Sophia Khaldoyanidi

Sophia Khaldoyanidi

The laboratory of Dr. Khaldoyanidi is focused on the basic biology of stem cells and on translational aspects of their use for tissue regeneration. The current projects include studies on multipotent stem cells, such as hematopoietic stem cells, mesenchymal stem cells and neural stem cells, as well as on pluripotent stem cell lines.

Sophia Khaldoyanidi

The laboratory of Dr. Khaldoyanidi is focused on the basic biology of stem cells and on translational aspects of their use for tissue regeneration. The current projects include studies on multipotent stem cells, such as hematopoietic stem cells, mesenchymal stem cells and neural stem cells, as well as on pluripotent stem cell lines.


Hyaluronan, a long-chain polysaccharide with a key role in bone marrow

Dr. Sophia Khaldoyanidi, Associate Member at Torrey Pines Institute for Molecular Studies (TPIMS), and her team of international collaborators recently discovered that the long-chain sugar molecule hyaluronan is important for the production of new blood cells in bone marrow. Millions of patients around the world suffer from acute and chronic illnesses caused by blood cell deficiencies resulting from damage to the bone marrow by chemotherapy, radiation, or disease. The new study, published in the July 20th, 2012 issue of the Journal of Biological Chemistry, could pave the way for new therapies that facilitate production of blood cells and improve the way that bone marrow stem cells are used to treat disease.

What is hyaluronan?

Dr. Khaldoyanidi’s team were interested in whether a long-chain polysaccharide called hyaluronan plays a role in supporting the production of new blood cells in the bone marrow, a process termed hematopoiesis. Hyaluronan is composed of repeating disaccharide units (N-acetyl-D-glucosamine and glucuronic acid) and is synthesized throughout the body by three hyaluronan synthase enzymes. Hyaluronan was initially thought to function simply by maintaining extracellular space. However, later studies showed that it participates in local extracellular matrix assembly by interacting with a variety of molecules, and is involved in the regulation of multiple cell functions, including cell proliferation and migration. As expected, hyaluronan concentrations are normally exquisitely regulated by synthetic and catabolic enzymes, but in some diseases, patients have abnormal serum levels of hyaluronan. Abnormalities in bone marrow hyaluronan levels can be induced by many external factors including radiation and chemotherapeutic treatments.

Stem cells and their microenvironment

Hematopoietic stem cells (HSCs) colonize the bone marrow during fetal development and remain there throughout life, generating a variety of lineage-specific progenitor cells that give rise to billions of blood cells every day. This process, termed hematopoiesis, is regulated by the local bone marrow microenvironment. The microenvironment is composed of several distinct cell types, including cells of mesenchymal origin, which communicate with each other and with HSCs through secreted regulatory molecules and cell surface interactions. The microenvironment influences many HSC decisions, including whether to undergo proliferation versus quiescence, self-renewal versus differentiation, or survival versus apoptosis. The health of this microenvironment is particularly important for patients undergoing bone marrow or stem cell transplantation, because the microenvironment regulates functions of donor HSCs in the recipient patient’s bone marrow.

“Although the quantity and quality of transplanted HSC are important for the recovery of hematopoiesis in patients, the functional status of the regulatory hematopoietic microenvironment is a critical parameter that determines the regenerative function of HSC,” said Dr. Khaldoyanidi. The success of HSC transplantation depends on the ability of the regulatory microenvironment to support hematopoiesis, which may be compromised during disease or following certain drug treatments. Thus, the hematopoietic microenvironment should be treated and allowed to recover prior to HSC transplantation. To do this effectively, it is important to understand which of the molecular pathways regulating the microenvironment’s functions are disrupted under specific pathological conditions.

Bone marrow cultures show hematopoietic cells (visible as small bright round cells) and components of the microenvironment (visible as a lower layer of dark and adherent cells). Cultures treated with the chemical 4-methylumbelliferone (4MU), an inhibitor of hyaluronan synthesis, (right) show a dramatic reduction in numbers of hematopoietic cells compared with untreated cultures (left).

How hyaluronan regulates HSCs

In the new study, Dr. Khaldoyanidi and her collaborators used a mouse engineered to delete the three hyaluronan synthase genes Has1, Has2, and Has3 (these mice are termed Prx1-Cre;Has2flox/flox;Has1–/–;Has3–/– triple knockout mice), which lacked hyaluronan in the bone marrow microenvironment. In these animals, hematopoietic progenitors — the cells that produce mature, functionally active blood cells — relocated from their normal niche in the bone marrow to sites such as the spleen and liver. In addition, hyaluronan-deficient bone marrow cells could not support growth of HSC in cell culture, which was consistent with the in vivo findings that hyaluronan is essential for HSC function.

