Malene Lindholm

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About me

I am a translational scientist with a PhD in medical science working at the intersection of cardiometabolic disease, bioinformatics and molecular biology, currently serving as junior faculty and Director of the Human Molecular Moonshot at Stanford University.

Articles

Article: BMC BIOLOGY. 2024;22(1):147
DNA methylation of exercise-responsive genes differs between trained and untrained men
Geiger C; Needhamsen M; Emanuelsson EB; Norrbom J; Steindorf K; Sundberg CJ; Reitzner SM; Lindholm ME
Journal article: CELL GENOMICS. 2024;4(6):100421
Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures
Nair VD; Pincas H; Smith GR; Zaslavsky E; Ge Y; Amper MAS; Vasoya M; Chikina M; Sun Y; Raja AN; Mao W; Gay NR; Esser KA; Smith KS; Zhao B; Wiel L; Singh A; Lindholm ME; Amar D; Montgomery S; Snyder MP; Walsh MJ; Sealfon SC
Journal article: CELL METABOLISM. 2024;36(6):1411-1429.e10
The mitochondrial multi-omic response to exercise training across rat tissues
Amar D; Gay NR; Jimenez-Morales D; Beltran PMJ; Ramaker ME; Raja AN; Zhao B; Sun Y; Marwaha S; Gaul DA; Hershman SG; Ferrasse A; Xia A; Lanza I; Fernandez FM; Montgomery SB; Hevener AL; Ashley EA; Walsh MJ; Sparks LM; Burant CF; Rector RS; Thyfault J; Wheeler MT; Goodpaster BH; Coen PM; Schenk S; Bodine SC; Lindholm ME
Journal article: NATURE. 2024;629(8010):174-183
Temporal dynamics of the multi-omic response to endurance exercise training
Journal article: NATURE METABOLISM. 2024;6(5):963-979
Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue
Many GM; Sanford JA; Sagendorf TJ; Hou Z; Nigro P; Whytock KL; Amar D; Caputo T; Gay NR; Gaul DA; Hirshman MF; Jimenez-Morales D; Lindholm ME; Muehlbauer MJ; Vamvini M; Bergman BC; Fernandez FM; Goodyear LJ; Hevener AL; Ortlund EA; Sparks LM; Xia A; Adkins JN; Bodine SC; Newgard CB; Schenk S; Adkins JN; Armenteros JJA; Amar D; Amper MAS; Ashley E; Asokan AK; Avila-Pacheco J; Bae D; Bamman MM; Bararpour N; Barnes J; Bergman BC; Bodine SC; Buford TW; Burant CF; Caputo T; Carbone NP; Carr SA; Chambers TL; Chavez C; Chiu R; Clish CB; Cutter GR; Dasari S; Dennis C; Evans CR; Fernandez FM; Gagne N; Gaul DA; Gay NR; Ge Y; Goodpaster BH; Goodyear LJ; Gritsenko MA; Hansen JR; Hennig KM; Hevener AL; Hirshman MF; Hou Z; Huffman KM; Hung C-J; Hutchinson-Bunch C; Ilkayeva O; Ivanova AA; Beltran PMJ; Jimenez-Morales D; Jin CA; Kachman MT; Keshishian H; Kraus WE; Lanza I; Lester B; Li JZ; Lindholm ME; Lira AK; Liu X; Maner-Smith KM; Many GM; May S; Monroe MR; Montgomery S; Moore RJ; Moore SG; Muehlbauer MJ; Nachun D; Nair KS; Nair V; Raja AN; Nestor MD; Newgard CB; Nigro P; Nudelman G; Ortlund EA; Petyuk VA; Piehowski PD; Pincas H; Qian W-J; Raskind A; Rasmussen BB; Rooney JL; Rushing S; Sagendorf TJ; Samdarshi M; Sanford JA; Schenk S; Sealfon SC; Smith KS; Smith GR; Snyder M; Sparks LM; Stowe CL; Talton JW; Teng C; Thalacker-Mercer A; Tracy R; Trappe TA; Vamvini M; Vasoya M; Vetr NG; Volpi E; Walkup MP; Walsh MJ; Wheeler MT; Whytock KL; Wu S; Xia A; Zaslavsky E; Zebarjadi N; Zhang T; Zhao B; Zhen J
Article: ISCIENCE. 2024;27(1):108638
Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training
Emanuelsson EB; Arif M; Reitzner SM; Perez S; Lindholm ME; Mardinoglu A; Daub C; Sundberg CJ; Chapman MA
Article: AGING CELL. 2024;23(1):e13859
Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle
Voisin S; Seale K; Jacques M; Landen S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Thompson J-LM; Doering TM; Lindholm ME; Walsh C; Davison G; Irwin R; McBride C; Hansson O; Asplund O; Heikkinen AE; Piirila P; Pietilainen KH; Ollikainen M; Blocquiaux S; Thomis M; Dawn CK; Sharples AP; Eynon N
Article: ANTIOXIDANTS. 2023;12(12):2043
