News!

4/25/2024: At the invitation of Dr. Jeff Morgan, Alexandra will give a talk at the Therapeutic Sciences Seminar Series at Brown University. Alexandra will discuss recent work from her lab on the development of advanced proteomic methods to advance ECM biomarker discovery. 

4/21/2024: We are seeking a talented candidate to fill the role of technician interested to work in a laboratory at the cutting edge of biomedical research. The successful candidate will join a dynamic team and will participate actively in the day-to-day management of the lab and contribute to the performance of various collaborative projects.

Click here for the complete job description.

Interested candidate should apply by May 10 via the UIC job board: https://uic.csod.com/ux/ats/careersite/1/home/requisition/9352?c=uic 

Graphic designed by pikisuperstar / Freepik

1/5/2024: Dharma's review entitled "Extracellular matrix dynamics: a key regulator of cell migration across length-scales and systems" is now published in the Cell Dynamics issue of Current Opinion in Cell Biology. 

Using examples taken from different organisms and pathophysiological states, this review discusses how ECM deposition and organization and the resulting mechanical and chemical signals contribute to modulating cell migration. 

Congratulations, Dharma!

12/6/2023: Alexandra is presenting the latest work from the lab on the development of enhanced mass-spectrometry-based approaches for in-depth profiling of the cancer ECM at the annual PI meeting of the NCI Innovative Molecular Analysis Technologies (IMAT) program.

12/5/2023: Announcing the deployment of 19 new human matrisome gene sets derived from our proteomic datasets on the cancer ECM and the first 15 murine matrisome gene sets in the Molecular Signature Database, MSigDB! All datasets are available on MSigDB and on the new dedicated page of the Matrisome portal. 

11/28/2023: 2 postdoctoral positions are available in our lab. More info and application guidelines available here. 

Graphic designed by pikisuperstar / Freepik

11/22/2023: Alexandra was invited to deliver the opening keynote lecture at the symposium of the training academy of the German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL) held in Berlin!  

11/17/2023: Our review  discussing the accomplishments, challenges, and future perspectives of the field of ECM proteomics and published in the Clinical Proteomics issue of Molecular and Cellular Proteomics is featured in ASBMB Today!

Read the feature piece at: https://www.asbmb.org/asbmb-today/science/111723/from-the-journals-mcp. 

11/8/2023: Alexandra joins the steering committee of the  Oncology Affinity Group initiative launched by the Chicago Biomedical Consortium! The overarching goal of the Oncology Affinity Group to accelerate scientific breakthroughs by leveraging team science in the oncology space across the 3 universities members of the CBC. Read more about the CBC Oncology Affinity Group: https://chicagobiomedicalconsortium.org/awards/affinity-groups-2/ 

10/27/2023: Big congrats to our own Adriana Duraki for using her artistic and pumpkin-carving skills to bring the lab’s idea to life. And big shout-out to the UIC Physiology and Biophysics Outreach Committee for organizing the first pumpkin carving contest!

10/13/2023: Leanna short talk entitled "Delineating the Timeline of SNED1 Fibrillogenesis and Assembly in the Extracellular Matrix " won second place at the 7th annual GEMS symposium. Congratulations, Leanna!

10/9/2023: With 3 selected short talks, 4 posters, and a session chaired by Alexandra, the Naba lab will have a great representation at the 2023 meeting of the American Society for Matrix Biology organized jointly with the Histochemical Society and the American Society for Investigative Pathology!

Read more about the event at: https://asip2023.asip.org/

10/3/2023: Alexandra will participate in a round table discussion on the Human Proteoform Project (HPfP) at the 2nd International Top-Down Proteomics Symposium organized at Northwestern University by the Consortium for Top-Down Proteomics. 

Read more about the event at: https://tdp2023.topdownproteomics.org/

9/11/2023: Dharma is short-listed to compete for the 2023 Iozzo post-doctoral trainee award at the upcoming meeting of the American Society for Matrix Biology. Congratulations, Dharma!

9/11/2023: Leanna's abstract entitled "Delineating the Timeline of SNED1 Fibrillogenesis and Assembly in the Extracellular Matrix " is selected for a short talk presentation at the upcoming meeting of the American Society for Matrix Biology (ASMB).

