BIOQUANT

Jan-Philipp Mallm

Over the last years the sequencing field has moved quickly and many methods have been developed that use deep-sequencing readouts to assess how the chromatin structure, epigenome and the transcriptome are linked.
Within the Heidelberg Center for Personalized Oncology (DKFZ-HIPO), the CHromatin And RNA Methods (CHARM) lab is dedicated to develop and adapt genome-wide chromatin and RNA methods for primary patient material. Workflows for different tumor entities, such as 3D cell culture, solid tumors and PBMCs, are carefully validated.

At this stage, ChIPseq of histone modifications, MNase-seq (to determine nucleosome positions), detection of accessible chromatin regions and tagmentation-based bisulfite sequencing have already been successfully applied within the HIPO program. A collection of validated antibodies for histone modifications and certain chromatin interacting proteins is available. Next, we plan to add the analysis of spatial genome folding via 3C/Hi-C methods. In addition, as a more long-term goal, we aim to establish and develop single-cell genomics, transcriptomics and epigenomics methods to address tumor heterogeneity.

All sequencing libraries are sequenced at the DKFZ High Throughput Sequencing Unit (GPCF) with subsequent data analysis by the HIPO bioinformatics group.

Our goal is to provide a comprehensive view on the regulation of the cancer genome to foster new strategies for personalized cancer treatment.

 

https://www.hipo-heidelberg.org

 

Scientific Background

  • Since 10/2014 Head of the Chromatin and RNA (CHARM) methods lab, Heidelberg Center for Personalized Oncology (HIPO)
  • 01/2013 - 09/2014 Postdoc in the Research Group Genome Organization & Function, research topic: Alteration of epigenetic modifications in CLL patients
  • 10/2008 - 12/2012 PhD student in the Research Group Genome Organization & Function, research topic: Chromatin features defining potency of embryonic stem cells and tumor initiating cells
  • 2008 Master in Molecular Biotechnology

  • 2005-2006 Visiting Student University of Sussex, UK

 

Publications

Mattout A, Aaronson Y, Sailaja BS, Raghu Ram EV, Harikumar A, Mallm JP, Sim KH, Nissim-Rafinia M, Supper E, Singh PB, Sze SK, Gasser SM, Rippe K, Meshorer E. Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells. Genome Biol. 2015 Sep 28; 16:213.

 

Junge KM, Bauer T, Geissler S, Hirche F, Thürmann L, Bauer M, Trump S, Bieg M, Weichenhan D, Gu L, Mallm JP, Ishaque N, Mücke O, Röder S, Herberth G, Diez U, Borte M, Rippe K, Plass C, Hermann C, Stangl GI, Eils R, Lehmann I. Increased vitamin D levels at birth and in early infancy increase offspring allergy risk-evidence for involvement of epigenetic mechanisms. J Allergy Clin Immunol. 2015 Aug 15.

 

Mallm JP, Rippe K. Aurora Kinase B Regulates Telomerase Activity via a Centromeric RNA in Stem Cells. Cell Rep. 2015 Jun 16;11:1667-78.

 

Campos B, Weisang S, Osswald F, Ali R, Sedlmeier G, Bageritz J, Mallm JP, Hartmann C, von Deimling A, Popanda O, Goidts V, Plass C, Unterberg A, Schmezer P, Burhenne J, Herold-Mende C. Retinoid resistance and multifaceted impairment of retinoic acid synthesis in glioblastoma. Glia. 2015 Oct; 63:1850-9.

 

Yearim A, Gelfman S, Shayevitch R, Melcer S, Glaich O, Mallm JP, Nissim-Rafinia M, Cohen AH, Rippe K, Meshorer E, Ast G. HP1 is involved in regulating the global impact of DNA methylation on alternative splicing. Cell Rep. 2015 Feb 24; 10:1122-34.

 

Hick M, Herrmann U, Weyer SW, Mallm JP, Tschäpe JA, Borgers M, Mercken M, Roth FC, Draguhn A, Slomianka L, Wolfer DP, Korte M, Müller UC. Acute function of secreted amyloid precursor protein fragment APPsα in synaptic plasticity.
Acta Neuropathol. 2015 Jan;129 :21-37.

 

Müller-Ott K, Erdel F, Matveeva A, Mallm JP, Rademacher A, Hahn M, Bauer C, Zhang Q, Kaltofen S, Schotta G, Höfer T, Rippe K. Specificity, propagation, and memory of pericentric heterochromatin. Mol Syst Biol. 2014 Aug 18;10:746.

 

Teif VB, Beshnova DA, Vainshtein Y, Marth C, Mallm JP, Höfer T, Rippe K. Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Res. 2014 Aug; 24:1285-95.

 

 

Jäger N, Schlesner M, Jones DT, Raffel S, Mallm JP, Junge KM, Weichenhan D, Bauer T, Ishaque N, Kool M, Northcott PA, Korshunov A, Drews RM, Koster J, Versteeg R, Richter J, Hummel M, Mack SC, Taylor MD, Witt H, Swartman B, Schulte-Bockholt D, Sultan M, Yaspo ML, Lehrach H, Hutter B, Brors B, Wolf S, Plass C, Siebert R, Trumpp A, Rippe K, Lehmann I, Lichter P, Pfister SM, Eils R. Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer. Cell. published online 17 October 2013.

 

Hahn M, Dambacher S, Dulev S, Kuznetsova AY, Eck S, Wörz S, Sadic D, Schulte M, Mallm JP, Maiser A, Debs P, von Melchner H, Leonhardt H, Schermelleh L, Rohr K, Rippe K, Storchova Z, Schotta G. Suv4-20h2 mediates chromatin compaction and is important for cohesin recruitment to heterochromatin. Genes Dev. 2013 Apr 15; 27:859-72.

 

Teif VB, Erdel F, Beshnova DA, Vainshtein Y, Mallm JP, Rippe K. Taking into account nucleosomes for predicting gene expression. Methods. 2013 Jul; 62:26-38.

 

Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K. Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol. 2012 Nov; 19:1185-92.

 

Caurdon-Herger M, Müller-Ott K, Mallm JP, Marth C, Schmidt U, Fejes-Tóth K, Rippe K. Coding RNAs with a non-coding function: maintenance of open chromatin structure. Nucleus. 2011 Sep;2: 410-424

 

Mallm JP, Tschäpe JA, Hick M, Filippov MA, Müller UC. Generation of conditional null alleles for APP and APLP2. Genesis. 2010 Mar;48:200-6.

 

Plaimas K, Mallm JP, Oswald M, Svara F, Sourjik V, Eils R, König R. Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol. 2008 Jul 24;2:67

 

Fatumo S, Plaimas K, Mallm JP, Schramm G, Adebiyi E, Oswald M, Eils R, König R. Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico. Infect Genet Evol. 2008 Jan 20.

 

 

Contact

Jan-Philipp Mallm

DKFZ & BioQuant Center

Chromatin and RNA methods (CHARM) lab

Im Neuenheimer Feld 267

69120 Heidelberg

Germany


BioQuant room 325, 3rd floor

Tel.: +49-6221-54-51257

Fax: +49 6221 54 51487


e-mail: jan-philipp.mallm (at) bioquant.uni-heidelberg.de

e-mail: j.mallm(a)dkfz.de