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Cancer ResearchDepartment of Thoracic Surgery

Division of Cancer Research

Department of Thoracic Surgery

News

30.08.2019 - Farewell

Today, we sadly say goodbye to Sonam with a lab outing to the city with guests from Heidelberg and alumni - all came to wish all the best to Sonam as founding member of our Freiburg lab. Thank you for all your hard work, your excellent ideas, your help to so many projects and your inspiration !  

09.07.2019 - Accepted

Our collaboration partner Manfred Jung sends good news: our cooperative manuscript on a novel Jumonji inhibitor has just been accepted for publication in ACS Chemical Biology. Congratulations !

16.05.2019 - Accepted

Again - excellent news:

Our manuscript on synonymous mutations in cancer has just been accepted for publication in Nature Communications !

Thanks to all contributors to this study - both, from our lab as well as from the Backofen lab in Freiburg.

Please check out the associated database SynMICdb to find and analyze synonymous mutations in a pan-Cancer panel.

17.04.2019 - Lab Outing

"FR 04" - formerly known as "L666" or simply "our lab" - is out again:
Today, we go to the exciting place of Denzlingen and play Minigolf with 3D glasses on under black light... this is not only great fun, but also guarantees a number of great pictures of our group. 
Afterwards, we take advantage of now having a "true Italian" in our midst and go for an authentic Italian dinner.

11.04.2019 - Accepted

And here is a big one:

Our manuscript on RNA Dependence has just been accepted for publication in Molecular Cell !

We are very happy and look forward to pursuing this new concept of RNA-dependent protein complexes further in the near future - job advertisements will be coming up...

CONGRATULATIONS first and foremost to Maiwen, who drives this project successfully, but also to all other contributors to the R-DeeP project in our lab as well as our collaboration partner in Dartmouth, Arminja Kettenbach, and her team.

You can already use our database to look for your favorite protein and its RNA Dependence in the R-DeeP database. This also mprovides a comprehensive resource for studies of RNA-binding proteins compiling results from 19 studies in one user-friendly spot.

Stay tuned - there will hopefully be more soon...

04.03.2019 - Accepted

News from Copenhagen: together with our collaboration partner Anders Lund, we just published a study about lncRNAs linked to autophagy in Oncogene - congratulations to Anders and his team.

24.12.2018 - Happy Holidays

Happy holidays and all the best wishes for the new year - to everyone interested in and contributing to and generously supporting our research to understand the RNA biology of lung Cancer and tumor genetics.

18.12.2018 - Christmas Lab Outing

One week to go - so, we also go on our Christmas Lab Outing. This year, we go Bowling and have dinner in between the strikes and spares. And one of our future lab members even won a game...

17.12.2018 - Accepted

Sonam's study about the role of the lncRNA linc00261 and its neighboring gene FOXA2 in lung cancer development and metastasis as well as in epithelial-to-mesenchymal transition (EMT) and lung cancer cell migration has been accepted in the new pertinent journal in our field: Non-coding RNA. Congratulations !

28.11.2018 - Magical Lab Outing

Tonight, we will watch the second part of the Magical Creatures in 3D and then have a drink on Sven's birthday last week. Lucky us that we have Ksenia, who can enlighten us and fill us in on the details we missed in the movie... 

17.11.2018 - Accepted

The end of a long journey: Anna's manuscript on the role of linc00673 in lung cancer cell senescence has been accepted today at RNA Biology - congratulations and thanks to everyone who contributed over the years.

01.11.2018 - Microprotein CASIMO1 in Breast Cancer ... quite some attention

Just three months ago, we published our study on the functional role of the microprotein CASIMO1 in breast cancer (Oncogene 2018).
Within this short period, the article has already received a lot of attention ranking in th 96th percentile of similarly aged publications:http://www.nature.com/articles/s41388-018-0281-5/metrics

Moreover, a figure from the CASIMO1 paper has been selected as "Picture of the Week" by Bild der Wissenschaft: https://www.wissenschaft.de/bildervideos/bild-der-woche/gruene-winzlinge-befeuern-krebs/ .

15.10.2018 - Accepted

Today, our review article on RNA motifs has been accepted for publication in Nature Structural & Molecular Biology.

19. - 21.09.2018 - Retreat in the Black Forest

These days, you will find us hiking and discussing science in Altglashütten in the Black Forest ... and really enjoying the weather on our joint retreat of the Heidelberg and the Freiburg labs.