Congratulations, Leanna!

9/11/2023: Nandini Kapoor, senior in our lab, has received a travel grant from the Honors College to attend the meeting of the American Society for Matrix Biology (ASMB) where she was selected to give a short oral presentation on MatrisomeDB. Congratulations, Nandini!

8/24/2023: Alexandra is invited to speak at the annual BioCity Turku symposium on the theme of "Sculpting Tissues - Cells, Matrix and Forces". Alexandra's talk, entitled "The extracellular matrix: from proteomic explorations to matritherapies", will focus on the latest work from the lab on the Matrisome Project. 

8/16/2023: It is official! Alexandra is promoted to Associate Professor with tenure in the Department of Physiology and Biophysics! 

8/10/2023: Our latest paper entitled "Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms" is now published in the Journal of Cell Science! Congratulations to Naba lab member James Considine and collaborators Petar Petrov and Valerio Izzi! You can read the full article at: https://doi.org/10.1242/jcs.261255.

8/9/2023: Our research proposal to study the "Mechanisms guiding the fibrillar assembly of SNED1 in the extracellular matrix" is funded!

You can read more about our project here: https://reporter.nih.gov/search/hl3JcX9NNkmQxt6sj_nDyw/project-details/10733534. 

7/26/2023: Hourly research specialist, laboratory technician, and project manager positions are available in our lab! These positions are ideal for new graduate or more experienced scientists alike, interested in contributing to cutting-edge research. Visit our recruitment page to learn how to apply!

7/19/2023: Alexandra contributed to a Perspective published in Nature Cell Biology discussing the goals of the NIH-funded Human BioMolecular Atlas Program (HuBMAP) which include the generation of spatial maps of functional tissue units across organs from diverse populations and the creation of tools and infrastructure to advance biomedical research. You can read the full article at: https://doi.org/10.1038/s41556-023-01194-w. 

7/10/2023: Leanna successfully passed her qualifying exam and is officially a PhD candidate! Leanna will be investigating the molecular mechanisms leading to SNED1 fibrillogenesis in the extracellular matrix. Congratulations, Leanna!

6/7/2023: Alexandra is invited to speak at the symposium celebrating the 50th anniversary of the discovery of fibronectin by Dr. Richard O. Hynes, Alexandra's postdoctoral mentor. Alexandra will present the latest work from the lab on the Matrisome Project and the lab's recent discoveries on the novel ECM protein, SNED1. 

5/30/2023: We are excited to welcome Adriana Duraki to the lab! 

Adriana received her Bachelor of Science with a major in  from the University of Illinois at Urbana-Champaign 's in Molecular and Cellular Biology. At UIC, she is enrolled in our Graduate Education in bioMedical Sciences program. Adriana is passionate about cancer research and her PhD project will focus on studying the roles of the ECM on tumors’ response to different therapeutic modalities.

Welcome Adriana!

5/22/2023: Nandini Kapoor, rising senior in our lab, has received a Liberal Arts and Sciences Undergraduate Research Initiative (LASURI) award for the 2023-2024 academic year! Nandini's research will focus on studying the role of the new ECM protein, SNED1, in cell adhesion. 

Congratulations, Nandini!

Learn more about the LASURI program here.

5/3/2023: Clarissa Gomez had the honor to deliver the student address  at the UIC Honors College convocation. You can watch here address on YouTube (jump to 1h51m31s)! 

4/28/2023: Clarissa Gomez did a fantastic job presenting her poster on MatrisomeDB at the UIC College of Medicine's senior thesis forum!

4/10/2023: Alexandra contributed to a study led by Dr. Romain Desert and Dr. Natalia Nieto that discovered ECM signatures characteristic of distinct hepatocellular carcinoma subtypes and that correlate with patients' outcome.  You can read the full story published in Hepatology at: https://doi.org/10.1097/HEP.0000000000000362.

4/4/2023: The Naba lab has multiple funded positions open at all levels. Visit this page for job descriptions and how to apply. 

3/14/2023: Nandini Kapoor, undergraduate research assistant in our lab received a $1,000 grant from the Honors College to study the molecular bases of cell adhesion to the extracellular matrix. Congratulations, Nandini!

