DNA Helix

Ludwig Lab

Stem Cell Dynamics and Mitochondrial Genomics

Profile

Our lab specializes in the development of single-cell multi-omic approaches which we use to answer key questions in stem cell, leukemia and mitochondrial genome biology.

In particular, we are interested in elucidating mechanisms relating to the activity, dynamics and regulation of hematopoietic stem cells. While hematopoiesis may present one of the best studied biological systems, it remains challenging to study the in vivo activity of individual stem cells in humans. To overcome this, we develop methods to detect naturally occurring sequence variation in the nuclear and mitochondrial genome. This allows us to study the unique mutational profiles of hematopoietic cells which we utilize as natural genetic barcodes to enable lineage tracing / assessment of clonal activity across the stem and progenitor cell pool. In conjunction with genomic readouts of cellular chromatin accessibility, gene and protein expression profiles, we aim to unravel fundamental principles of stem cell dynamics and (de-)regulation in health and disease states, including leukemia. 

Moreover, an interrelated key objective of the group is to better understand how mitochondrial genotypes contribute to metabolic and cellular phenotypes in the context of congenital disorders, an aging immune system and more generally human biology.

The lab is part of the joint 'Single Cell Approaches for Personalized Medicine' Research Focus Area of the Berlin Institute of Health and the Max-Delbrück Center/Berlin Institute of Medical Systems Biology. We are affiliated with the clinical departments of Hematology, Oncology and Tumor Immunology at the Charité medical school and foster close collaborations with the clinical and biomedical research community.

Team

Research

Our lab currently works on a number of research topics in the areas of single cell genomics, hematology/oncology and mitochondrial genetics & genome biology:

Single-cell multi-omics methods

We have developed a range of single-cell-based technologies that enable the concomitant measurements of multiple modalities from the same cells to maximize the phenotypic depth of information for cellular profiling. For instance, we have combined high-throughput accessible chromatin profiling with whole mitochondrial genome sequencing for clonal tracing and the study of mitochondrial genetics (mitochondrial single-cell ATAC-seq, mtscATAC-seq). We further contributed to enabling the simultaneous profiling of surface marker and intracellular proteins (ATAC with Select Antigen Profiling by sequencing, ASAP-seq). We have integrated gene activity-based readouts from chromatin accessibility, mRNA expression and cellular proteins, thereby allowing to address the central aspects of gene regulation (DOGMA-seq). Together with computational approaches, these methods allow us to comprehensively study human genetics and biomedical questions in health and disease contexts.

Related publications

Show all related publications ►

  1. Lareau CA*#, Ludwig LS*# et al. (2020) Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature Biotechnology. DOI: 10.1038/s41587-020-0645-6
  2. Mimitou EP*, Lareau CA*, Chen KY* et al. (2021) Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nature Biotechnology (accepted in principle). Preprint DOI: 10.1101/2020.09.08.286914
  3. Fiskin E, Lareau CA, Ludwig LS et al. Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATAC. Preprint DOI: 10.1101/2020.10.01.322420

*Equal contribution
#Co-corresponding author

Hematopoiesis & hematopoietic stem cell biology

A major focus of the lab is the study of hematopoiesis, a process that gives rise to a diverse repertoire consisting of millions of blood cells every second. Conceivably, this is a highly regulated process that is controlled by hematopoietic stem cell activity in the bone marrow. A number of recent studies suggests that the hematopoietic stem cell pool is highly heterogenous. By leveraging genomic sequence variation as natural genetic barcodes, we have previously demonstrated the utility of somatic mitochondrial mutations to resolve clonal processes in the human bone marrow at high resolution and scale. By combining single-cell multi-omic technologies with cell biological approaches and insights from clinical observations and human genetics, we aim to uncover fundamental mechanisms of hematopoietic stem cell biology, underlying clonal dynamics and its (dys-)regulation in diseases such as leukemia.

Related publications

Show all related publications ►

  1. Ludwig LS*#, Lareau CA*, Ulirsch JC* et al. (2019) Lineage tracing in humans enabled by mitochondrial mutations and single cell genomics. Cell. DOI: 10.1016/j.cell.2019.01.022
  2. Ulirsch JC*, Lareau CA*, Bao EL*, Ludwig LS et al. (2019) Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nature Genetics. DOI: 10.1038/s41588-019-0362-6
  3. Khajuria RK, Munschauer M*, Ulirsch JC*, Fiorini C*, Ludwig LS* et al. (2018) Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis. Cell. DOI: 10.1016/j.cell.2018.02.036

*Equal contribution
#Co-corresponding author

Mitochondrial genetics and genomics

Mitochondria play a central role in metabolism and are unique organelles that carry their own genome, encoding a subset of proteins, tRNAs and ribosomal RNAs essential to their function. Critically, mutations in the mitochondrial genome are associated with a multitude of congenital disorders and clinical phenotypes. Recently, we have shown that single-cell genomic approaches can be effectively used to study such disorders and, more generally, mechanisms of mitochondrial genetics that are characterized by high mitochondrial DNA copy number and unique modes of replication/inheritance. Moreover, we have demonstrated the high prevalence of somatic mitochondrial DNA mutations that may contribute to a series of human phenotypes. Using cell biological, single-cell multi-omics and computational approaches, we aim to advance our understanding of the pleiotropic function of the mitochondrial genome in shaping human and cellular phenotypes.

