Close

Dissecting Mammalian Spermatogenesis Using Spatial Transcriptomics

Haiqi Chen, Evan Murray, Anisha Laumas, Jilong Li, Xichen Nie, Jim Hotaling, Jingtao Guo, Bradley R. Cairns, Evan Z. Macosko, C. Yan Cheng, Fei Chen

Posted on: 7 January 2021

Preprint posted on 17 October 2020

Article now published in Cell Reports at http://dx.doi.org/10.1016/j.celrep.2021.109915

I told my supervisor that we need space - in my experiments. Using spatial transcriptomics to dissect mammalian spermatogenesis.

Selected by Martin Estermann

Background:

One of the main testicular functions is to produce male gametes (sperm cells), which are crucial for sexual reproduction. Two main compartments are distinguishable in the testis, the seminiferous tubules, fine coiled tubular structures where spermatogenesis takes place, and the peritubular space. The tubules contain layers of germ cells, that develop into sperm cells (also known as spermatozoa), in close association with Sertoli cells. Steroidogenic Leydig cells, macrophages and other interstitial cells are located in the space between the tubules.

Spermatogenesis is a controlled process that begins postnatally and culminates with the production of the first sperm at the onset of sexual maturity. In mice, the seminiferous tubules periodically cycle through 12 stages (I-XII) that are defined by the combination of germ cells present. Recently, testicular single-cell RNA sequencing (scRNA-seq) studies showed that not only the germ cells are stage specific but other cells like Sertoli cells also vary from stage to stage.

scRNA-seq introduced a fundamental change in the focus of the research and gene expression. Instead of using the whole organ as a research unit, it is partitioned to the smallest structural and functional unit, the single cell. One of the main issues concerning single-cell technologies is that spatial and tissue organization information is lost when generating a single-cell suspension. Spatial transcriptomics was developed as a new methodology to overcome this problem. Briefly, frozen tissue sections are placed on a slide containing barcoded spots (bead array) that provide a specific spatial orientation. The cells in the tissue sections are permeabilized, allowing mRNA to be bound to the most proximal barcode, followed by cDNA synthesis and sequencing. The barcode sequence associates each transcript with a spatial position, assigning mRNA expression to different tissue regions (Fig. 1).

The authors used spatial transcriptomics in mouse and human testis to develop a spatial transcriptome atlas for mammalian spermatogenesis, being able to assign information of cell type, seminiferous tubule, and stage to each bead with high accuracy. Furthermore, the authors provided evidence for the diagnostic value of this technology by characterizing the testicular disorganization in a diabetic mouse model.


Fig 1. Spatial transcriptomics workflow. (Preprint Fig. 1A and B).

Key findings

 1) Spatial transcriptome atlas for mouse spermatogenesis

Mouse 10 um frozen testicular sections were captured into a slide-seq array and subjected to spatial transcriptomics, detecting around 30,000 beads (“cells”) per array. The different beads were assigned with a cell type and were mapped into the array, which reflected the structure of the testicular seminiferous tubules (Fig. 2A). After the cell type assignment, the array was partitioned into the distinctive seminiferous tubules (Fig. 2B) and classified into one of the four major stages of seminiferous tubules using known stage-dependent markers: stages I-III, IV-VI, VII-VIII or IX-XII (Fig. 2C).

Stage-specific Sertoli and germ cells are well characterized in the literature, but the cells in the testicular interstitium and the peritubular space remain largely unexplored. The authors were able to identify transcriptomic signatures of stage specific Leydig (steroidogenic) cells (Fig. 2D) and macrophages (Fig. 2E) never reported before.

Fig 2. Mouse testicular spatial transcriptomics. (A) Spatial mapping of testicular cell types in mouse section. ES: elongated/elongating spermatid, RS: round spermatid, SPC: spermatocyte, SPG: spermatogonium. (B) Digital segmentation of the seminiferous tubules. (C) Spatial mapping of the four stage clusters. (D) Schematic representation of the spatial localization and marker genes for each stage dependent Leydig cell. (E) Schematic representation of the spatial localization and marker genes for each stage dependent macrophage. (Preprint Fig. 1C, 1F, 1H, 3A, 3C and 3D).