3/13/2023: Alexandra was invited to contribute a review to the 2023 issue of Molecular and Cellular Proteomics on Clinical Proteomics discussing the accomplishments, challenges, and future perspectives of the field of ECM proteomics. You can read the full text at: https://doi.org/10.1016/j.mcpro.2023.100528

3/10/2023: MD/PhD student, Fred Lee, successfully defended his thesis! During his PhD training, Fred contributed to develop novel proteomic methods to uncover new facets of the ECM and of our favorite ECM protein, SNED1. Congratulations, Fred!

3/6/2023: Ikram Isa, biomedical engineering major (class of '24), was awarded a Chancellor’s Undergraduate Research Award from the Office of the Vice Provost for Undergraduate Affairs and Academic Programs to pursue her research on the ECM in the lab. Congratulations, Ikram!

More info on the Chancellor’s Undergraduate Research Award can be found here.

3/1/2023: Alexandra is presenting a poster describing the latest release of MatrisomeDB at the annual meeting of the US chapter of the Human Proteome Organization (HUPO). 

2/5/2023: At the invitation of Dr. Ambra Pozzi and Dr. Jim Norman, Alexandra will be presenting the latest work from the lab on the novel ECM protein SNED1 and its roles in cancer and development at the Gordon Research Conference on "Fibronectin, Integrins, and Related Molecules". 

1/30/2023: At the invitation of Dr. Anne Marie Malfait, Alexandra will be presenting the latest work from the lab on ECM proteomics and MatrisomeDB at the seminar series of the newly established Chicago Center on Musculoskeletal Pain. 

01/03/2023: The Special Issue of Matrix Biology guest-edited by Alexandra and Dr. Suneel Apte is out! 2022 marks a decade since the conceptualization and delineation of the modern “matrisome” by Dr. Naba, a term which is now broadly accepted within the ECM community, and has better defined the field for non-ECM biologists. To jump-start the next decade of matrisome research, we assembled reviews and primary research papers spanning the full range of -omic applications to provide a forward-looking view of matrisome research. Read our editorial at https://doi.org/10.1016/j.matbio.2022.12.003 and the full issue at https://www.sciencedirect.com/science/article/pii/S0945053X22001524

11/20/2022: Our manuscript describing the new release of MatrisomeDB is now published in the 2023 Database issue of Nucleic Acids Research and available online at: https://doi.org/10.1093/nar/gkac1009. Congratulations to all co-authors from the Naba lab: Clarissa Gomez, Nandini Kapoor, James Considine, and our collaborators in the Gao lab: Tom Gao, Xinhao Shao and Chris Grams!

10/24/2022: Dharma received a travel grant from the journal Disease Models and Mechanisms to present his work at the 2022 Cell Bio meeting of the American Society for Cell Biology (ASCB) and the European Molecular Biology Organization (EMBO). 

Congratulations Dharma! 

9/20/2022: Congratulations to our collaborator Dr. Javier Bravo-Cordero and his team for the publication of their paper entitled "A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling" in Cell Reports.  We contributed to this study by analyzing the secretome of dormant (srGAP1 low) and proliferative (srGAP1 high) breast cancer cells and showed that srGAP1 low cells secreted higher amount of TGF-β2. 

You can read the full article at https://doi.org/10.1016/j.celrep.2022.111358. 

9/19/2022: Alexandra will be presenting the latest work from the lab on the development of advanced proteomic methods for in-depth profiling of the tumor ECM  at the upcoming "The Landscape of Post-Translational Modifications in Tumor Biology Meeting" sponsored by the Division of Cancer Biology of the National Cancer Institute. More about the workshop here. 

9/15/2022: Hot off the press! Our study in collaboration with Dr. John Varga (University of Michigan) and Dr. Maria Teves (Virginia Commonwealth University) demonstrating, for the first time, a role for the cilia protein SPAG17 in scleroderma was published in the Journal of Investigative Dermatology. Congratulations to first author Paulene Sapao, to co-author Fred Lee, MD/PhD student in the Naba lab, and the entire team! And thank you to the Chicago Biomedical Consortium, for having supported this project in its the early stage.

You can read the full article at https://doi.org/10.1016/j.jid.2022.08.052.

