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Chromatin accessibility of circulating CD8⁺ T cells differentiates disease severity in IgA nephropathy
Rodrigues, J. C., Haas, M. & Reich, H. N. IgA nephropathy. Clin. J. Am. Soc. Nephrol. 12(4), 677–86 (2017).

Google Scholar
Tomino, Y. Predictors of prognosis in IgA nephropathy. Kaohsiung J. Med Sci. 28(10), 517–20 (2012).

Google Scholar
Joo, Y. S. et al. External validation of the international prediction tool in Korean patients with immunoglobulin a nephropathy. Kidney Res. Clin. Pract. 41(5), 556–66 (2022).

Google Scholar
Yao, X. et al. MicroRNAs in IgA nephropathy. Ren Fail. 43(1), 1298–310 (2021).

Google Scholar
Zhang, Y., Yang, H., Jiang, M. & Nie, X. Exploring the pathogenesis and treatment of IgA nephropathy based on epigenetics. Epigenomics. 15(19), 1017–26 (2023).

Google Scholar
Shema, E., Bernstein, B. E. & Buenrostro, J. D. Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. Nat. Genet. 51(1), 19–25 (2019).

Google Scholar
Spitz, F. & Furlong, E. E. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13(9), 613–26 (2012).

Google Scholar
Ahmed, N. et al. Multi-omic analysis of longitudinal acute myeloid leukemia patient samples reveals potential prognostic markers linked to disease progression. Front. Genet. 15, 1442539 (2024).

Google Scholar
Araki, Y., Fann, M., Wersto, R. & Weng, N. P. Histone acetylation facilitates rapid and robust memory CD8 T cell response through differential expression of effector molecules (eomesodermin and its targets: perforin and granzyme B). J. Immunol. 180(12), 8102–8 (2008).

Google Scholar
Ma, S. et al. Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell. 183(4), 1103–16 (2020).

Google Scholar
Xie, S. et al. T cell responses in immune-mediated IgA nephropathy. J. Leukoc. Biol. 116(3), 523–35 (2024).

Google Scholar
Ruszkowski, J. et al. T cells in IgA nephropathy: role in pathogenesis, clinical significance and potential therapeutic target. Clin. Exp. Nephrol. 23(3), 291–303 (2019).

Google Scholar
Pei, G. et al. Renal interstitial infiltration and tertiary lymphoid organ neogenesis in IgA nephropathy. Clin. J. Am. Soc. Nephrol. 9(2), 255–64 (2014).

Google Scholar
Zheng, Y. et al. Single-cell transcriptomics reveal immune mechanisms of the onset and progression of IgA nephropathy. Cell Rep. 33(12), 108525 (2020).

Google Scholar
Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods. 14(10), 959–62 (2017).

Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9(4), 357–9 (2012).

Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26(6), 841–2 (2010).

Google Scholar
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9(9), R137 (2008).

Google Scholar
Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 489(7414), 57–74 (2012).

Google Scholar
Shin, H. M. et al. Chromatin accessibility of circulating CD8(+) T cells predicts treatment response to PD-1 blockade in patients with gastric cancer. Nat. Commun. 12(1), 975 (2021).

Google Scholar
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26(1), 139–40 (2010).

Google Scholar
Budczies, J. et al. Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization. PLoS One. 7(12), e51862 (2012).

Google Scholar
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 38(4), 576–89 (2010).

Google Scholar
Ivanek OBaR. seqLogo: Sequence logos for DNA sequence alignments. (2023).
Kramer, A., Green, J., Pollard, J. Jr. & Tugendreich, S. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 30(4), 523–30 (2014).

Google Scholar
Yi, M., Nissley, D. V., McCormick, F. & Stephens, R. M. ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications. Sci. Rep. 10(1), 10258 (2020).

Google Scholar
Wertheimer, A. M. et al. Aging and cytomegalovirus infection differentially and jointly affect distinct circulating T cell subsets in humans. J. Immunol. 192(5), 2143–55 (2014).

Google Scholar
Mizutani, S. et al. Loss of RUNX1/AML1 arginine-methylation impairs peripheral T cell homeostasis. Br. J. Haematol. 170(6), 859–73 (2015).

Google Scholar
Doering, T. A. et al. Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. Immunity. 37(6), 1130–44 (2012).

Google Scholar
Paley, M. A. et al. Progenitor and terminal subsets of CD8+ T cells cooperate to contain chronic viral infection. Science. 338(6111), 1220–5 (2012).

Google Scholar
Man, K. et al. Transcription factor IRF4 promotes CD8(+) T cell exhaustion and limits the development of memory-like T cells during chronic infection. Immunity. 47(6), 1129–41 (2017).

Google Scholar
Chandele, A. et al. Formation of IL-7Ralphahigh and IL-7Ralphalow CD8 T cells during infection is regulated by the opposing functions of GABPalpha and Gfi-1. J. Immunol. 180(8), 5309–19 (2008).

Google Scholar
Simundic, A.-M. Diagnostic accuracy—part 1: basic concepts: sensitivity and specificity, ROC analysis STARD statement. Point Care. 11(1), 6–8 (2012).

Google Scholar
Deng, Q. et al. The emerging epigenetic role of CD8+T cells in autoimmune diseases: a systematic review. Front. Immunol. 10, 856 (2019).