“Many past studies have hinted at a role for hyaluronan in hematopoiesis. Focus on the biology of hyaluronan in this fundamental process was rewarded when the recent report by Goncharova and co-workers confirmed that hyaluronan is essential for bone marrow hematopoiesis. The study is one of the more comprehensive efforts in years to determine if this polysaccharide plays a key role in allowing people to make many types of new blood cells every day,” said Dr. Paul H. Weigel, Professor and Chairman at the University of Oklahoma Health Sciences Center and President of the International Society of Hyaluronan Sciences ( “These research findings are important because they bring us closer to a future ability to manipulate the complicated cellular pathways that utilize and respond to hyaluronan, in order to improve the efficacy of using stem cells to treat a variety of diseases.”

“It is an interesting and important study that demonstrates that hyaluronan has important and essential roles in bone marrow stem cell niches that foster hematopoietic progenitor cells. Here at the Cleveland Clinic we have shown that progenitors for osteogenic lineage in human bone marrow isolates can be significantly enriched by selecting for cells with hyaluronan coats. This paper has now been accepted in Annals of Biomedical Engineering, and would complement and compliment Sophia’s study,” said Dr. Vincent Hascall, Professor at the Cleveland Clinic Lerner Research Institute.

Once Dr. Khaldoyanidi’s team had shown that hyaluronan was needed for normal bone marrow function, the researchers used the chemical 4-methylumbelliferone (4MU) to inhibit the production of hyaluronan by cultured bone marrow cells. They showed that 4MU decreased the expression of hyaluronan synthases (HAS2 and HAS3), inhibited hyaluronan synthesis, and eliminated hematopoiesis in the culture dish. Further studies demonstrated that endogenously produced hyaluronan was needed for the production of chemokines and growth factors, which in turn were necessary for the motility of hematopoietic cells. Hyaluronan was also found to be involved in regulating interactions of the hematopoietic cells with the vasculature under conditions of physiological blood flow.

This and other studies have shown that too much or too little hyaluronan in bone marrow caused hematopoietic abnormalities. Thus, in healthy tissues, the body maintains optimal hyaluronan levels through complex machinery that fine-tunes hyaluronan synthesis, binding, retention, accumulation, degradation, and clearance. Collectively, this new study suggests that the tissue-associated hyaluronan in bone marrow might be clinically relevant and reflect the biological health of the hematopoietic microenvironment.

Faculty of 1000

The study was evaluated by the Faculty of F1000, in which the world's leading scientists and clinicians identify and evaluate the most important articles in biology and medical research. On average, 1500 new evaluations are selected each month, which is about 2% of all published articles in the biological and medical sciences.

“This is a highly prestigious distinction that highlights the quality of Dr. Khaldoyanidi's scientific work,” said Dr. Robert Sackstein, a leading bone marrow transplant physician-scientist and Professor,Harvard Medical School. “Dr. Khaldoyanidi's elegant studies provide seminal evidence of the key role of hyaluronan in the hematopoietic microenvironment. The work has profound implications for clinical practice, as it suggests that maintenance of marrow hyaluronan levels could improve blood cell development.” Dr. Hascall concurred. “The fact that the Faculty of 1000 is now paying attention to hyaluronan research is great. As most of us in the field know, it has been difficult at times to get the broader research community to pay attention to hyaluronan matrices and their roles in normal and pathological processes,” he said.

For patients undergoing treatment in preparation for stem cell transplantation, the team suggests it may prove clinically useful to monitor hyaluronan recovery to help pinpoint the optimal time for stem cell transplantation. The scientists believe that biologically active hyaluronan polymers or hyaluronan synthesis inhibitors may prove useful in the clinic to correct misbalanced hyaluronan levels.

“Our findings suggest that hyaluronan is a biologically active component of the hematopoietic microenvironment and is involved in regulating hematopoietic homeostasis,” said Dr. Khaldoyanidi. “This is a very difficult time for biomedical research funding, but I am optimistic that our team will be able to continue this important project, which is on the edge of glycobiology and stem cell biology, to bring our understanding of hyaluronan biology to the next level.” The researchers in Dr. Khaldoyanidi’s group believe that further research is required to bring the recent advances in hyaluronan basic research generated in many laboratories over the past decade to the level that could finally benefit patients, i.e. to the bedside.