2) Spatial transcriptome atlas for human spermatogenesis

The next challenge was to apply this pipeline to human testicular samples, spatially mapping human testicular cell types (Fig 3A). In order to validate these results, the authors used the Human Protein Atlas database to corroborate the expression pattern of different spermatogonia genes into the seminiferous tubules (Fig. 3B). This resulted in around 74% of match, with the remaining 26% not being present in the protein database or showing non-specific immunostaining. An example of four genes with differential expression from the lumen (left) to the basement membrane (right) can be found in Fig. 3B.

Recently, human testicular single-cell RNA sequencing revealed 5 transcriptional states of human spermatogonia (0-4). Using the described expression markers, two different microenvironments of spermatogonia coexist in the same seminiferous tubule, one containing mostly state 0 spermatogonia (naïve/stem cell) and the other containing states 1-4 and the remaining state 0 (Fig. 3C).

Fig 3. Human testicular spatial transcriptomics. (A) Spatial mapping of testicular cell types in human section. ES: elongated/elongating spermatid, RS: round spermatid, SPC: spermatocyte, SPG: spermatogonium. (B) Spatial expression patterns of the genes ACTRT3, ACRBP, CLDN11 and GSTA1 from the spatial transcriptomic atlas and the human protein atlas. (C) Spatial mapping of the five human spermatogonia germ cells. (Preprint Fig. 4 A, B and D).

3) Testicular spatial transcriptomics in diabetes-induced testicular injuries

Several reports indicate that diabetes mellitus results in disturbances in the male reproductive system, but the exact mechanism is still unknown. To evaluate if the slide-seq workflow could be applied to study testicular diseases, leptin-deficient diabetic mice (ob/ob) testis were compared with wild type testis (WT), using spatial transcriptomics (Fig. 4A). Differential expression analysis identified a downregulation of elongating/elongated spermatids genes such as Smcp and Odf1 (Fig. 4B). This is consistent with the loss of elongated spermatids in ob/ob testes. Furthermore, mitochondrial genes were elevated, a condition associated with mitochondrial dysfunction and mtDNA damage.

A disorganization in the seminiferous tubules structure was also detected in the ob/ob mice testes. To quantify these changes, a purity score was generated, taking into account the spatial mixing of the elongated spermatids beads with beads of other cell types (Fig. 4C). In the wild type mice, the elongated spermatids beads clustered in the centre of the seminiferous tubule, showing a high purity score (0.63). In contrast, in ob/ob seminiferous tubules, the elongated spermatids beads were likely to make contacts with beads of other cell types, reflecting a lower purity score (0.44) and a structural disorganization.

Fig 4. Diabetes causes disruption in the testicular seminiferous tubules. (A) Spatial mapping of the testicular cell types in wild type (WT) and leptin-deficient diabetic (ob/ob) samples. ES: elongated/elongating spermatid, RS: round spermatid, SPC: spermatocyte, SPG: spermatogonium. (B) Spatial expression pattern of Smcp and Odf1 genes in a representative WT and ob/ob seminiferous tubule. (C) Elongated spermatid purity score for each Slide-seq bead in a representative WT and ob/ob seminiferous tubule. (Preprint Fig. 5A, C and S11).

Why I choose this paper:

One of the main issues around single-cell technologies is that spatial and tissue organization information is lost when generating a single-cell suspension. Spatial transcriptomics was developed as a new methodology to overcome this problem. This study demonstrated the utility of this emerging technique by characterizing testicular spermatogenesis in mouse and human tissue with high accuracy. Furthermore, the authors provided evidence for the diagnostic value of this technology by characterizing the testicular disorganization in a diabetic mouse model. The spatial atlases generated can be useful to identify cellular and molecular changes associated with different diseases.

The used protocol can easily be adapted to other tissues, animal models or human samples and provides the first workflow that could be used in the clinic. Tissue biopsies from testicular cancer, infertility or differences of sex development (DSDs) could potentially be subjected to spatial transcriptomics in the near future.

 

Future directions / questions for the authors:

  • Sertoli and germ cells grow in really close association, how hard was it for you to differentiate both cell types? How often did you find Sertoli and sperm cells transcripts in the same bead?
  • In your opinion, what would be the next step required to bring spatial transcriptomics into a clinical setting?

 

doi: https://doi.org/10.1242/prelights.26837

Read preprint (1 votes)

Have your say

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

Also in the bioinformatics category:

Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods

Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders

Selected by 11 November 2024

Benjamin Dominik Maier

Bioinformatics

Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted

Miguel Reina-Campos, Alexander Monell, Amir Ferry, et al.