Google Scholar
Uchimura, K. et al. The effects of CD40- and interleukin (IL-4)-activated CD23+ cells on the production of IL-10 by mononuclear cells in Graves’ disease: the role of CD8+ cells. Clin. Exp. Immunol. 128(2), 308–12 (2002).

Google Scholar
Xing, L. et al. CD8+HLA-DR+ T cells are increased in patients with severe aplastic anemia. Mol. Med. Rep. 10(3), 1252–8 (2014).

Google Scholar
Blanco, P. et al. Increase in activated CD8+ T lymphocytes expressing perforin and granzyme B correlates with disease activity in patients with systemic lupus erythematosus. Arthritis Rheum. 52(1), 201–11 (2005).

Google Scholar
Jung, S. & Baek, J. H. The potential of T cell factor 1 in sustaining CD8(+) T lymphocyte-directed anti-tumor immunity. Cancers (Basel). 13(3), 515 (2021).

Google Scholar
Grenningloh, R. et al. Ets-1 maintains IL-7 receptor expression in peripheral T cells. J. Immunol. 186(2), 969–76 (2011).

Google Scholar

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It might seem unappetising or even gross to some, but experts say shoppers looking for a nutritious boost in their diet should consider offal.

Animal organs can be high in iron and other essential nutrients, and experts believe the benefits of the meat are being overlooked.

As cost-of-living pressures force one in five Australians to miss meals, they are urging consumers and industry not to undervalue its potential.

Eating animal organ meats, or offal, such as liver, tripe, or brain, is considered sustainable as it reduces the waste of animal by-products. (ABC Capricornia: Claudia Sullivan)

Iconic chef’s first foray into cooking

One Australian who fondly remembers offal-based meals, like sheep’s brain is celebrity chef, author, businesswoman and health advocate Maggie Beer.

Ms Beer said she found offal “irresistible”, and it was also the first dish she ever cooked.

“I was pan-frying chicken livers. I was seven, and my father said, ‘Stop picking at those, there’ll be none left for anyone else,’” Ms Beer said.

“[It] was such a special treat … and a total respecting of an animal by using every part,” she said.

Maggie Beer smiles at the camera while standing in a grove of trees, a bright sunset lighting the field behind her. — Celebrated chef Maggie Beer has been working to change the culture of food in aged care and the quality of life of those living there. (Supplied: Maggie’s Orchard)

The acclaimed chef has been campaigning to improve the quality of food served in aged-care facilities.

She said that because of the special memories some seniors associated with animal by-products, the food would make a great addition to any retirement home menu.

For anyone interested in cooking an animal by-product, she recommended pan-fried sheep’s brain.

“[Start by] poaching the brains and then letting them chill. Then cook them in nut brown butter with capers and parsley, and a good squeeze of lemon,” she said.

“That, to me, is one of the great dishes of the world.“

Still in demand at home and overseas

Australia exported 234,000 tonnes of edible offal in 2024, according to Meat and Livestock Australia.

While this amount was outstripped by the 1.3 million tonnes of beef exported, it is still substantial and in league with the 359,000 tonnes of lamb and 255,000 tonnes of mutton exported.

Even in Rockhampton, Australia’s beef capital, there are still loyal consumers of sheep’s brain.

Butcher Bill Douglas worked long days to find mostly locally sourced products, including animal organ meat.

Man dressed in a black collared t-shirt holds up different cuts of meat, infront of a refrigerated display of more meat. — Bill Douglas is working around the clock to supply as much locally sourced produce as possible. (ABC Capricornia: Claudia Sullivan)

“We sell it mostly to elderly people. They come in just for it,” Mr Douglas said.

“[If] we don’t have it … we make sure we have it later on in the week for them, and they’ll come back for it.”

Offal was not his most popular item, but he said there was a persistent demand.

“It’s getting harder and harder to get [with] fewer places actually selling it,” he said.

More research needed to avoid ‘haemorrhaging nutrients’

Veterinary scientist Robyn Alders has researched food and nutrition security for more than 30 years, and said more data was needed to understand our eating habits and attitudes.

A woman holiding a chicken in her arms in a village in Tanzania with a group of villagers in traditional dress looking on — Robyn Alders AO has been working in the field of global food and nutritional security for decades, as seen in her work introducing vaccinations to chickens in Tanzania in 2012. (Supplied: Sally Ingleton)

She said the data submitted by the United Nations research focused on animal muscle rather than nutrient-dense organs.

“It’s something that they are actively trying to change right now,” Dr Alders said.

“Everyone’s aware now that our system is haemorrhaging nutrients if we’re not taking organ meats into account,” she said.

“Our diet has drifted. We’re consuming a lot of junk food, and we’re eating only the muscle. That gives us a certain range of nutrients.”

A bite has been taken out of a golden yellow pastry pie drizzled with tomatoe sauce, showing the meat inside. — Robyn Elders says that for earlier generations, the consumption of organ meat through dishes like steak and kidney pie was very common. (ABC Capricornia: Claudia Sullivan)

Dr Alders said offal could be beneficial to the 25 per cent of pregnant women in Australia who were anaemic, often due to iron deficiency.

“Organ foods, such as liver, are very high in iron. [And that] iron … is what we call bioavailable. It’s in a form that the body can use immediately, which means you get good uptake.”

Dr Alders also said it was not clear why we were consuming less organ meat, but she had heard a few theories.

“One [could] be that as more of us are urbanised, we’re more removed from the systems that sustain us and feed us, and people simply don’t like the sight of organ meat,” she said.