Milk micro-RNA information and lactation

New Signals in milk?

- Markers of milk and lactation status ? - Signal infant development ?

Comparative analysis of milk miRNA data…

Christophe Lefèvre, BioDeakin,. Deakin University, Geelong VIC Australia

Biogenesis of miRNA

MicroRNAs are produced from either their own genes or from introns.

~22 nt (18-24)

Mode of Action of miRNAs

*RISC: RNA-induced silencing complex

Function of miRNAs • MiRNAs constitute an important new class of regulatory bio-molecules. • implicated, through their broad post transcriptional inhibitory effect on gene

expression in the control of : – Differentiation – metabolism – cell morphology – polarity – migration – signal transduction – cellular communication – organogenesis – developmental processes * Found in most multicellular organism (also found in green alga Chlamydomonas reinhardtii, casting shadow on previous suggestions that miRNAs might have helped to drive evolution to a multicellular state, Chen et. Al. Genes Dev. 21, 1190–1203 (2007)).

Biogenesis of secreted miRNAs

exosome signalling

Antigen presentation

Blood coagulation

Neuron gene transfer

=> Alternative secretion of proteins Shuttle for RNA, proteins, infectious agents: Shuttle for miRNAs (function still to be established)?

- Inflammation -Tumor growth (EGFRvIII)

-Cell invasion through ECM remodeling (MMPs) …

Identification of human milk miRNAs • The MicroRNA Spectrum in 12 Body Fluids J. A. Weber, D. H. Baxter, S. Zhang, D. Y. Huang, K. H. Huang, Ming Jen Lee, D. J. Galas and K. Wang. Clinical Chemistry 56:11 and Genetics 1733–1741 (2010)

- MicroRNAs are ubiquitous in all the body fluid types tested. - Fluid type–specific miRNAs may have functional roles associated with the surrounding tissues.

* miR-518c* was uniquely detected in breast milk and is also highly expressed in the placenta

Identification of human milk miRNAs

• microRNA as a new immune-regulatory agent in breast milk. Kosaka et al.. Silence 2010, 1:7

- high expression levels of immune-related miRNAs in the first 6 months of lactation.

- miRNAs are stable even in very acidic conditions, indicating that breast milk allows dietary intake of miRNAs by infants.

- Present in CD63 micro-vesicle exosome fraction =>breast milk may modulate the development of the infant's immune system. =>suggests the transfer of genetic material as miRNA from human to human occurs by means other than through sexual reproduction.

Specificity of milk miRNA

Immune-related miRNA levels in human breast milk (n = 5) and serum (n = 6) of healthy subjects measured by qRT-PCR. Kosaka et al. Silence 2010 1:7 doi:10.1186/1758-907X-1-7

miRNAs in bovine milk

Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products. Chen et. Al, Cell research 2010. - 245 miRNAs in raw milk - individual miRNAs can be significantly altered during lactation process - may be a more accurate indicator to reflect the quality alteration of milk -7 miRNAs that have a relatively consistent expression throughout lactation expression profile of these 7milk-specific miRNAs can serve as an ideal biomarker for discriminating poor-quality or “manipulated” milk from pure raw milk, as well as for the quality control of commercial milk products, such as fluid milk and powdered formula milk. The findings provide a basis for understanding the physiological role of milk miRNAs and a new potential standard for determining the quality of raw milk or milk-related commercial products.

Identification of milk miRNAs bovine milk

Isolation of bovine milk-derived microvesicles carrying mRNAs and microRNAs. Hata et. Al, BBRC 396 2010, 528-533. - 1700 and 1000 ng of total RNA, in which small RNAs were major components, was contained inside the microvesicles isolated from 6 ml of colostrum and mature milk, despite high RNase activity in the milk. - Moreover, a considerable amount of mammary gland and immune-related microRNAs were present in the milk-derived microvesicles. - Acidification of milk to mimic gastrointestinal tract did not mostly affected RNA yield and quality. - The milk related gene transcripts were detected in cultured cells when incubated with milk-derived microvesicles, suggesting cellular uptake of the microvesicle RNA contents.

“Our findings suggest that bovine breast milk contains RNAs capable for being transferred to living cells and involved in the development of calf’s gas- trointestinal and immune systems”.

Role of miRNAs in mammary gland development

• Characterisation of microRNA expression in post-natal mouse mammary gland development. S. Avril-Sassen et. al. BMC Genomics 2009, 10:548

- One third (n = 102) of all murine miRNAs analysed were detected during mammary gland development - MicroRNAs were expressed in likely co-regulated clusters during mammary gland development. Breast cancer-associated

miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation provide new avenues for research into mammary gland biology and generate candidates for functional validation.