Selected by 22 August 2024

Marina Schernthanner

Bioinformatics

Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

Nikolai Hecker , Niklas Kempynck , David Mauduit, et al.

Selected by 02 July 2024

Rodrigo Senovilla-Ganzo

Bioinformatics

Also in the cell biology category:

Motor Clustering Enhances Kinesin-driven Vesicle Transport

Rui Jiang, Qingzhou Feng, Daguan Nong, et al.

Selected by 16 November 2024

Sharvari Pitke

Biophysics

Cellular signalling protrusions enable dynamic distant contacts in spinal cord neurogenesis

Joshua Hawley, Robert Lea, Veronica Biga, et al.

Selected by 15 November 2024

Ankita Walvekar

Developmental Biology

Green synthesized silver nanoparticles from Moringa: Potential for preventative treatment of SARS-CoV-2 contaminated water

Adebayo J. Bello, Omorilewa B. Ebunoluwa, Rukayat O. Ayorinde, et al.

Selected by 14 November 2024

Safieh Shah, Benjamin Dominik Maier

Epidemiology

Also in the developmental biology category:

Cellular signalling protrusions enable dynamic distant contacts in spinal cord neurogenesis

Joshua Hawley, Robert Lea, Veronica Biga, et al.

Selected by 15 November 2024

Ankita Walvekar

Developmental Biology

Actin-based deformations of the nucleus control multiciliated ependymal cell differentiation

Marianne Basso, Alexia Mahuzier, Syed Kaabir Ali, et al.

Selected by 30 October 2024

Ryan Harrison

Developmental Biology

HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos

Estefania Sanchez-Vasquez, Marianne E. Bronner, Magdalena Zernicka-Goetz

Selected by 11 October 2024

Anchel De Jaime Soguero

Developmental Biology

Also in the genetics category:

Intracellular diffusion in the cytoplasm increases with cell size in fission yeast

Catherine Tan, Michael C. Lanz, Matthew Swaffer, et al.

Selected by 18 October 2024

Leeba Ann Chacko, Sameer Thukral

Cell Biology

Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA

Brett T. Wisniewski, Laura L. Lackner

Selected by 30 August 2024

Leeba Ann Chacko

Cell Biology

The bat Influenza A virus subtype H18N11 induces nanoscale MHCII clustering upon host cell attachment

Maria Kaukab Osman, Jonathan Robert, Lukas Broich, et al.

Selected by 20 August 2024

Mitchell Sarmie, Mohammed A. Jalloh

Immunology

Also in the genomics category:

A fine kinetic balance of interactions directs transcription factor hubs to genes

Apratim Mukherjee, Samantha Fallacaro, Puttachai Ratchasanmuang, et al.

Selected by 23 July 2024

Deevitha Balasubramanian

Genomics

Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

Nikolai Hecker , Niklas Kempynck , David Mauduit, et al.

Selected by 02 July 2024

Rodrigo Senovilla-Ganzo

Bioinformatics

Modular control of time and space during vertebrate axis segmentation

Ali Seleit, Ian Brettell, Tomas Fitzgerald, et al.

AND

Natural genetic variation quantitatively regulates heart rate and dimension

Jakob Gierten, Bettina Welz, Tomas Fitzgerald, et al.

Selected by 24 June 2024

Girish Kale, Jennifer Ann Black

Developmental Biology

Also in the immunology category:

Alzheimer’s Disease Patient Brain Extracts Induce Multiple Pathologies in Vascularized Neuroimmune Organoids for Disease Modeling and Drug Discovery

Yanru Ji, Xiaoling Chen, Meek Connor Joseph, et al.

Selected by 07 November 2024

Manuel Lessi

Neuroscience

Global coordination of protrusive forces in migrating immune cells

Patricia Reis-Rodrigues, Nikola Canigova, Mario J. Avellaneda, et al.

Selected by 10 October 2024

yohalie kalukula

Biophysics

Integrin conformation-dependent neutrophil slowing obstructs the capillaries of the pre-metastatic lung in a model of breast cancer

Frédéric Fercoq, Gemma S. Cairns, Marco De Donatis, et al.

Selected by 07 October 2024

Simon Cleary

Cancer Biology

Also in the molecular biology category:

Green synthesized silver nanoparticles from Moringa: Potential for preventative treatment of SARS-CoV-2 contaminated water

Adebayo J. Bello, Omorilewa B. Ebunoluwa, Rukayat O. Ayorinde, et al.

