About

Jeffrey D. Macklis is the Max and Anne Wien Professor of Life Sciences in the Department of Stem Cell and Regenerative Biology and the Center for Brain Science at Harvard University. He also holds a professorship in Neurology (Neuroscience) at Harvard Medical School. Professor Macklis directs the Developmental and Regenerative Neuroscience Laboratory, where his research focuses on the molecular development of cortical projection neurons, growth cone biology, induced neurogenesis and transplantation, directed differentiation of pluripotent stem cells, and the development of new technologies and tools. His work aims to understand the mechanisms underlying neuronal development, regeneration, and repair, with a particular emphasis on the nervous system's dynamic processes. The Macklis Laboratory is engaged in cutting-edge research to elucidate the genetic and epigenetic factors that influence neuronal growth, axon targeting, and the molecular pathways involved in neurodevelopmental and neurodegenerative conditions.

Research topics

• Neuroscience
• Biology
• Anatomy
• Genetics
• Medicine

Selected publications

• Developmental dynamics and axonal transport of cerebral cortex projection neuron mRNAs <i>in vivo</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-23 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Appropriate development of long-range nervous system circuitry requires dynamic regulation of subcellular mRNA localization, but little is known about how specific neuron subtypes control this critical process in vivo . Here, we employ an integrated genetic and temporally controlled approach to investigate in vivo developmental mRNA dynamics in somata and axons of a prototypical cerebral cortex projection neuron subtype, callosal projection neurons (CPN), which connect the cortical hemispheres to integrate sensorimotor information, and regulate high-level associative cognition and behavior. We identify cis-regulatory elements that are associated with mRNA turnover in CPN somata, including specific 3’ untranslated regions (UTRs), and elucidate distinct modes of axon transport in CPN axons for function-specific mRNA classes. Together, these findings elucidate how developing CPN control subcellular mRNA localization, and how dysregulation of these processes might lead to neurodevelopmental and/or neurodegenerative disorders. More broadly, this work identifies general mRNA localization mechanisms that likely function across projection neuron subtypes, and in other polarized cells.

  PublisherOA PDFDOI

• Bcl11b orchestrates subcerebral projection neuron axon development via cell-autonomous, non-cell-autonomous, and subcellular mechanisms

  eLife · 2025-04-24

  preprintOpen accessSenior author

  Summary Both cell-intrinsic competency and extracellular cues regulate axon projection, but mechanisms that coordinate these elements remain poorly understood. Subcerebral projection neurons (SCPN) extend their primary axons from cortex through subcortical structures, including the striatum, targeting the brainstem and spinal cord. We identify that the transcription factor Bcl11b/Ctip2 functions in multiple independent neuron populations to control SCPN axon development. Bcl11b expressed by SCPN is required cell-autonomously for axonal outgrowth and efficient entry into the internal capsule within the striatum, while Bcl11b expressed by medium spiny neurons (MSN) non-cell-autonomously regulates SCPN axon fasciculation within the internal capsule and subsequent pathfinding. Further, integrated investigation of Bcl11b-null SCPN with transcriptomic, immunocytochemical, and in vivo growth cone purification approaches identifies that Cdh13 is localized along axons and on growth cone surfaces of SCPN in vivo, and mediates Bcl11b regulation of SCPN axonal outgrowth. Together, these results demonstrate that Bcl11b controls multiple aspects of SCPN axon development by coordinating intrinsic SCPN cell autonomous subcellular mechanisms and extrinsic MSN non-cell-autonomous mechanisms.

