[Preprint] The central nervous systems proteogenomic and spatial imprint upon systemic viral infections with SARS-CoV-2, 2023, Radke et al

[SNT Gatchaman]

The central nervous systems proteogenomic and spatial imprint upon systemic viral infections with SARS-CoV-2

Spoiler: Radke et al

Josefine Radke, Jenny Meinhardt, Tom Aschman, Robert Lorenz Chua, Vadim Farztdinov, Soren Lukkassen, Foo Wei Ten, Friebel Ekaterina, Naveed Ishaque, Jonas Franz, Valerie Helena Huhle, Ronja Mothes, Kristin Peters, Carolina Thomas, Simon Streit, Regina von Manitius, Peter Kortvelyessy, Stefan Vielhaber, Dirk Reinhold, Anja Hauser, Anja Osterloh, Philipp Enghard, Jana Ihlow, Sefer Elezkurtaj, David Horst, Florian Kurth, Marcel A Muller, Nils C Gassen, Julia Schneider, Katharina Jechow, Bernd Timmermann, Camila Fernandez-Zapata, Chotima Bottcher, Werner Stenzel, Emanuel Wyler, Victor Corman, Christine Stadelmann-Nessler, Markus Ralser, Roland Eils, Frank L Heppner, Michael Mulleder, Christian Conrad, Helena Radbruch

In COVID-19 neurological alterations are noticed during the systemic viral infection. Various pathophysiological mechanisms on the central nervous system (CNS) have been suggested in the past two years, including the viral neurotropism hypothesis. Nevertheless, neurological complications can also occur independent of neurotropism and at different stages of the disease and may be persistent. Previous autopsy studies of the CNS from patients with severe COVID-19 show infiltration of macrophages and T lymphocytes, especially in the perivascular regions as well as pronounced microglial activation, but without signs of viral encephalitis. However, there is an ongoing debate about long-term changes and cytotoxic effects in the CNS due to the systemic inflammation.

Here, we show the brain-specific host response during and after COVID-19. We profile single-nucleus transcriptomes and proteomes of brainstem tissue from deceased COVID-19 patients who underwent rapid autopsy. We detect a disease phase-dependent inflammatory type-I interferon response in acute COVID-19 cases. Integrating single-nucleus RNA sequencing and spatial transcriptomics, we could localize two patterns of reaction to severe systemic inflammation. One neuronal with direct focus on cranial nerve nuclei and one diffusely affecting the whole brainstem, the latter reflecting a bystander effect that spreads throughout the vascular unit and alters the transcriptional state of oligodendrocytes, microglia and astrocytes.

Our results indicate that even without persistence of SARS-CoV-2 in the CNS, the tissue activates highly protective mechanisms, which also cause functional disturbances that may explain the neurological symptoms of COVID-19, triggered by strong systemic type-I IFN signatures in the periphery.

Link

 

[Jacob Richter]

The central nervous systems proteogenomic and spatial imprint upon systemic viral infections with SARS-CoV-2

Spoiler: Radke et al

Josefine Radke, Jenny Meinhardt, Tom Aschman, Robert Lorenz Chua, Vadim Farztdinov, Soren Lukkassen, Foo Wei Ten, Friebel Ekaterina, Naveed Ishaque, Jonas Franz, Valerie Helena Huhle, Ronja Mothes, Kristin Peters, Carolina Thomas, Simon Streit, Regina von Manitius, Peter Kortvelyessy, Stefan Vielhaber, Dirk Reinhold, Anja Hauser, Anja Osterloh, Philipp Enghard, Jana Ihlow, Sefer Elezkurtaj, David Horst, Florian Kurth, Marcel A Muller, Nils C Gassen, Julia Schneider, Katharina Jechow, Bernd Timmermann, Camila Fernandez-Zapata, Chotima Bottcher, Werner Stenzel, Emanuel Wyler, Victor Corman, Christine Stadelmann-Nessler, Markus Ralser, Roland Eils, Frank L Heppner, Michael Mulleder, Christian Conrad, Helena Radbruch

In COVID-19 neurological alterations are noticed during the systemic viral infection. Various pathophysiological mechanisms on the central nervous system (CNS) have been suggested in the past two years, including the viral neurotropism hypothesis. Nevertheless, neurological complications can also occur independent of neurotropism and at different stages of the disease and may be persistent. Previous autopsy studies of the CNS from patients with severe COVID-19 show infiltration of macrophages and T lymphocytes, especially in the perivascular regions as well as pronounced microglial activation, but without signs of viral encephalitis. However, there is an ongoing debate about long-term changes and cytotoxic effects in the CNS due to the systemic inflammation.

Here, we show the brain-specific host response during and after COVID-19. We profile single-nucleus transcriptomes and proteomes of brainstem tissue from deceased COVID-19 patients who underwent rapid autopsy. We detect a disease phase-dependent inflammatory type-I interferon response in acute COVID-19 cases. Integrating single-nucleus RNA sequencing and spatial transcriptomics, we could localize two patterns of reaction to severe systemic inflammation. One neuronal with direct focus on cranial nerve nuclei and one diffusely affecting the whole brainstem, the latter reflecting a bystander effect that spreads throughout the vascular unit and alters the transcriptional state of oligodendrocytes, microglia and astrocytes.

