Germ cell biology, developmental programming and epigenetic inheritance of disease – Qiaolin Deng's research group

Our research group at FyFa is interested in understanding the developmental principles of the germline in health and disease. Moreover, we focus on how the parental effects are transmitted via developmental programming and germline moderation to future offspring, a process known as epigenetic inheritance. High-throughput sequencing, stem cell differentiation modeling, 3D organoid culture and transgenic mouse models are our frequently used tools among others.


Our research

Illustration of the germline cycle
The germline cycle.

Germ cells are often considered immortal. They are sole messengers to relay genetic and epigenetic information across generations to perpetuate life. The germline cycle is long with specification starting from early gastrulation to gametogenesis continuing after birth. Errors occurring at any stage during this process can lead to devastating and long-lasting effects. With recent technological advances in single-cell sequencing, our knowledge of germline development in mammals has expanded considerably in recent times but some questions are remained. Among them, we aim to answer (1) what regulate progenitor competence and then define cell quality to opt into germline specification? (2) How is migration correlated with epigenetic remodeling? (3) How certain genetic mutations affect gametogenesis? Read more about our research and ongoing projects here


Selected publications

Full list of publications

See the full publication list here

Staff and contact

Group leader

All members of the group


  • Han Hui-Pin (postdoc)
  • Ahmed Reda (postdoc)
  • Veeramohan Veerapandian (postdoc)
  • Menghan Wang (postdoc)
  • Shangli Cheng (postdoc)
  • Julio Agulia Benitez (postdoc)
  • Geng Chen (postdoc)
  • Yu Pei (PhD student)
  • Alice Larsson (master student)
  • Christina An Binh Nordentoft (master student)
  • Alisa Luo (biomedicine student)
  • Tom van Leeuwen (master student)
  • Hannah Schöler (master student)
  • Mathias Ahlqvist (master student)
  • Olli Ainasoja (master student)

Our collaborators

  • Elisabet Stener-Victorin, Dept. Physiology and Pharmacology, KI
  • Jan-Bernd Stukenborg, Dept. Women and Children’s health, KI
  • Martin Enge, Dept. Oncology and Pathology, KI
  • Kenny Rodriguez-Wallberg, Dept. Clinical Science, Intervention and Technology, KI
  • Sergiu-Bogdan Catrina, Dept. Molecular Medicine and Surgery, KI
  • Eva Hedlund, Dept. Biochemistry and Biophysics, Stockholm University
  • Xingqi Chen, Dept. Immunology, Genetics and Pathology, Uppsala University
  • Jun Wu, UT Southwestern Medical center, USA
  • Jiayu Cheng, School of Life Sciences, Tongji University, China
  • Weida Li, School of Life Sciences, Tongji University, China
  • Eszter Vanky, Institute for Clinical and Molecular Medicine, NTNU, Norway
  • Sandra Haider, Reproductive Biology Unit, Medical University of Vienna

Research projects

While specific projects may change over time, our dedication to the following research fields remains constant.

Interestingly, two waves of epigenetic remodeling occur after fertilization to ensure the totipotency of the blastocyst for somatic lineage specification and to ascertain “clean slate” of germ cells for erasing any potentially harmful epigenetic modifications acquired by parents. The evolutionary advantage of these processes is to enable the organism to adapt to changing environmental conditions and minimize the risk of epigenetic inheritance of harmful traits. However, the degree of completeness and faithfulness of these processes still remain to be investigated. More and more studies have shown that parental health condition predisposes their offspring to develop diseases such as obesity, diabetes, cardiovascular disease, and behavioral disorders, which contributes to increased prevalence of chronic diseases. This process is referred to as developmental programming and epigenetic inheritance of diseases. Despite of increasing amount of epidemiological evidence, mechanistic understanding is still sparse. Here, we aim to answer (1) how parental health condition affects the germline that further transmit phenotypic traits? (2) how placenta responds to adverse uterine environment that in turn systematically modify cellular and physiological function of the offspring? (3) can we systematically model maternal disease signature with offspring key organ signature?

We are among those pioneers to apply and develop single-cell RNA sequencing (Smart-seq, Smart-seq2, LCM-seq etc). More tools to answer all these interesting questions are mouse disease models, human iPSC culture and differentiation, organoid culture, human sample cohorts and registry data together with other key cellular and molecular assays.

Research filed I: Develop culture platform to differentiate germ cells towards maturation with epigenetic remodeling for the purpose of disease modeling and mechanistic understanding

Microscope picture of a hPGCLC sphere culture
Sphere culture for hPGCLCs expressing TFAP2C (green), Mitotracher (red), DAPI (blue).