Researchers involved in this study were: Valentina Goncharova, Ingrid Schraufstatter, Tatiana Povaliy, Valentina Wacker, Audrey de Ridder, and Sophia Khaldoyanidi from Torrey Pines Institute for Molecular Studies, San Diego, CA; Naira Serobyan from La Jolla Institute for Molecular Medicine, San Diego, CA; Shinji Iizuka and Yu Yamaguchi from Sanford-Burnham Medical Research Institute, La Jolla CA; Irina A. Orlovskaja from Institute of Clinical Immunology, Novosibirsk, Russia; Naoki Itano from Kyoto Sangyo University, Kyoto, Japan; and Koji Kimata from Aichi Medical University, Nagakute, Japan.

Original paper: Hyaluronan expressed by the hematopoietic microenvironment is required for bone marrow hematopoiesis. Goncharova V, Serobyan N, Iizuka S, Schraufstatter I, de Ridder A, Povaliy T, Wacker V, Itano N, Kimata K, Orlovskaja IA, Yamaguchi Y, Khaldoyanidi S. J Biol Chem. 287, 25419–25433, 2012. PMID: 22654110

Research Focus

Dr. Khaldoyanidi’s laboratory is focused on the basic biology of stem cells, and on translational aspects of their use for tissue regeneration. The current projects include studies on somatic multipotent stem cells, including hematopoietic stem cells (HSC), mesenchymal stem cells (MSCs), and neural stem cells (NSCs), as well as on pluripotent stem cell (PSC) lines.

The fate of stem cells depends on their interactions with the local microenvironment, i.e. the niche. One of Dr. Khaldoyanidi’s research interests is to identify the cells that contribute to the complex structure of the hematopoietic niche in bone marrow. Her laboratory is also studying the non-cellular compartment of the niche, which includes extracellular matrix molecules, chemokines, anaphylotoxins, and cholinergic mediators. Ongoing studies are investigating the molecular mechanisms by which these factors mediate their effects on the fate of stem cells and on the cross-talk between stem cells and the niche.

Multipotent stem cells, or other differentiated cells derived from pluripotent stem cells, are of potential use for tissue regeneration. One current problem is to generate the desired cells in sufficient quantities for transplantation. The critical issue, which has been insufficiently addressed, is to improve the efficiency of PSC differentiation into the desired specific lineage. Dr. Khaldoyanidi’s laboratory is studying how extracellular matrix components, produced by PSCs, regulate the fate of PSCs.

Transplantation of stem cells is necessary for treatment of many pathological conditions. When cells are administered systemically, the efficiency of transplantation depends on the ability of the stem cells to home to the target organ. Dr. Khaldoyanidi’s laboratory has established a new in vitro method, based on a 3-dimesional (3D) flow chamber device, to investigate the effects of the organ-specific microenvironment on stem cell - endothelial cell interactions under physiological shear stress conditions. The device allows the discrete steps of the cell-cell interaction to be studied, including rolling on, adhesion to, and transmigration of the stem cells across an endothelial layer. This approach will contribute to our understanding of the mechanisms that regulate stem cell migration, and may lead to the development of treatments that either enhance or prevent homing of cells into the target organ.



  • 1983 - 1989: Medical State University, Novosibirsk, Russian Federation, M.D. (Pediatrics)
  • 1989 - 1993: Institute of Clinical Immunology, Novosibirsk, Russian Federation, Ph.D. (Immunology/Hematology)
  • 2005 - 2006: The Burnham Institute for Medical Research, Stem Cell Center, sabbatical; La Jolla, California, USA


  • 1993 - 1995: Guest Scientist, German Cancer Research Center (DKFZ), Heidelberg, Germany
  • 1995 - 1998: Guest Scientist, Institute for Genetics (IGEN), Karlsruhe Research Center (FZK), Karlsruhe, Germany
  • 1998 - 1999: Postdoctoral Fellow, Laboratory for Hematopoiesis Research, Medical Biology Institute, La Jolla, CA, USA
  • 1999 - 2001: Research Scientist, Department of Vascular Biology, LJIMM, La Jolla, CA, USA
  • 2001 - 2007: Assistant Professor, Department of Vascular Biology, LJIMM, San Diego, CA, USA
  • 2005 - 2007: Director, Stem Cells and Regenerative Medicine Program, LJIMM, San Diego, CA, USA
  • 2007 - Present: Associate Member, Torrey Pines Institute for Molecular Studies, San Diego, CA