9/13/2022: Our lab has received a 3-year R21 grant from the National Cancer Institute's Innovative Molecular Analysis Technologies (IMAT) program . 

Our proposal in collaboration with Dr. Tom Gao's lab (UIC College of Pharmacy) aims to develop enhanced mass-spectrometry-based approaches for in-depth profiling of the cancer extracellular matrix. Learn more about our project here.

Postdoctoral and predoctoral positions to work on this exciting project will open soon. Contact Dr. Naba if you are interested!

9/1/2022: Clarissa Gomez, senior in the lab, was awarded a Cancer Federation, Inc scholarship from the University of Illinois Cancer Center for her excellence in cancer research. Congratulations, Clarissa!

8/3/2022: The Naba lab has multiple funded positions open at all levels. Visit this page for job descriptions and how to apply. 

8/3/2022: The source codes for #MatrisomeAnnotator and #MatrisomeAnalyzer are now available on GitHub: https://github.com/Matrisome

7/26/2022: Leanna Leverton, 1st-year graduate student in the lab received a T32 pre-doctoral fellowship from the Vascular Biology, Signaling and Therapeutics (VBST) training program. Congratulations, Leanna!

7/23/2022: Clarissa Gomez, undergraduate research assistant in the lab won an award for outstanding oral presentation with honorable mention at the 2022 Illinois Summer Research Symposium. Clarissa's research, supported by the UIC Summer Research Opportunity Program (SROP) proposed to facilitate cancer biomarker discovery by leveraging the content of MatrisomeDB.  

6/21/2022: Our lab has received a 4-year U01 grant from the NIH to join the HubMAP consortium. Our proposal developed in collaboration with Dr. Tom Gao's lab (UIC College of Pharmacy) entitled "Thinking outside the cell" will leverage HuBMAP data to build the human ECM atlas. You can learn more about our project here.

Postdoctoral and predoctoral positions to work on this exciting project will open soon. Contact Dr. Naba if you are interested!

6/20/2022: Alexandra was named mentor of the Vascular Biology, Signaling and Therapeutics (VBST) training program led by Dr. Kitajewski and Dr. Wary and supported by a T32 award from the National, Heart, Lung, and Blood Institute (HL144459) .  

6/17/2022: Martin Davis, past lab manager of our lab, will join the University of Illinois College of Medicine's entering class of 2022 this fall and was awarded a $60,000 Research Scholarship for having demonstrated excellence in research. Congratulations, Martin! 

6/14/2022: Alexandra collaborated with the laboratory of Dr. Farach-Carson at UT Houston, School of Dentistry, to explore the  FANTOM5 SSTAR dataset and define the pattern of expression of ECM genes across physiological systems. The resulting publication entitled "Systematic Analysis of Actively Transcribed Core Matrisome Genes Across Tissues and Cell Phenotypes" is now published in Matrix Biology. Congratulations to first authors Tristen Tellman and Merve Dede, and to the entire team! You can read the full article at https://doi.org/10.1016/j.matbio.2022.06.003.

6/1/2022: Alexandra contributed to  a perspective piece entitled "New views of old proteins: clarifying the enigmatic proteome" published in Molecular and Cellular Proteomics. 

In this perspective, we discuss how functional proteomic tools, methods, and datasets can be integrated to accelerate the development of comprehensive spatio-molecular tissue maps to generate new biological insights. You can read the review at https://doi.org/10.1016/j.mcpro.2022.100254.

5/23/2022: Alexandra will present the latest work from the lab focused on the "computational and experimental profiling of the mutational landscape of the cancer matrisome" at the 2022 Midwest Tumor Microenvironment Meeting. More information on the meeting can be found here: https://www.kumc.edu/midwesttme.html.

5/6/2022: Anna Barqué received her PhD from the Graduate Education in Biomedical Science program during the commencement ceremony of the UIC College of Medicine. Congratulations Anna! Scroll to 1:51:45 to see Anna receive her hood!

5/4/2022: Ali Thahab, undergraduate research assistant in the lab, graduated summa cum laude from the UIC Honors College. Congratulations Ali! Scroll to 1:39:19 to see Ali receive his gold stole!

