell sequencing paints diverse pictures of the brain

The new frontier in understanding human and mammalian brain development

K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas

Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma

Retinoblastoma outcomes in Europe: a prospective analysis of 483 patients from 40 countries

Neuronal vulnerability and multilineage diversity in multiple sclerosis

Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2

Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system

The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer

Profiling human brain vascular cells using single-cell transcriptomics and organoids

A study of the mutational landscape of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma

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