Comparing the Blood Response to Hyperbaric Oxygen with High-Intensity Interval Training-A Crossover Study in Healthy Volunteers
Kjellberg A; Lindholm ME; Zheng X; Liwenborg L; Rodriguez-Wallberg KA; Catrina S-B; Lindholm P
Article: CIRCULATION-GENOMIC AND PRECISION MEDICINE. 2021;14(6):e003419
Mono- and Biallelic Protein-Truncating Variants in Alpha-Actinin 2 Cause Cardiomyopathy Through Distinct Mechanisms
Lindholm ME; Jimenez-Morales D; Zhu H; Seo K; Amar D; Zhao C; Raja A; Madhvani R; Abramowitz S; Espenel C; Sutton S; Caleshu C; Berry GJ; Motonaga KS; Dunn K; Platt J; Ashley EA; Wheeler MT
Article: NATURE COMMUNICATIONS. 2021;12(1):3471
Time trajectories in the transcriptomic response to exercise - a meta-analysis
Amar D; Lindholm ME; Norrbom J; Wheeler MT; Rivas MA; Ashley EA
Article: MEDICINE & SCIENCE IN SPORTS & EXERCISE. 2020;52(8):1679-1690
Exercise Induces Different Molecular Responses in Trained and Untrained Human Muscle
Moberg M; Lindholm ME; Reitzner SM; Ekblom B; Sundberg C-J; Psilander N
Article: JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE. 2020;11(4):887-898
An epigenetic clock for human skeletal muscle
Voisin S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Doering TM; Thompson J-LM; Benedict C; Cedernaes J; Lindholm ME; Craig JM; Rowlands DS; Sharples AP; Horvath S; Eynon N
Article: CELL REPORTS. 2020;31(12):107808
Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women
Chapman MA; Arif M; Emanuelsson EB; Reitzner SM; Lindholm ME; Mardinoglu A; Sundberg CJ
Article: CONTEMPORARY CLINICAL TRIALS COMMUNICATIONS. 2018;10:148-153
Metabolic and functional changes in transgender individuals following cross-sex hormone treatment: Design and methods of the GEnder Dysphoria Treatment in Sweden (GETS) study
Wiik A; Andersson DP; Brismar TB; Chanpen S; Dhejne C; Ekstrom TJ; Flanagan JN; Holmberg M; Kere J; Lilja M; Lindholm ME; Lundberg TR; Maret E; Melin M; Olsson SM; Rullman E; Wahlen K; Arver S; Gustafsson T
Article: NATURE COMMUNICATIONS. 2018;9(1):1612
Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study
DeBoever C; Tanigawa Y; Lindholm ME; McInnes G; Lavertu A; Ingelsson E; Chang C; Ashley EA; Bustamante CD; Daly MJ; Rivas MA
Article: PLOS GENETICS. 2016;12(9):e1006294
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts
Lindholm ME; Giacomello S; Solnestam B; Fischer H; Huss M; Kjellqvist S; Sundberg CJ
Article: EXPERIMENTAL PHYSIOLOGY. 2016;101(1):28-32
Skeletal muscle hypoxia-inducible factor-1 and exercise
Lindholm ME; Rundqvist H
Article: BMC GENOMICS. 2015;16(1):475
The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling
Lindskog C; Linne J; Fagerberg L; Hallstrom BM; Sundberg CJ; Lindholm M; Huss M; Kampf C; Choi H; Liem DA; Ping P; Varemo L; Mardinoglu A; Nielsen J; Larsson E; Ponten F; Uhlen M
Article: EPIGENETICS. 2014;9(12):1557-1569
An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training
Lindholm ME; Marabita F; Gomez-Cabrero D; Rundqvist H; Ekstrom TJ; Tegner J; Sundberg CJ
Article: FASEB JOURNAL. 2014;28(10):4571-4581
The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing
Lindholm ME; Huss M; Solnestam BW; Kjellqvist S; Lundeberg J; Sundberg CJ
Article: AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY, INTEGRATIVE AND COMPARATIVE PHYSIOLOGY. 2014;307(3):r248-r255
Negative regulation of HIF in skeletal muscle of elite endurance athletes: a tentative mechanism promoting oxidative metabolism
Lindholm ME; Fischer H; Poellinger L; Johnson RS; Gustafsson T; Sundberg CJ; Rundqvist H
Article: EPIGENETICS. 2013;8(3):333-346
An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform
Marabita F; Almgren M; Lindholm ME; Ruhrmann S; Fagerstrom-Billai F; Jagodic M; Sundberg CJ; Ekstrom TJ; Teschendorff AE; Tegner J; Gomez-Cabrero D
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All other publications