17.09.2018 - 1000th citation of MALAT1

And our paper on the initial discovery of MALAT1 (Oncogene 2003) has reached another milestone in the Web of Science: 1000 citations !
Thank you to everyone who acknowledges our research in this way.

12.09.2018 - Publon Awards for Peer Review

Again, Sven has been recognized by Publons for his efforts in peer reviewing with awards in the categories as a top reviewer in "General Science" (worldwide #8), "Biology & Biochemistry" (#29) and "Biochemistry, Genetics and Molecular Biology" (#30). 

31.07.2018 - MALAT1 - the first ncRNA in the Cancer Gene Census

MALAT1 - the long non-coding RNA, which we first discovered and named as a marker associated with lung cancer metastasis (Oncogene 2003) and later characterized as an essential factor in lung cancer metastasis (Cancer Res 2013) - has now been listed as a proven cancer gene in the Cancer Gene Census. It is hence the first non-coding RNA which reached this status!

Further reading on MALAT1 and ncRNAs in metastasis:
Onogene 2003, Genome Res 2011, RNA Biol 2012, Cancer Res 2013, J Mol Med 2013, Int J Cancer 2016

19.07.2018 - Accepted

Good news from our collaboration partner Kannanganattu Prasanth at the University of Illinois: our first joint manuscript on the role of long non-coding RNAs in cell cycle regulation has just been accepted at Nucleic Acids Research (new IF: 12). Congratulations and thank you for including us in this productive collaboration!

P.S.: Now, this is the fifth original article with an impact factor above 10 this year for our lab ... and we are just in July... and although our scientifically most impactful paper this year so far (from our perspective) did not even make it into this category, but is certainly worth reading ... 

14.05.2018 - Accepted

Today, Marcel's paper entitled "The lncRNA CASC9 and RNA binding protein HNRNPL form a complex and co-regulate genes linked to AKT signaling" has been accepted for publication in Hepatology.

Congratulations - and what a great way to get your data published before submitting your PhD thesis!
We will all celebrate next week another 13 impact points for our lab... and more to come as the very positive presubmission inquiries in the last weeks let us hope for.

10.04.2018 - Lab Inning

This time, our lab outing takes place in the lab: Pizza and a movie ... and a nice Belgian cake for dessert... now, we know where to find the fantastic beasts and are prepared for part II in the fall.

02.04.2018 - Accepted

Happy news for happy Easter:

Today, our manuscript entitled "The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation" has been accepted for publication in Oncogene. Congratulations and a big thank you to everyone who participated in this study and especially to Maria for her great dedication and perseverance throughout this project and to Matthias for driving the revision home! It has been a really long journey starting about nine years ago with a process of multiple submissions and revisions spanning about two years.

In this study, we describe the first microprotein derived from a putative lncRNA in cancer. We call it CASIMO1, identified it in breast cancer and characterize its cellular and molecular functions as well as interaction partners in detail.
You may wonder why this has not been published earlier and in a higher impact journal - well, we have been wondering about the same over the last years. But hence now, it is even more important, that many of you interested in our research have a look at it and judge for yourself... and if you like it: cite it frequently whenever you are looking at small ORFs in putative lncRNAs.
After all, our initial discovery of MALAT1 had also "only" been published in Oncogene and has now been cited 911 times according to the Web of Science.

21.03.2018 - Accepted

And another one: our collaboration partners Sonia Forcales and Manuel Perucho from Barcelona just informed us that our joint manuscript entiled "A novel long non-coding RNA from NBL2 pericentromeric macrosatellite forms a perinucleolar aggregate structure in colon cancer" has just been accepted at Nucleic Acids Research
By the way: this is our tenth publication in NAR (IF 10.2) in the last five years...

28.02.2018 - Lab Outing & Farewell of a Master

It is cold outside - really, really cold. So, this is the ideal whether for a hot dinner inside. Hence, we have Raclette tonight - and celebrate Angela's Master defense and sadly say good-by to her.

26.02.2018 - Accepted - 10 points for CCI + CCCF

Good news from our collaboration partner Dr. Claudio Mussolino: our joint manuscript on the use of designer epigenome modifiers in clinically relevant human cells has just been accepted for publication in Nucleic Acids Research. Congratulations !

This is a prime example of the fruitful collaboration of our group as part of the Comprensive Cancer Center Freiburg (CCCF) together with several groups at the Center for Chronic Immunodeficiency (CCI) which are housed together in the new Center for Translational Cell Research in Freiburg (ZTZ).