The 32nd Physiology Awards Night that took place on March 31st, 2022 brought a lot of excitement for our lab! Fred Lee (G3, MSTP) received the 2021 John and Kathy Solaro Endowed Graduate Fellowship and Anna Barqué (G5, GEMS), the Mark R Lambrecht Award for Scholarship and Commitment. Congratulations, Fred and Anna!

Alexandra was awarded a 2021 HOPE (Honoring Our Professors' Excellence) Award.

Started in 2015, the HOPE awards are presented by Campus Housing to recognize faculty who have made a lasting impact on the lives of Housing residents.

Clarissa will present her work in collaboration with Pam Kreeger's lab (U. Wisconsin, Madison) on the role of the ECM during high-grade serous ovarian cancer progression at the 2022 UIC Undergraduate Research Forum. Clarissa's work in the lab was supported by a UIC Honors College Research Grant, a LASURI grant, and funding from the UIC Summer Research Opportunities Program (SROP) and Graduate Pathways to Success (GPS) program. 

Our lab is excited to announce that Anna Barqué successfully defended her Ph.D thesis entitled "The Extracellular Matrix Protein SNED1 Regulates Neural Crest Cell Phenotype and Carniofacial Development".  Congratulations, Dr. Barqué!

In September 2021, the American Society for Matrix Biology (ASMB) organized a hybrid scientific meeting, integrating in-person and virtual formats, to discuss the latest developments in ECM research. In this meeting report written by the Outreach committee of the ASMB chaired by Dr. Naba, we highlight exciting scientific advances that emerged from the meeting. In addition, we discuss how the ASMB incorporated mentoring, career development, and diversity, equity, and inclusion initiatives. Finally, we reflect on the hybrid scientific conference format and how it will help the ASMB accomplish its mission moving forward. 

Read the full report here: https://doi.org/10.1242/bio.059156

Our paper in collaboration with Dr. Bravo-Cordero (Mount Sinai Medical School) demonstrating that "A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy" is now published in Nature Cancer. 

Read it here: https://www.nature.com/articles/s43018-021-00291-9 

Our paper in collaboration with Dr. Pam Kreeger and Dr. Kristyn Masters (Department of Biomedical Engineering, U. Wisconsin-Madison) and funded by the National Cancer Institute on the "Multi-modal Profiling of the Extracellular Matrix of Human Fallopian Tubes and Serous Tubal Intraepithelial Carcinomas" is now published in the Journal of Histochemistry and Cytochemistry. 

Read it here: https://doi.org/10.1369/00221554211061359

Do not miss Anna's virtual poster presentation available on-demand throughout the meeting!

Click here for more information: https://www.ascb.org/cellbio2021/ and read Anna's abstract here: https://www.abstractsonline.com/pp8/#!/10458/presentation/3418 

Click here for more information: https://www.sidekudostutkijat.fi/the-joint-nordic-matrix-biology-meeting 

Click here for more information: https://www.mbsanz.org/events-1/VICmeeting

Click here for more information: https://www.scgdb.org/annual-meeting

We are excited to welcome Dr. Dharma Pally to the Naba lab! Dharma received his PhD from the Indian Institute of Science in Bangalore where he trained in Dr. Bhat's lab. For his postdoctoral training in the lab, Dharma will lead a project aimed at understanding the roles of our favorite ECM protein, SNED1, in breast cancer metastasis. Welcome Dharma!

Congratulations to Anna Barqué (G5, GEMS) and Fred Lee (G3, MSTP) for being selected to give short talks at the upcoming meeting of he American Society for Matrix Biology (ASMB)! See the program of the meeting here.

On August 26, Alexandra will participate in a panel discussion on reviewing scientific paper organized by #THEMeshwork. More info and link to sign up for the event: https://www.eventbrite.com/e/the-good-practice-of-reviewing-or-how-to-avoid-being-reviewer-3-tickets-164898637263 

Our annual tradition took us this year to downtown Chicago where we enjoyed a round of mini-golf, tacos, and a stroll along the River walk. This year was bitter-sweet as we bid farewell to our fantastic lab manager, Martin Davis, who is heading to medical school! It was also the occasion to celebrate our successes, end the summer term, and enjoy a day off before the new term starts.

The Naba lab is ready for the 2021-2022 academic year!