Preprint: BIORXIV. 2023;BIORXIV
Multi-omic identification of key transcriptional regulatory programs during endurance exercise training.
Smith GR; Zhao B; Lindholm ME; Raja A; Viggars M; Pincas H; Gay NR; Sun Y; Ge Y; Nair VD; Sanford JA; Amper MAS; Vasoya M; Smith KS; Montgomery S; Zaslavsky E; Bodine SC; Esser KA; Walsh MJ; Snyder MP; MoTrPAC Study Group
Preprint: BIORXIV. 2023;BIORXIV
Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue.
Many GM; Sanford JA; Sagendorf TJ; Hou Z; Nigro P; Whytock K; Amar D; Caputo T; Gay NR; Gaul DA; Hirshman M; Jimenez-Morales D; Lindholm ME; Muehlbauer MJ; Vamvini M; Bergman B; Fern Ndez FM; Goodyear LJ; Ortlund EA; Sparks LM; Xia A; Adkins JN; Bodine SC; Newgard CB; Schenk S; MoTrPAC Study Group
Preprint: BIORXIV. 2023;BIORXIV
The mitochondrial multi-omic response to exercise training across tissues.
Amar D; Gay NR; Jimenez-Morales D; Beltran PMJ; Ramaker ME; Raja AN; Zhao B; Sun Y; Marwaha S; Gaul D; Hershman SG; Xia A; Lanza I; Fernandez FM; Montgomery SB; Hevener AL; Ashley EA; Walsh MJ; Sparks LM; Burant CF; Rector RS; Thyfault J; Wheeler MT; Goodpaster BH; Coen PM; Schenk S; Bodine SC; Lindholm ME; MoTrPAC Study Group
Preprint: BIORXIV. 2022
Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle
Voisin S; Seale K; Jacques M; Landen S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Thompson J-LM; Doering TM; Lindholm ME; Walsh C; Davison G; Irwin R; McBride C; Hansson O; Asplund O; Heikkinen AE; Piirilä P; Pietiläinen KH; Ollikainen M; Blocquiaux S; Thomis M; Coletta DK; Sharples AP; Eynon N
Preprint: BIORXIV. 2022
Temporal dynamics of the multi-omic response to endurance exercise training across tissues
Group MS; Amar D; Gay NR; Beltran PMJ; Adkins JN; Armenteros JJA; Ashley E; Avila-Pacheco J; Bae D; Bararpour N; Burant C; Clish C; Cutter G; Dasari S; Dennis C; Evans CR; Fernández FM; Gaul D; Ge Y; Gerszten R; Goodyear LJ; Hou Z; Ilkayeva O; Ivanova AA; Jimenez-Morales D; Kachman MT; Keshishian H; Kraus WE; Lanza IR; Li J; Lindholm ME; Lira AC; Many GM; Marwaha S; Miller ME; Muehlbauer MJ; Nair KS; Nair VD; Raja AN; Newgard C; Ortlund EA; Piehowski PD; Presby DM; Qian W-J; Rooney JL; Sanford JA; Savage E; Sealfon SC; Smith GR; Smith KS; Steep A; Stowe CL; Sun Y; Tracy R; Vetr NG; Walsh MJ; Wu S; Zhang T; Zhao B; Zhen J; Albertson BG; Amper MAS; Balci AT; Bamman M; Barton ER; Bergman B; Bessesen D; Booth F; Bouverat B; Buford TW; Caputo T; Chambers TL; Chavez C; Chikina M; Chiu R; Cicha M; Coen PM; Cooper D; Cornell E; Dalton KP; De Sousa LO; Farrar R; Gadde K; Gagne N; Goodpaster BH; Gritsenko MA; Guevara K; Haddad F; Hansen JR; Harris M; Hastie T; Hennig KM; Hershman SG; Hevener