20.01.2018 - 500 citations for MALAT1

Good news from the Web of Science:

Our publication on the important role of MALAT1 in lung cancer metastasis has now been cited more than 500 times since its publication in Cancer Research in 2013.

It is thus the fifth publication from our lab reaching this milestone.

24.12.2017 - Happy holidays

Happy Holidays, merry Christmas and all the best wishes for the new year 2018 !
We would like to thank all our colleagues and collaborators for their Support in the past year and look Forward to a fruitful next year.

13.12.2017 - Farewell & Christmas Lab Outing

December is here ... and we go for our Christmas lab outing: an evening of Bowling and a nice dinner at the new restaurant "Das Quartier" not far away from our lab. At the same time, we are sad to say good-bye to Yogita, who will move to Scandinavia soon. 

11.12.2017 - Funding

Good news from the German Research Foundation (DFG):
Our grant proposal on novel types of mutations in tumor suppressor genes outside of the coding region will be funded for the next three years.

 

08.12.2017 - Top 0.01%

In these days, when almost everything is rated as "outstanding" and "excellent" and within the "top 10%", it sometimes helps to look at real numbers again:

Almost five years ago, our manuscript on the important role of the lncRNA MALAT1 in lung cancer metastasis has been accepted for publication and was printed in Cancer Research in February 2013. Not even five years after its publication, we are proud to see that it has already been cited 485 times - and we would like to thank our colleagues in the scientific community for this unanimous appreciation of our work.

To put this number into perspective: Out of all 9.010.590 scientific papers published worldwide in the last five years, our paper ranks #857, so at the top 0,0095% ...

 

24.11.2017 - Lab outing to the space

For our November lab outing, we chose a very special place to go and see: our galaxy. The Planetarium Freiburg took all of us on an exciting cruise through the milky way, before we indulged into more earthy pleasures cruising from the Indian Curryhouse to the cocktails at Brasil.

 

08.11.2017 - Visibility & Impact

The scientific community values our contributions as expressed in citing of our work: in the first ten months of this year alone, all our publications together have been cited more than 1000 times. We are very happy about the visibility and the impact that our scientific articles apparently reach.

 

19.10.2017 - ZTZ Happy Hour

Today, it is our turn:
Everyone in the ZTZ is welcome to join for the Happy Hour organized by our lab starting at 17:00 - but not on the second floor, but outside under the blue sky on the new ZTZ deck. Enjoy food and drinks and Ksenia's favorite Pub Quiz...

 

04.10.2017 - Accepted

Three in a row ... original research articles these are:

Today, Ashish's manuscript on the inverse but independent regulation of pairs of sense mRNAs and their antisense lncRNAs during the DNA damage response got accepted for publication in Nucleic Acids Research! Congratulations - thereby, one of the studies going on for the longest time in our lab has found "a good home". Thanks to the many who made valuable contributions over the years...

For all those interested in statistics:

This is now the tenth publication from our lab this year and the fifth one with an impact factor above 10. So, 2017 is a productive year for us - and stay tuned: there is much more to come.

02. - 04.10.2017 - Retreat

The two Diederichs divisions from Heidelberg and Freiburg are going on their annual joint retreat!

So, do not wonder if the labs are empty these days - we are in Bad Herrenalb in the Black Forest and make big plans for the next exciting science.

02.10.2017 - Accepted

21.09.2017 - Accepted

12.09.2017 - Publons Peer Review Award

24.08.2017 - Accepted

26.06.2017 - Welcome

13.04.2017 - Accepted

10.04.2017 - Accepted

01.03.2017 - One year in Freiburg

01.02.2017 - Lab Outing

25.01.2017 - Accepted

01.01.2017 - A new year

24.12.2016 - Happy holidays

16.12.2016 - 1000 Citations

Our review article on microRNA Biogenesis in Nature Cell Biology has reached 1000 citations in Web of Science! Also, our review on long non-coding RNAs in cancer published in RNA Biology has already been cited 400 times. Thanks to everyone who acknowledged our work by citing it.

Also our original research has reached several milestones with 650 citations for the discovery of MALAT1 (Oncogene) and more than 300 citations for its functional characterization (Cancer Research) as well as the discovery of Argonaute protein functions in microRNA biogenesis and regulation (Cell).

14.12.2016 - Lab Outing ... to the Movies

Tonight, we will learn about fantastic beasts and where to find them.

05.12.2016 - Christmas Lab Outing

Today, we had a great time at the Christmas Market in Strasbourg.