• miR-212 and miR-132 are required for epithelial stromal interactions necessary for mouse mammary gland development. A. Ucar et. Al. NATURE GENETICS

VOLUME 42 | NUMBER 12 | DECEMBER 2010. via regulation of stromal MMP-9 production. • A microRNA, miR-101a, controls mammary gland development by regulating

cyclooxygenase-2 expression. Tanaka et. Al. Differentiation, Volume 77, Issue 2, February 2009, Pages 181-187

• MiR-126-3p regulates progesterone receptors and involves development and lactation of mouse mammary gland. Wei Cui, Qingzhang Li, Li Feng and Wei Ding. MOLECULAR AND CELLULAR BIOCHEMISTRY Volume 355, Numbers 1-2, 17-25

• miR-214 regulates Lactoferrin expression and pro-apoptotic function in mammary epithelial cells. Y. Liao et. Al. Journal of Nutrition, 2010 p 1552.

• Selective release of microRNA species from normal and malignant mammary epithelial cells. L. Pigatiet. Al. PLOS one Volume 5, 10 p , 2010 p 1552.

Plant food miRNA is detected in blood and regulate gene expression

• Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.Lin Zhang et al. Cell Research (2011) :1-20.

• 30 miRNAs from plants detected in human, cow and mice serum (5% of sequences) • miR168a and miR156a 0.5% of total serum RNA reads • > Half in microvesicles • Transfected Caco cells express miRNA168a/AGO2 in microvesicules which can be taken by HEPG2

cells (with improved efficiency of transfer) • 2O’-methylation confer some extra stability • Diet effect confirmed (rice miRNA 168a) • Plant miRNAs found in many tissue including liver (up to ~853 copies/cell, with some selectivity) • miRNA168a targets LDL receptor adaptor protein 1 in exon4 and can decrease plasma removal

(increase plasma LDL cholesterol) • Plant miRNA are stable pH 2, 37C, 6 hours

• =>miRNAs in food can regulate target gene expression in mammals • =>food miRNAs are resistant to digestion, can cross the intestinal epithelia, to be secreted in

circulating microvesicles allowing tissue uptake of functional miRNAs • => miRNA can be transferred from one species to another

The case for micro-RNA signaling in milk and dairy sciences

• Role in mammary function established • Present in milk • Some selectivity and compartment distribution • Can cross the gastro-intestinal barrier and regulate gene expression

⇒May have a role in infant immunity and development.

Emerging role of miRNAs in Dairy sciences and industry: ⇒A new way to look at lactation ⇒New milk quality markers providing a new and deep insight into milk synthesis and function…

Milks micro-RNA in the mammalian kingdom • Sequencing in human, pig, cow, buffalo, goat • Sequencing in marsupial wallaby

s

* Agilent peaks in monotremes, seal, alpaca…

Comparative analysis of sequencing data >100/M (10-4) in >3 samples, DSAP annotation (cow UMD3.1) except for cow data

Comparative analysis of sequencing data >100/M (10-4) in >3 samples, DSAP annotation (cow UMD3.1) except for cow data

Outsider Lactation test? - failure - performance

Comparative analysis of sequencing data >100/M (10-4) in >3 samples, DSAP annotation (cow UMD3.1) except for cow data

Mir-148a

< 4 samples

Mir-148a

Technical? Annotation? Raw data: not available!

milk selection effect? (>240 miRs)

Intra-specific correlation

Colostrum/milk

Buffalo colostrum exoquick/whey

(cm-a only) miR-223

Buffalo colostrum Buffalo milk human milk

Pig day0 milk Cow colostrum

Human /pig day 0

Pig high

Human high

Cow milk/colostrum(blue) or serum(red)

Wallaby

Buffalo milk human pig

Milk markers

Some species enriched milk miRNAs

conclusion • All mammals drink milk miRNA • miRNA profiling is a powerful technique for

milk/lactation testing • Some features of miRNA composition are likely to be

highly conserved while others are variable within and between species

• Challenges remain to reveal the full potential of miRNA profiling for lactation research and the dairy industry – Distribution, biogenesis, activity of milk miRNA

• open data policies and funding will facilitate comparative approaches…

Comparative Lactation Biology Mir-Milk: an interactive milk miRNA browser

for collaborative comparative lactation genomics? Bioinf:

Amit Kumar Philip Church Adam Wong Lab: Sanjana Kuruppath Khanh Phuong Ngo Vengama Naidu Modepalli Kevin Nicholas

New Signals in milk?