A; Hirshman MF; Hsu F-C; Huffman KM; Hung C-J; Hutchinson-Bunch C; Jackson BE; Jankowski C; Jin CA; Johannsen NM; Ke BG; Kohrt WM; Kramer KS; Leeuwenburgh C; Lessard SJ; Lester B; Liu X; Lu C-J; Makarewicz NS; Maner-Smith KM; Mani; Marjanovic N; Marshall A; May S; Melanson E; Monroe ME; Moore RJ; Moore S; Moreau KL; Mundorff CC; Musi N; Nachun D; Nestor MD; Newton RL; Nicklas B; Nigro P; Nudelman G; Pahor M; Pearce C; Petyuk VA; Pincas H; Powers S; Radom-Aizik S; Ramachandran K; Ramaker ME; Ramos I; Rankinen T; Raskind A; Rasmussen BB; Ravussin E; Rector RS; Rejeski WJ; Richards C; Rirak S; Robbins JM; Rubenstein AB; Ruf-Zamojski F; Rushing S; Sagendorf TJ; Samdarshi M; Schauer IE; Schwartz R; Seenarine N; Soni T; Sparks LM; Teng C; Thalacker-Mercer A; Thyfault J; Tibshirani R; Trappe S; Trappe TA; Uppal K; Vangeti S; Vasoya M; Volpi E; Vornholt A; Walkup MP; Williams J; Xia A; Yan Z; Yu X; Zang C; Zaslavsky E; Zebarjadi N; Bodine SC; Carr S; Esser K; Montgomery SB; Schenk S; Snyder MP; Wheeler MT
Conference publication: ACTA PHYSIOLOGICA. 2022;236:57
Do muscles have memory?Molecular effects of training, detraining and retraining
Lindholm ME
Preprint: BIORXIV. 2020
Mono- and bi-allelic protein truncating variants in alpha-actinin 2 cause cardiomyopathy through distinct mechanisms
Lindholm M; Jimenez-Morales D; Zhu H; Seo K; Amar D; Zhao C; Raja A; Madhvani R; Espenel C; Sutton S; Caleshu C; Berry G; Motonaga K; Dunn K; Platt J; Ashley E; Wheeler M
Conference publication: CIRCULATION. 2020;142(Suppl_3)
Abstract 14355: Mono- and Biallelic Structural Variants in Alpha-actinin 2 Cause Contractile Dysfunction and Cardiomyopathy in Humans
Lindholm ME; Zhu H; Seo K; Jimenez-Morales D; Zhao C; Ashley EA; Wheeler MT
Review: CELL. 2020;181(7):1464-1474
Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise
Sanford JA; Nogiec CD; Lindholm ME; Adkins JN; Amar D; Dasari S; Drugan JK; Fernandez FM; Radom-Aizik S; Schenk S; Snyder MP; Tracy RP; Vanderboom P; Trappe S; Walsh MJ
Conference publication: CIRCULATION. 2020;142
Mono- and Biallelic Structural Variants in Alpha-actinin 2 Cause Contractile Dysfunction and Cardiomyopathy in Humans
Lindholm ME; Zhu H; Seo K; Jimenez-Morales D; Zhao C; Ashley EA; Wheeler MT
Preprint: BIORXIV. 2019
Differential response trajectories to acute exercise in blood and muscle
Amar D; Lindholm M; Norrbom J; Wheeler M; Rivas M; Ashley E
Preprint: BIORXIV. 2019
An epigenetic clock for human skeletal muscle
Voisin S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Doering TM; Thompson JM; Benedict C; Cedernaes J; Lindholm ME; Craig JM; Rowlands DS; Sharples AP; Horvath S; Eynon N