  PublisherDOI

• Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors

  eLife · 2025-08-05

  preprintOpen accessSenior author

  Corticospinal neurons (CSN) centrally degenerate in amyotrophic lateral sclerosis (ALS), along with spinal motor neurons, and loss of voluntary motor function in spinal cord injury (SCI) results from damage to CSN axons. For functional regeneration of specifically affected neuronal circuitry in vivo, or for optimally informative disease modeling and/or therapeutic screening in vitro, it is important to reproduce the type or subtype of neurons involved. No such appropriate in vitro models exist with which to investigate CSN selective vulnerability and degeneration in ALS, or to investigate routes to regeneration of CSN circuitry for ALS or SCI, critically limiting the relevance of much research. Here, we identify that the HMG-domain transcription factor Sox6 is expressed by a subset of NG2+ endogenous cortical progenitors in postnatal and adult cortex, and that Sox6 suppresses a latent neurogenic program by repressing proneural Neurog2 expression by progenitors. We FACS-purify these progenitors from postnatal mouse cortex and establish a culture system to investigate their potential for directed differentiation into CSN. We then employ a multi-component construct with complementary and differentiation-sharpening transcriptional controls (activating Neurog2, Fezf2, while antagonizing Olig2 with VP16:Olig2). We generate corticospinal-like neurons from SOX6+/NG2+ cortical progenitors, and find that these neurons differentiate with remarkable fidelity compared with corticospinal neurons in vivo. They possess appropriate morphological, molecular, transcriptomic, and electrophysiological characteristics, without characteristics of the alternate intracortical or other neuronal subtypes. We identify that these critical specifics of differentiation are not reproduced by commonly employed Neurog2-driven differentiation. Neurons induced by Neurog2 instead exhibit aberrant multi-axon morphology and express molecular hallmarks of alternate cortical projection subtypes, often in mixed form. Together, this developmentally-based directed differentiation from cortical progenitors sets a precedent and foundation for in vitro mechanistic and therapeutic disease modeling, and toward regenerative neuronal repopulation and circuit repair.

  PublisherDOI

• Author response: Bcl11b orchestrates subcerebral projection neuron axon development via cell-autonomous, non-cell-autonomous, and subcellular mechanisms

  2025-04-24

  peer-reviewOpen accessSenior author

  Both cell-intrinsic competency and extracellular cues regulate axon projection, but mechanisms that coordinate these elements remain poorly understood. Subcerebral projection neurons (SCPN) extend their primary axons from cortex through subcortical structures, including the striatum, targeting the brainstem and spinal cord. We identify that the transcription factor Bcl11b/Ctip2 functions in multiple independent neuron populations to control SCPN axon development. Bcl11b expressed by SCPN is required cell-autonomously for axonal outgrowth and efficient entry into the internal capsule within the striatum, while Bcl11b expressed by medium spiny neurons (MSN) non-cell-autonomously regulates SCPN axon fasciculation within the internal capsule and subsequent pathfinding. Further, integrated investigation of Bcl11b-null SCPN with transcriptomic, immunocytochemical, and in vivo growth cone purification approaches identifies that Cdh13 is localized along axons and on growth cone surfaces of SCPN in vivo, and mediates Bcl11b regulation of SCPN axonal outgrowth. Together, these results demonstrate that Bcl11b controls multiple aspects of SCPN axon development by coordinating intrinsic SCPN cell autonomous subcellular mechanisms and extrinsic MSN non-cell-autonomous mechanisms.

  PublisherDOI

• Bcl11b orchestrates subcerebral projection neuron axon development via cell-autonomous, non-cell-autonomous, and subcellular mechanisms

  eLife · 2025-04-24 · 1 citations

  preprintOpen accessSenior author

  Summary Both cell-intrinsic competency and extracellular cues regulate axon projection, but mechanisms that coordinate these elements remain poorly understood. Subcerebral projection neurons (SCPN) extend their primary axons from cortex through subcortical structures, including the striatum, targeting the brainstem and spinal cord. We identify that the transcription factor Bcl11b/Ctip2 functions in multiple independent neuron populations to control SCPN axon development. Bcl11b expressed by SCPN is required cell-autonomously for axonal outgrowth and efficient entry into the internal capsule within the striatum, while Bcl11b expressed by medium spiny neurons (MSN) non-cell-autonomously regulates SCPN axon fasciculation within the internal capsule and subsequent pathfinding. Further, integrated investigation of Bcl11b-null SCPN with transcriptomic, immunocytochemical, and in vivo growth cone purification approaches identifies that Cdh13 is localized along axons and on growth cone surfaces of SCPN in vivo, and mediates Bcl11b regulation of SCPN axonal outgrowth. Together, these results demonstrate that Bcl11b controls multiple aspects of SCPN axon development by coordinating intrinsic SCPN cell autonomous subcellular mechanisms and extrinsic MSN non-cell-autonomous mechanisms.