Related publications

Show all related publications ►

  1. Walker MA*, Lareau CA*, Ludwig LS* et al. (2020) Purifying selection against pathogenic mitochondrial DNA in T cells. New England Journal of Medicine. DOI: 10.1056/NEJMoa2001265
  2. Lareau CA*#, Ludwig LS*# et al. (2020) Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature Biotechnology. DOI: 10.1038/s41587-020-0645-6
  3. Ludwig LS*#, Lareau CA*, Ulirsch JC* et al. (2019) Lineage tracing in humans enabled by mitochondrial mutations and single cell genomics. Cell. DOI: 10.1016/j.cell.2019.01.022

*Equal contribution
#Co-corresponding author

Publications

News

Jobs

We are immediately looking for a

Postdoctoral researcher (computational biology, data science)

We are seeking a highly motivated post-doctoral fellow with a background in computational biology/data science to join the team of Dr. Leif S. Ludwig, centrally located at the Berlin Institute of Medical Systems Biology (BIMSB) in Berlin-Mitte, Germany. Our lab is part of the new Focus Area 'Single Cell Approaches for Personalized Medicine' and specializes in the development of single cell multi-omic technologies and their application in stem cell & leukemia research in hematology/oncology and mitochondrial genome biology. The successful applicant will work closely with an international, interdisciplinary, and highly collaborative group, including clinicians, biologists and computational biologists across the BIMSB/MDC & BIH/Charité community, providing a range of opportunities to learn new skills. The ideal candidate has a strong computational/ analytical background, experience with single cell genomics data analysis and the ability to integrate and work within a team of scientists.

Your responsibilities:

  • Processing, quality control and analysis of high-dimensional single cell multi-omics data from clinical and biological samples in an integrated manner (e.g. transcriptome, accessible chromatin, protein expression, somatic nuclear and mitochondrial mutations).
  • Assess, integrate and develop new methodologies related to single cell multi-omics data analyses.
  • Identify cell types and cell programs among heterogeneous cell populations.
  • Identify genomic features such as gene expression and mutational signatures characteristic of disease samples.
  • Document progress, communicate and present analyses to group, institute members and collaborators verbally and in writing.
  • Work with members of the group and collaborators as well as independently with respect to experimental design, data analysis, visualization and interpretation.

Requirements:

  • We are looking for a motivated computational biologist / data scientist who is well organized, creative and excited by new challenges. Excellent communications skills and a working knowledge of English are essential (lab and institute language is English). The ideal candidate will have the following qualifications:
  • PhD or equivalent in a quantitative discipline (e.g. computational biology, computer science, statistics, mathematics, physics). Candidates with a MSc, or MD and significant experience in computational analyses will also be considered for the position.
  • Experience in working independently in several of the above-mentioned responsibilities using respective tools (e.g. Seurat, Scanpy).
  • Experience with big data management, statistical analysis and data summary visualization.
  • Background in statistics and statistical models.
  • Strong self-motivation, organizational skills and ability to lead and develop scientific projects.
  • Scientific curiosity, analytical thinking and interest in contributing to projects.
  • Keen interest in learning new skills, research techniques, data processing and analysis/interpretation of results.
  • Ability to work in a team of young scientists, to be flexible, and flourish in a fast-paced environment.
  • Strong communication and interpersonal skills, ability to work collaborate effectively with expert individuals of different backgrounds in a multidisciplinary team.

We offer:

  • A collaborative research environment that en-courages and supports scientific curiosity, in-novation, and development of its team mem-bers
  • Remuneration according to E13 TVöD VKA-K: The grouping takes into consideration the qualifications and the personal circumstances of the candidate
  • Appointment duration: initially until 31.10.2023 with the possibility of extension
  • Family - friendly, flexible working hours

We live diversity!

BIH strongly encourages qualified women to apply. Severely disabled applicants and those with equal status will be given preferential consideration in cases of equal suitability.

Please submit your application by email to juliane.großkopf@bih-charite.de by 15.08.2021, quoting the reference number BIH-66.21.
 

About the Berlin Institute of Health (BIH) at the Charité

 

The mission of the Berlin Institute of Health (BIH) is medical translation: transferring biomedical research findings into novel approaches to personalized prediction, prevention, diagnostics and therapy and, conversely, using clinical observations to develop new research ideas. The aim is to deliver relevant medical benefits to patients and the population at large. The BIH is also committed to establishing a comprehensive translational ecosystem as translational research area at Charité – one that places emphasis on a system-wide understanding of health and disease and that promotes change in the biomedical research culture. The BIH is funded 90 percent by the Federal Ministry of Education and Research (BMBF) and 10 percent by the State of Berlin. The two founding institutions, Charité – Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), were independent member entities within the BIH until 2020. As of 2021, the BIH has been integrated into Charité as the so-called third pillar; the MDC is privileged partner of the BIH.


You can find more information about us and BIH at

www.bihealth.org
www.bihealth.org/en/research/focus-areas/single-cell-technologies
www.mdc-berlin.de/Ludwig
www.bihealth.org/en/research/research-group/stem-cell-dynamics-mitochondrial-genomics/