22.11.2016 - Celebrations

Meet us for dinner and drinks tonight in the "Brasil" to celebrate a big birthday tomorrow... 

24.10.2016 - Welcome

Patrick Frey starts his rotation in our lab for four weeks as an SGBM rotation student working with Chul-Min. Welcome!

12.10.2016 - Accepted

Good news from Barcelona: our joint manuscript with Manel Esteller's group has been accepted for publication in PNAS. Congratulations!

23.09.2016 - Accepted

Today, our manuscript on the use of CRISPR-based technologies for non-coding RNAs (as well as any other gene ...) -  the challenges and potential pitfalls as well as the required controls to circumvent these  - has been accepted by Nucleic Acids Research!

Congratulations to Ashish and Ksenia as well as Matthias and Marcel - and many thanks to everyone else who contributed to this quick and successful Project.

21.09.2016 - Vacant position for technician

Job opening !!! Please have a look at our site "Open Positions"... 

10.08.16 - Lab Outing

After our lab meeting today, we will go for our August lab outing... if you want to discuss science and beyond, you can meet uns in the "Extrablatt" tonight...

28.07.16 - Lab Inning

The Lab Outing for July is more a Lab Inning: our latest addition to the lab comes to visit. Sadly, there are no lab coats in size 50 for toddlers...

27.07.16 - FEBS Anniversary Prize

And another recognition of our research work: today, the Federation of European Biochemical Societies (FEBS) has awarded Sven with the 2016 Anniversary Prize!

09.06.16 - New future lab member arrived...

Congratulations!

04.06.16 - Accepted

Good news from our collaboration partners in Israel, Aldema Sas-Chen and Yosef Yarden: our manuscript on the role of LIMT, a novel lncRNA that inhibits metastasis in breast cancer, got accepted in EMBO Molecular Medicine. Congratulations!

25.05.16 - Birthday Lab Outing

This month's lab outing is something special: we celebrate (into) Ksenia's birthday! Karma in Freiburg - known to many, but not yet to us will host us for the evening.

18.05.16 - Housewarming, part II

After the official opening ceremony and the housewarming party for the entire building, we will now have the second part of the housewarming activities... with a much more selective group of attendees: the left half of the second floor... come and join in. 

11.05.16 - Sonam's review published

Sonam's review on the role of lncRNAs in migration, invasion and metastasis was published in the International Journal of Cancer.

10.05.16 - Dinner

After an intense day and the shock in the middle of the seminar, we earned our dinner and test out the Mexican restaurant next door... good food, but since there was a large group ahead of us, we had to wait for a long time before we could get back to the lab.

10.05.16 - Seminar at SFB 992

Today, Sven presents our projects at the SFB 992 "Medical Epigenetics" here in Freiburg.

Surprise right in the middle of the presentation: Sven's computer dies... an improvised Q&A session and a quick replacement from Ksenia save the seminar...

03.05.16 - "Ein klein Deutschkurs"

A surprise in the morning... a seminar in German for our international lab, but we took as "ein klein Deutschkurs"... and repeated the content of the instructions later in our lab Meeting in English.

02.05.16 - Cell culture

After the equipment of our lab is now almost complete and we spent the last months with a lot of planning and bioinformatical analyses for our running projects, we have started the cell culture today. Finally, our lab is fully operational.

01.05.16 - EMBO Mol Med Review

Right in time for our reunion meeting in Heidelberg, the review article written in the summer academy last year has now appeared in print in EMBO Molecular Medicine. Enjoy reading!

29.04.16 - Accepted

Good news from our partner lab at the DKFZ: Nucleic Acids Research has accepted our manuscript on splicing isoforms of the microRNA processing factor Drosha for publication. Congratulations to Steffen and Steffi, the shared first authors of this story!

22.04.16 - ZTZ Housewarming

The Center for Translational Cell Research (ZTZ) will celebrate housewarming today! All members of this new center join for short presentations from each group in the building, a rallye through the ZTZ and an evening with food, music, dancing and GATTACA (geneticists will know why the title is in capital letters).

20.04.16 - Research Meeting Thoracic Surgery

The Department of Thoracic Surgery meets today in the ZTZ lecture hall for its research meeting. Members of the new division and clinical fellows present and discuss their latest exciting results from basic science and clinical studies.

13.04.16 - Lab Outing: Bowling

A new month - a new lab outing. Tonight, we will all go Bowling since this is not that far from the lab. Now, everyone knows Sven's story about the Homer Simpson bowling socks ... and who can really master thie pins.