  PublisherDOI

• Author response: Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors

  2025-08-05

  peer-reviewOpen accessSenior author

  Corticospinal neurons (CSN) centrally degenerate in amyotrophic lateral sclerosis (ALS), along with spinal motor neurons, and loss of voluntary motor function in spinal cord injury (SCI) results from damage to CSN axons. For functional regeneration of specifically affected neuronal circuitry in vivo, or for optimally informative disease modeling and/or therapeutic screening in vitro, it is important to reproduce the type or subtype of neurons involved. No such appropriate in vitro models exist with which to investigate CSN selective vulnerability and degeneration in ALS, or to investigate routes to regeneration of CSN circuitry for ALS or SCI, critically limiting the relevance of much research. Here, we identify that the HMG-domain transcription factor Sox6 is expressed by a subset of NG2+ endogenous cortical progenitors in postnatal and adult cortex, and that Sox6 suppresses a latent neurogenic program by repressing proneural Neurog2 expression by progenitors. We FACS-purify these progenitors from postnatal mouse cortex and establish a culture system to investigate their potential for directed differentiation into CSN. We then employ a multi-component construct with complementary and differentiation-sharpening transcriptional controls (activating Neurog2, Fezf2, while antagonizing Olig2 with VP16:Olig2). We generate corticospinal-like neurons from SOX6+/NG2+ cortical progenitors, and find that these neurons differentiate with remarkable fidelity compared with corticospinal neurons in vivo. They possess appropriate morphological, molecular, transcriptomic, and electrophysiological characteristics, without characteristics of the alternate intracortical or other neuronal subtypes. We identify that these critical specifics of differentiation are not reproduced by commonly employed Neurog2-driven differentiation. Neurons induced by Neurog2 instead exhibit aberrant multi-axon morphology and express molecular hallmarks of alternate cortical projection subtypes, often in mixed form. Together, this developmentally-based directed differentiation from cortical progenitors sets a precedent and foundation for in vitro mechanistic and therapeutic disease modeling, and toward regenerative neuronal repopulation and circuit repair.

  PublisherDOI

• Cortical projection neurons with distinct axonal connectivity employ ribosomal complexes with distinct protein compositions

  eLife · 2025-10-01 · 1 citations

  articleOpen accessSenior author

  Abstract Diverse subtypes of cortical projection neurons (PN) form long-range axonal projections that are responsible for distinct sensory, motor, cognitive, and behavioral functions. Translational control has been identified at multiple stages of PN development, but how translational regulation contributes to formation of distinct, subtype-specific long-range circuits is poorly understood. Ribosomal complexes (RCs) exhibit variations of their component proteins, with an increasing set of examples that confer specialized translational control. Here, we directly compare the protein compositions of RCs in vivo from two closely related cortical neuron subtypes–cortical output “subcerebral PN” (SCPN) and interhemispheric “callosal PN” (CPN)– during establishment of their distinct axonal connectivity. Using retrograde labeling of subtype-specific somata, purification by fluorescence-activated cell sorting, ribosome immunoprecipitation, and ultra-low-input mass spectrometry, we identify distinct protein compositions of RCs from these two subtypes. Strikingly, we identify 16 associated proteins reliably and exclusively detected only in RCs of SCPN. 11 of these proteins have known interaction with components of ribosomes; we further validated ribosome interaction with protein kinase C epsilon (PRKCE), a candidate with roles in synaptogenesis. PRKCE and a subset of SCPN-specific candidate ribosome-associated proteins also exhibit enriched gene expression by SCPN. Together, these results indicate that ribosomal complexes exhibit subtypespecific protein composition in distinct subtypes of cortical projection neurons during development, and identify potential candidates for further investigation of function in translational regulation involved in subtype-specific circuit formation.