The use of pluripotent stem cells for in vitro differentiation provides a most valuable approach to study human germ cell specification and to uncover genetic and epigenetic dysregulations associated with infertility. Our previous and recent work has demonstrated the establishment of formative pluripotency conditions for direct specification of primordial germ cell-like cells (PGCLCs) (Cheng Cell Reports 2019, Luo Cell Reports 2023). Building on this work, we plan to further develop in vitro differentiation platform using organoid co-culture to investigate the impact of genetic mutations on fertility.

Microscope picture of a LT-hPGCLC coculture
Long-term (LT)-hPGCLC culture for 2 months with fetal gonadal somatic cells.

Specifically, our research has shown focus on understanding the role of X-chromosome activity and mitochondrial dynamics in germ cell development.

Research field II: Characterize the spatiotemporal regulation of germ cell migration and reveal the mechanisms of quality selection for gametogenesis

Germ cell migration is accompanied by extensive DNA demethylation and histone protein modification. We still know little about how these two sophisticated processes are coordinated. Furthermore, majority of migrating germ cells undergo apoptosis without further commitment to gametogenesis. We aim to use genetic mouse models, lineage tracing, single-cell sequencing among others to reveal gene function and mitochondrial dynamics during migration, epigenetic resetting, and meiosis entry. Especially, we are focusing on human genetic mutations implicated in infertility/subfertility.

Three pictures in a row showing Migrating PGCS
Whole-mount immunostaining of PGCs. (A) Migrating PGCs in the E9.5 mouse embryo showing OCT4 staining. (B) Migrating PGCs in the E10.5 mouse embryo showing OCT4 and DPPA3 double positive staining. (C) PGCs in embryonic gonads in the E12.5 mouse embryo double positive for DPPA3 and XXX.
During pregnancy, environmental factors, such as exposure to maternal androgen or AMH excess adversely affect placental function and could result in epigenetic changes that affect the somatic and germ cells of the growing fetus. For example, histone modifications, DNA methylation and transcriptional regulation by non- coding RNAs might predispose both female and male offspring to develop reproductive and metabolic abnormalities as well as neuropsychiatric disorders. F0, the pregnant woman with PCOS; F1, her first-generation offspring; F2, her second-generation offspring. (Stener-Victorin E and Deng Q, Nat Rev Endocrinol 2021 Sep;17(9):521-533) Photo: n/a

Research field III: Investigate the role of germline transmission in epigenetic inheritance of diseases

Women are born with a pool of primary follicles, some of which are periodically matured for fertilization. Throughout a woman's reproductive life, the number and quality of the remaining follicles gradually decline, leading to a decrease in fertility and an increased risk of reproductive disorders. Besides genetics, environmental factors can affect the health and function of the oocytes through dynamic interaction with niche cells. We are particularly interested in how maternal endocrine diseases such as polycystic ovarian syndrome (PCOS) and type I diabetes impact transcriptome and metabolism of oocytes, which in turn affects their offspring health across generations independent of uterine environmental effects. We are using diseased mouse models, IVF and surrogacy, and single-cell sequencing together with phenotyping and molecular assays.  

Research field IV: Investigate the molecular basis of maternal-fetal communication in maternal endocrine diseases and their effects on offspring future health

Functional placentation and endometrial receptivity are essential to maintain a healthy pregnancy and influence fetal development. We have previously showed that reproductive and metabolic traits of maternal PCOS can be transmitted across generations (Risal, Pei Nature Medicine 2019). To further delineate the role of adverse uterine environment versus germline transmission, we are carrying on several projects to study the role of the placenta in developmental programming and offspring’s future health. As increasing evidence has shown that the placenta is not functioned as a passive barrier, instead actively responds and adapts to uterine environment to impact fetal development. It is important to elucidate molecular adaptation of placentas in maternal endocrine diseases in function to maternal clinical features including hormone profiles. We also aim to mediate the placental function and prevent the developmental programming. To address these questions, mouse disease models, single-cell sequencing of human placentas as well placental organoids based chemical screening are applied to systematically examine molecular and phenotypic traits of mother, placentas and offspring and build molecular link underlying the developmental programming effects.

A: Human placenta section with H&E staining showing villous tree morphology.              B: Human placental organoid culture
A: Human placenta section with H&E staining showing villous tree morphology. B: Human placental organoid culture.