01.04.16 - Welcome

Dr. Chul-Min Yang from the NIH joins us today as a new postdoctoral fellow: Welcome!

10.03.16 - Lab Outing March

Our first - of hopefully many - lab outings is taking place. Since many of us are new to Freiburg, we enjoy a guided tour through the old town followed by a nice dinner in town.

05.03.16 - Chairs

The title says it all... little things can make us very happy these days.

03.03.16 - SGBM

Today, Sven has been appointed as principal investiogator in the Spemann Graduate School of Biology and Medicine (SGBM).

01.03.16 - Start reloaded

Now, the new building of the ZTZ at Breisacher Str. 115 in Freiburg is indeed move-in ready (for the largest part) and our group really starts: Sven, Sonam and Ksenia join from the DKFZ in Heidelberg and Andrea Becker joins the lab as a new member while Olga Mayer has already been part of the Department of Thoracic Surgery.

At the top of our wish list yet to come: chairs!

17.02.16 - Accepted

Now, it is for everyone to see what Sven did last summer:

He was leading a group of 22 talented students from all life sciences in a summer academy organized jointly by the German Academic Scholarship Foundation and the Young Academy held at the Moastery of Roggenburg. Within only one week, they searched through more than 2100 scientific publications to distill the first of its kind review article on the topic of "The dark matter of the cancer genome: Aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations". Today, this manuscript has been accepted for publication in the journal EMBO Molecular Medicine.

04.02.16 - Accepted

Today, Sonam's review on the role of lncRNAs in migration, invasion and metastasis was accepted for publication in the International Journal of Cancer. Congratulations!

15.01.16 - SFB 850 Cell Migration

Sonam presents her project on the role of lncRNAs in cell migration, metastasis and EMT at the SFB 850 "Control of Cell Motility in Morphogenesis, Cancer Invasion and Metastasis". Congratulations on a successful presentation!

01.01.16 - Start

Today, is officially the first day of the new Division of Cancer Research in the Department of Thoracic Surgery at the Medical Faculty and Medical Center of the University of Freiburg.

But... no space for us, so the "real" start of our division will be in March when the brandnew building will hopefully be move-in ready.

Division of Cancer Research

Department of Thoracic Surgery

Center for Translational Cell Research (ZTZ)
Breisacher Str. 115
D-79106 Freiburg

 

Prof. Dr. Sven Diederichs

Division Head

Phone:
+49 761 270-77571
E-Mail:
lung-cancer-research
@uniklinik-freiburg.de
 

More than 70% of the human Genome (blue) is transcribed into RNA forming the Transcriptome (red), while only less than 2% of the genome are needed to produce all proteins in a human cell constituting the Proteome (yellow).

RNA Biology

A particular emphasis of our research lies on the Molecular Biology of RNA and its associated molecules.

Recent insights into RNA biology induced a paradigm shift towards the recognition of RNAs as functionally important molecules - beyond serving as messengers for protein-encoding genes. A large fraction of the human genome is transcribed into RNA (more than 70%), while only 2% are protein-encoding. Non-protein-coding RNAs execute important functions in the cell. Very short non-coding RNAs, the microRNAs, play important roles in gene regulation. The tumor-suppressive or oncogenic role of many microRNAs and their frequent deregulation in tumors allow a first glimpse of the striking role that non-coding RNAs could play in cancer. Novel long non-coding RNAs (ncRNA, lncRNA, lincRNA) fulfill important functions in epigenetic regulation, chromatin remodeling or splicing. Taken together, the human cell contains many more RNAs than previously anticipated and many of them might just await their discovery as functionally important molecules in cancer.

Our research focuses on long non-coding RNAs (lncRNAs) and their role in cancer. Based on expression profiling using microarrays as well as deep RNA sequencing of the whole transcriptome, we elucidate the cellular and molecular functions of differentially regulated ncRNAs in cancer using innovative techniques like the CRISPR/Cas9 system, in vivo RNA Affinity Purification and our own customized siRNA and CRISPR libraries targeting specifically lung cancer-associated lncRNAs. Our RNAi screens have uncovered numerous lncRNAs controlling several hallmarks of cancer including cancer cell viability, mitosis and Migration.

An emerging Topic of particular importance in our lab are RNA-Protein complexes, especially the new concept of RNA Dependence: R-DeeP (Mol Cell 2019).