Selected by 14 November 2024

Safieh Shah, Benjamin Dominik Maier

Epidemiology

Non-disruptive inducible labeling of ER-membrane contact sites using the Lamin B Receptor

Laura Downie, Nuria Ferrandiz, Megan Jones, et al.

Selected by 15 October 2024

Jonathan Townson

Cell Biology

HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos

Estefania Sanchez-Vasquez, Marianne E. Bronner, Magdalena Zernicka-Goetz

Selected by 11 October 2024

Anchel De Jaime Soguero

Developmental Biology

Also in the physiology category:

Geometric analysis of airway trees shows that lung anatomy evolved to enable explosive ventilation and prevent barotrauma in cetaceans

Robert L. Cieri, Merryn H. Tawhai, Marina Piscitelli-Doshkov, et al.

Selected by 26 November 2024

Sarah Young-Veenstra

Evolutionary Biology

Precision Farming in Aquaculture: Use of a non-invasive, AI-powered real-time automated behavioural monitoring approach to predict gill health and improve welfare in Atlantic salmon (Salmo salar) aquaculture farms

Meredith Burke, Dragana Nikolic, Pieter Fabry, et al.

Selected by 11 September 2024

Jasmine Talevi

Animal Behavior and Cognition

Gestational exposure to high heat-humidity conditions impairs mouse embryonic development

Avinchal Manhas, Amritesh Sarkar, Srimonta Gayen

Selected by 08 July 2024

Girish Kale, preLights peer support

Developmental Biology

preLists in the bioinformatics category:

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

 



List by Alex Eve

Antimicrobials: Discovery, clinical use, and development of resistance

Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.

 



List by Zhang-He Goh

Also in the cell biology category:

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

The Society for Developmental Biology 82nd Annual Meeting

This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.

 



List by Joyce Yu, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

BioMalPar XVI: Biology and Pathology of the Malaria Parasite

[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria

 



List by Dey Lab, Samantha Seah

1

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Cellular metabolism

A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.

 



List by Pablo Ranea Robles

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

MitoList

This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.

 



List by Sandra Franco Iborra

Biophysical Society Annual Meeting 2019

Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA

 



List by Joseph Jose Thottacherry

ASCB/EMBO Annual Meeting 2018

This list relates to preprints that were discussed at the recent ASCB conference.

 



List by Dey Lab, Amanda Haage

Also in the developmental biology category:

BSDB/GenSoc Spring Meeting 2024

A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.

 



List by Joyce Yu, Katherine Brown

GfE/ DSDB meeting 2024

This preList highlights the preprints discussed at the 2024 joint German and Dutch developmental biology societies meeting that took place in March 2024 in Osnabrück, Germany.

 



List by Joyce Yu

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

The Society for Developmental Biology 82nd Annual Meeting

This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.

 



List by Joyce Yu, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

 



List by Alex Eve

Society for Developmental Biology 79th Annual Meeting

Preprints at SDB 2020

 



List by Irepan Salvador-Martinez, Martin Estermann

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EDBC Alicante 2019

Preprints presented at the European Developmental Biology Congress (EDBC) in Alicante, October 23-26 2019.

 



List by Sergio Menchero et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

 



List by Alex Eve

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Young Embryologist Network Conference 2019

Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London

 



List by Alex Eve

Pattern formation during development

The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.

 



List by Alexa Sadier

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the genetics category:

BSDB/GenSoc Spring Meeting 2024

A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.

 



List by Joyce Yu, Katherine Brown

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Also in the genomics category:

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the immunology category:

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

 



List by Alex Eve

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Antimicrobials: Discovery, clinical use, and development of resistance

Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.

 



List by Zhang-He Goh

Also in the molecular biology category:

2024 Hypothalamus GRC

This 2024 Hypothalamus GRC (Gordon Research Conference) preList offers an overview of cutting-edge research focused on the hypothalamus, a critical brain region involved in regulating homeostasis, behavior, and neuroendocrine functions. The studies included cover a range of topics, including neural circuits, molecular mechanisms, and the role of the hypothalamus in health and disease. This collection highlights some of the latest advances in understanding hypothalamic function, with potential implications for treating disorders such as obesity, stress, and metabolic diseases.

 



List by Nathalie Krauth

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

MitoList

This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.

 



List by Sandra Franco Iborra
Close