Our results indicate that even without persistence of SARS-CoV-2 in the CNS, the tissue activates highly protective mechanisms, which also cause functional disturbances that may explain the neurological symptoms of COVID-19, triggered by strong systemic type-I IFN signatures in the periphery.

Link

Thanks for sharing. I find this area of research hard to follow in the details as a non-expert but my intuitive sense/lived experience of ME/CFS always brings me back to this sort of mechanism as a likely candidate. If anyone has the knowledge and experience to provide informed comment on this paper I'd really welcome that.

 

[SNT Gatchaman]

Post-mortem arm —

We analyzed autopsy tissue samples from n = 23 male and n = 7 female individuals. [...] Patients with COVID-19 (n = 21) were divided into two groups, namely ‘acute’ (n = 10; median age: 77.5 years, age range: 63 - 91 years) and ‘late’ (n = 11, median age: 78 years, age range: 56 - 92 years) depending on whether death occurred within 14 days from the beginning of symptoms or more than 14 days, respectively.

CSF evaluation arm —

In a retrospective study, we collected CSF samples from patients with a PCR-proven SARS- CoV-2 infection (nasopharyngeal swab testing) who underwent lumbar puncture to rule out CNS pathologies such as autoimmune encephalitis or meningitis, involving a total of n = 38 COVID-19 patients, as well as patients with herpes simplex virus (HSV) encephalitis (n = 10) and non-inflammatory controls (n = 28). [...] We divided the COVID-19 cohort into two subgroups, namely ‘PCTlow’ and ‘PCThigh’ depending on serum procalcitonin (PCT) levels. Low PCT levels (<0.5 μg/L) are a surrogate for non-septic conditions, whereas elevated PCT levels (>1.0 μg/L) indicate a high likelihood of systemic bacterial infection.

Some selected quotes —

various pathophysiological mechanisms of COVID-19-associated effects on the CNS have been suggested in the past two years, including the neurotropism hypothesis. This hypothesis is based on the detection of viral RNA, while active replication of SARS-CoV-2 or intact viral particles have not yet been shown in the CNS. Nevertheless, existing histological and molecular data implicate immune activation and inflammation within the CNS as well as dysregulation of CNS-specific cells primarily caused by indirect systemic effects.

So far, there is no robust proof of SARS-CoV-2 entering the brain along the cranial nerves, reaching cardio-respiratory control centers in the brainstem. However, there is neurophysiological evidence of SARS-CoV-2-related brainstem involvement in severe COVID-19 patients, especially at the medullary level.

Taken together, our snRNA-seq results demonstrated that within the brainstem, glutamatergic neurons and endothelial cells respond to systemic inflammation in addition to reactive microglia, irrespectively of active SARS-CoV-2 replication.

Reactive microglia signatures were not restricted to areas of immune-reactive neurons and found diffusely throughout the white matter.

Endothelial cells and macrophages showed the strongest interferon related signature. Therefore, we focused on the perivascular space as an immune-regulatory unit in more detail.

In addition to the strong type I IFN signature described above, capillary endothelial cells in the brainstem of patients with an acute disease course showed a significant increase in the expression of transforming growth factor-ß (TGF-ß) coding gene TGFB1. [...] These alterations suggested an increased leakiness of the blood brain barrier (BBB)

In fact, the perivascular space is the main homeostatic niche for tissue-resident memory T cells. The alterations of the vascular unit pointed to an increased immune cell recruitment from the periphery with upregulation of integrins but with reduced local reactivation in the perivascular space due to downregulation of MHC molecules

Our results demonstrate a proinflammatory CNS microenvironment during systemic COVID-19 infection with significant upregulation of IFN-stimulated genes and proteins as well as significant downregulation of genes and expressed proteins associated with synaptic organization and myelination. However, we did not see a marked increase in T cell numbers or additional microglial populations as previous studies probably due to our control group with also multi-organ failure, superinfection and to some degree neurodegenerative diseases similar to the COVID-19 groups

While there is no robust evidence for a direct infection of endothelial cells by SARS-CoV-2, multiple studies suggest capillary damage in various organs and functional impairment of the microvasculature has been implicated in the pathogenesis of COVID-19 acutely in the pandemic. We didn't find overt signs of neurovascular damage, increased thrombosis, endothelial destruction or bleedings in our brainstem samples. However on a transcriptional level, besides the response to interferon, we find signs of BBB damage.

Actually, high serum levels of TGF are detected in the first two weeks of SARS-CoV-2 infection and NK cells show a dominant TGF response signature, which seems to inhibit NK cell function and early control of the virus. Furthermore, we find a downregulation of MHC class I molecules (e.g. HLA-A, -B, -C, -DRA) in endothelial cells in the brainstem, which may also be explained by the activation of TGF signaling