Conference publication: JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY. 2019;73(9):1027
NOVEL ALPHA-ACTININ 2 MUTATIONS ARE ASSOCIATED WITH CARDIOMYOPATHY AND HYPERTROPHY IN HUMAN CARDIAC TISSUE AND IPSC-DERIVED CARDIOMYOCYTES
Lindholm M; Zhu H; Huang Y; Ashley EA; Wheeler M
Conference publication: EUROPEAN JOURNAL OF HUMAN GENETICS. 2019;27:1310
Structural variants in Alpha-actinin 2 are associated with cardiomyopathy and hypertrophy in human cardiac tissue and iPSC-derived cardiomyocytes
Lindholm ME; Zhu H; Huang Y; Ashley EA; Wheeler M
Preprint: SSRN ELECTRONIC JOURNAL. 2019
Differential Response Trajectories to Acute Exercise in Blood and Muscle
Amar D; Lindholm ME; Norrbom J; Wheeler MT; Rivas M; Ashley EA
Conference publication: FASEB JOURNAL. 2016;30
Endurance Training Alters Expression of Over 3000 Isoforms and 34 Novel Transcripts in Human Skeletal Muscle
Lindholm M; Giacomello S; Solnestam BW; Fischer H; Kjellqvist S; Huss M; Sundberg CJ
Thesis / dissertation: 2015
The search for human skeletal muscle memory : exercise effects on the transcriptome and epigenome
Lindholm, Maléne
Conference publication: ACTA PHYSIOLOGICA. 2014;211:38
The human skeletal muscle transcriptome - sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing
Lindholm ME; Huss M; Solnestam BW; Kjellqvist S; Lundeberg J; Sundberg CJ
Conference publication: FASEB JOURNAL. 2013;27(S1):1134.1
Endurance training changes the DNA methylation pattern in human skeletal muscle
Lindholm ME; Marabita F; Gomez‐Cabrero D; Fischer H; Tegnér J; Sundberg CJ
Conference publication: FASEB JOURNAL. 2012;26:533.3
Human skeletal muscle histone modifications in response to six weeks of endurance training
Ydfors M; Lindholm M; Sundberg CJ
Conference publication: FASEB JOURNAL. 2012;26:1086.11
Variation of global mRNA expression in biopsies from the same human muscle
Sundberg CJB; Lindholm M; Solnestam BW; Lundberg J; Fischer H
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Grants

Exercise-induced cardiac adaptation in hypertrophic cardiomyopathy
National Heart Lung and Blood Institute
1 July 2022 - 31 December 2024
Genome-scale mechanisms of adaptation in long-term exercise trained humans – skeletal muscle and adipose tissue crosstalk assessed through spatial transcriptomics analysis
Swedish Research Council
1 January 2019 - 31 December 2021

Employments

Affiliated to Research, Department of Physiology and Pharmacology, Karolinska Institutet, 2023-2026

Degrees and Education

Degree Of Doctor Of Philosophy, Department of Physiology and Pharmacology, Karolinska Institutet, 2015
Master Of Medical Science, Karolinska Institutet, 2009

About me

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