Professional Affiliations

  • American Society of Hematology, since 1998
  • International Society of Experimental Hematology, since 2000
  • International Society for Hyaluronan Science, Since 2007
  • International Society for Stem Cell Research, Since 2008

Selected Publications

Selected Publications (10 of 42)

  1. Khaldoyanidi, S.K.; Moll, J.; Karakhanova S.S.; Herrlich, P.; Ponta, H. Hyaluronate-enhanced hematopoiesis: Two different receptors trigger the release of interleukin-1beta and interleukin-6 from bone marrow macrophages. Blood (1999), 94(3), 940-949
  2. Khaldoyanidi, S., Karakhanova S., Sleeman, J., Herrlich, P., Ponta, H. CD44 variant specific antibodies trigger hemopoiesis by selective release of cytokines from bone marrow macrophages. Blood, (2002),99(11):3955-3961
  3. Matrosova V, Orlovskaya I, Serobyan N. and Khaldoyanidi S. Hyaluronic acid facilitates recovery of hematopoiesis impaired by 5-fluouracil administration. Stem Cells, 2004;22:544-555
  4. Franz-Josef Mueller, Naira Serobyan, Ingrid U. Schraufstatter, Richard DiScipio, Jeanne F. Loring, Evan Y. Snyder and Sophia K. Khaldoyanidi. Adhesive interactions between human neural stem cells and inflamed human vascular endothelium are mediated by integrins. 2006, Stem Cells, 24(11):2367-72.
  5. Irina Orlovskaya, Ingrid Schraufstatter, Jeanne Loring and Sophia Khaldoyanidi. Hematopoietic differentiation of embryonic stem cells. Methods, 2008; 45:159-167
  6. Sophia Khaldoyanidi. Directing stem cell homing. 2008, Cell Stem Cell, 2:198-200.
  7. Nadezhda Omelyanchuk, Irina A. Orlovskaya, Ingrid U. Schraufstatter and Sophia K. Khaldoyanidi. Key Players in the Gene Networks Guiding ESCs toward Mesoderm. Journal of Stem Cells, 2009; .4(3):147-160
  8. Schraufstatter, I.U., DiScipio, R.G., Zhao, M. and Khaldoyanidi, S.K. C3a and C5a are chemotactic factors for human mesenchymal stem cells, which cause prolonged ERK1/2 phosphorylation. J. Immunol., 2009, 182: 3827-3836.
  9. Ingrid Schraufstatter, Naira Serobyan, Richard DiScipio, Natalia Feofanova, Irina Orlovskaya and Sophia Khaldoyanidi. Hyaluronan stimulates mobilization of mature hematopoietic cells but not hematopoietic progenitors. Journal of Stem Cells, 2009:4(4):191-202.
  10. Ingrid U. Schraufstatter, Naira Serobyan, Jeanne Loring and Sophia K. Khaldoyanidi. Hyaluronan is required for generation of hematopoietic cells during differentiation of human embryonic stem cells. Journal of Stem Cells, 2010, 14:81-91, 2005.


  1. Pending - Device for evaluating in vitro cell migration under flow conditions, and methods of use thereof. United States Patent Application Serial No. 11/395,812. United States Attorney Docket No. 8059-003 PR (filed March 31, 2004)

Honors & Awards

  • Medical State University, Novosibirsk, Stipend of Excellence 1983-1989
  • Boehrihger Ingelheim, Germany, Guest Scientist Award 1993
  • German Cancer Research Center, Heidelberg, Germany, Guest Scientist Award 1994-1995
  • Forschungszentrum Karlsruhe, Germany, Guest Scientist Award 1995-1998
  • American Society of Hematology, travel Award 1999
  • International Society of Hematology, travel Award 2003
  • International Drug Discovery Science and Technology, Honorary Member, 2004
  • International Society of Hematology, Member of the Month, October 2006


  • Stem Cells
  • British Journal of Haematology
  • International Journal of Biochemistry and Cell Biology
  • International Journal of Biological Macromolecules
  • Journal of Immunological Methods
  • Oncogen
  • PNAS


  • Frontiers in Bioscience
  • Grant reviewer: Universite du Luxemnourg, 2006
  • PhM Research Management Group, 2007
  • NIH, since 2008