  PublisherDOI

• Cortical projection neurons with distinct axonal connectivity employ ribosomal complexes with distinct protein compositions

  eLife · 2025-10-01

  articleOpen accessSenior author

  Abstract Diverse subtypes of cortical projection neurons (PN) form long-range axonal projections that are responsible for distinct sensory, motor, cognitive, and behavioral functions. Translational control has been identified at multiple stages of PN development, but how translational regulation contributes to formation of distinct, subtype-specific long-range circuits is poorly understood. Ribosomal complexes (RCs) exhibit variations of their component proteins, with an increasing set of examples that confer specialized translational control. Here, we directly compare the protein compositions of RCs in vivo from two closely related cortical neuron subtypes–cortical output “subcerebral PN” (SCPN) and interhemispheric “callosal PN” (CPN)– during establishment of their distinct axonal connectivity. Using retrograde labeling of subtype-specific somata, purification by fluorescence-activated cell sorting, ribosome immunoprecipitation, and ultra-low-input mass spectrometry, we identify distinct protein compositions of RCs from these two subtypes. Strikingly, we identify 16 associated proteins reliably and exclusively detected only in RCs of SCPN. 11 of these proteins have known interaction with components of ribosomes; we further validated ribosome interaction with protein kinase C epsilon (PRKCE), a candidate with roles in synaptogenesis. PRKCE and a subset of SCPN-specific candidate ribosome-associated proteins also exhibit enriched gene expression by SCPN. Together, these results indicate that ribosomal complexes exhibit subtypespecific protein composition in distinct subtypes of cortical projection neurons during development, and identify potential candidates for further investigation of function in translational regulation involved in subtype-specific circuit formation.

  PublisherDOI

• Dynamic subtype- and context-specific subcellular RNA regulation in growth cones of developing neurons of the cerebral cortex

  Nature Neuroscience · 2025-12-29 · 1 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Cortical projection neurons with distinct axonal connectivity employ ribosomal complexes with distinct protein compositions

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-23 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Diverse subtypes of cortical projection neurons (PN) form long-range axonal projections that are responsible for distinct sensory, motor, cognitive, and behavioral functions. Translational control has been identified at multiple stages of PN development, but how translational regulation contributes to formation of distinct, subtype-specific long-range circuits is poorly understood. Ribosomal complexes (RCs) exhibit variations of their component proteins, with an increasing set of examples that confer specialized translational control. Here, we directly compare the protein compositions of RCs in vivo from two closely related cortical neuron subtypes–cortical output “subcerebral PN” (SCPN) and interhemispheric “callosal PN” (CPN)– during establishment of their distinct axonal connectivity. Using retrograde labeling of subtype-specific somata, purification by fluorescence-activated cell sorting, ribosome immunoprecipitation, and ultra-low-input mass spectrometry, we identify distinct protein compositions of RCs from these two subtypes. Strikingly, we identify 16 associated proteins reliably and exclusively detected only in RCs of SCPN. 11 of these proteins have known interaction with components of ribosomes; we further validated ribosome interaction with protein kinase C epsilon (PRKCE), a candidate with roles in synaptogenesis. PRKCE and a subset of SCPN-specific candidate ribosome-associated proteins also exhibit enriched gene expression by SCPN. Together, these results indicate that ribosomal complexes exhibit subtypespecific protein composition in distinct subtypes of cortical projection neurons during development, and identify potential candidates for further investigation of function in translational regulation involved in subtype-specific circuit formation.

  PublisherDOI

Recent grants

• NIH Grant K08HD000859

  NIH · $191k · 1991

• Neocortical Precursor Transplant for Circuitry Repair

  NIH · $2.9M · 2000–2012

• NIH Grant R29HD028478

  NIH · $616k · 1996

• Molecular Mechanisms of CTIP2 Function in Corticospinal Motor Neuron Development

  NIH · $1.8M · 2012–2018

• Molecular Controls over Neurogenesis, Subtype Development, and Diversity of Cortical Output Projection Neurons

  NIH · $5.4M · 2002–2023

Frequent coauthors

• Alexandros Poulopoulos

  Harvard University

  100 shared

• Abdulkadir Özkan

  94 shared

• Paola Arlotta

  Harvard University Press

  81 shared

• Jason G. Emsley

  Dalhousie University

  75 shared

• Bradley J. Molyneaux

  Brigham and Women's Hospital

  68 shared

• Sanjay S. P. Magavi

  60 shared

• Denis Jabaudon

  University Hospital of Geneva

  51 shared

• Eiman Azim

  Salk Institute for Biological Studies

  51 shared

Labs

• Macklis LaboratoryPI